124 results on '"Rajeev K, Varshney"'
Search Results
2. The putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness
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Qier Liu, Yun Zhao, Shanjida Rahman, Maoyun She, Jingjuan Zhang, Rongchang Yang, Shahidul Islam, Graham O’Hara, Rajeev K. Varshney, Hang Liu, Hongxiang Ma, and Wujun Ma
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Abstract
Key message The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. Abstract The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of ‘Westonia’ × ‘Kauz’. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat ‘Westonia’. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed. more...
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- 2023
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3. Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean
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Javaid Akhter Bhat, Benjamin Karikari, Kehinde Adewole Adeboye, Showkat Ahmad Ganie, Rutwik Barmukh, Dezhou Hu, Rajeev K. Varshney, and Deyue Yu
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Plant Breeding ,Phenotype ,Haplotypes ,Genetics ,Soybeans ,General Medicine ,Polymorphism, Single Nucleotide ,Agronomy and Crop Science ,Genome, Plant ,Linkage Disequilibrium ,Genome-Wide Association Study ,Biotechnology - Abstract
Key message Plant height of soybean is associated with a haplotype block on chromosome 19, which classified 211 soybean accessions into five distinct groups showing significant differences for the target trait. Abstract Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height. more...
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- 2022
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4. Estimating the potential to close yield gaps through increased efficiency of chickpea production in Ethiopia
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Shalander Kumar, Abhishek Das, Michael Hauser, Geoffrey Muricho, Tulu Degefu, Asnake Fikre, Chris Ojiewo, Setotaw Ferede, and Rajeev K. Varshney
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Development ,Agronomy and Crop Science ,Food Science - Abstract
This is the accepted manuscript version of the work published in its final form as Kumar, S., Das, A., Hauser, M., Muricho, G., Degefu, T., Fikre, A., Ojiewo, C., Ferede, S., & Varshney, R. K. (2022). Estimating the potential to close yield gaps through increased efficiency of chickpea production in Ethiopia.Food Security. https://doi.org/10.1007/s12571-022-01285-w Deposited byshareyourpaper.organdopenaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailinghelp@openaccessbutton.org. more...
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- 2022
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5. Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops
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Shabir H. Wani, Mukesh Choudhary, Rutwik Barmukh, Pravin K. Bagaria, Kajal Samantara, Ali Razzaq, Jagdish Jaba, Malick Niango Ba, and Rajeev K. Varshney
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Gene Editing ,Insecta ,fungi ,Genetics ,Animals ,food and beverages ,Genomics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Abstract
Key message Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Abstract Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops. more...
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- 2022
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6. QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
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Vikas Singh, Pallavi Sinha, Jimmy Obala, Aamir W. Khan, Annapurna Chitikineni, Rachit K. Saxena, and Rajeev K. Varshney
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Genetics ,Genetics (clinical) - Abstract
To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement. more...
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- 2022
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7. Genetic mapping of drought tolerance traits phenotyped under varying drought stress environments in peanut (Arachis hypogaea L.)
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Subhasini Ghosh, Supriya S. Mahadevaiah, S. Anjan Gowda, Sunil S. Gangurde, Mangesh P. Jadhav, Anil A. Hake, P. Latha, T. Anitha, V. P. Chimmad, Kiran K. Mirajkar, Vinay Sharma, Manish K. Pandey, Kenta Shirasawa, Spurthi N. Nayak, Rajeev K. Varshney, and Ramesh S. Bhat more...
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Genetics ,Plant Science ,Horticulture ,Agronomy and Crop Science - Published
- 2022
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8. The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data
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Kristy Hobson, Rajeev K. Varshney, Timothy D. Colmer, Julie E. Hayes, Judith Atieno, Tim Sutton, Ute Baumann, Duong T. Nguyen, Manish Roorkiwal, Helen Bramley, Yongle Li, and Angela L. Pattison
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Germplasm ,Genetics ,education.field_of_study ,biology ,Population ,Haplotype ,food and beverages ,General Medicine ,Quantitative trait locus ,biology.organism_classification ,Inbred strain ,Genetic marker ,Seedling ,education ,Agronomy and Crop Science ,Biotechnology ,Genetic association - Abstract
QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple diversity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two diversity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1–FTa2–FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and diversity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the diversity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology. more...
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- 2021
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9. Regulatory non-coding RNAs: a new frontier in regulation of plant biology
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Sadhana Singh, Arun K. Pandey, Rajeev K. Varshney, Hikmet Budak, Rakesh Kumar, Satendra K. Mangrauthia, Ankit Jain, Sailaja Bhogireddy, and Himabindu Kudapa
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Small interfering RNA ,RNA, Untranslated ,Stress response ,RNA ,Review ,Crop improvement ,General Medicine ,Computational biology ,Plants ,Ribosomal RNA ,Biology ,Plant biology ,Degradation ,MicroRNAs ,microRNA ,Genetics ,Nucleic acid ,RNA, Long Noncoding ,Regulatory non-coding RNAs ,RNA, Small Interfering ,IsomiRs ,Biogenesis ,Function (biology) - Abstract
Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s10142-021-00787-8. more...
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- 2021
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10. Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits
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Vikas K. Singh, Rajeev K. Varshney, Abhishek Bohra, Arvind Kumar, Pallavi Sinha, and Jochen C. Reif
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Crops, Agricultural ,0106 biological sciences ,Breeding program ,Climate Change ,Population ,Review ,Biology ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,Genetics ,Selection, Genetic ,education ,Alleles ,Selection (genetic algorithm) ,030304 developmental biology ,Gene Editing ,0303 health sciences ,Genetic diversity ,education.field_of_study ,Population size ,Genetic Variation ,Genomics ,General Medicine ,Heritability ,Plant Breeding ,Phenotype ,Risk analysis (engineering) ,Genetic gain ,Trait ,Gene-Environment Interaction ,Nutritive Value ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Abstract Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits. more...
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- 2021
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11. Rapid delivery systems for future food security
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David Edwards, Abhishek Bohra, Michael W. Bevan, Manish Roorkiwal, Rajeev K. Varshney, Annapurna Chitikineni, Rutwik Barmukh, Kadambot H. M. Siddique, Arvind Kumar, Janine Croser, Muhammad Farooq, Lee T. Hickey, Wolfram Weckwerth, A. Harvey Millar, Wallace Cowling, José Crossa, and Hon-Ming Lam more...
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Food security ,business.industry ,Internet privacy ,Biomedical Engineering ,MEDLINE ,Molecular Medicine ,Developing country ,Bioengineering ,Business ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2021
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12. Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement
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Chad E. Niederhuth, Himabindu Kudapa, Vikas K. Singh, Gaurav Agarwal, Manish K. Pandey, Abirami Ramalingam, Henry T. Nguyen, Gunvant Patil, Rajeev K. Varshney, Vanika Garg, Divya Choudhary, Ramanjulu Sunkar, Baozhu Guo, and Pallavi Sinha more...
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Crops, Agricultural ,Epigenomics ,0106 biological sciences ,0301 basic medicine ,Plant Development ,Computational biology ,01 natural sciences ,DNA sequencing ,Histones ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genetics ,Epigenetics ,Phenotypic plasticity ,biology ,General Medicine ,Methylation ,DNA Methylation ,Plants ,Chromatin ,Histone Code ,Plant Breeding ,030104 developmental biology ,Histone ,DNA methylation ,biology.protein ,sense organs ,Protein Processing, Post-Translational ,010606 plant biology & botany - Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits. more...
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- 2020
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13. Fatty acid desaturase-2 (ahFAD2) mutant alleles in peanut (Arachis hypogaea L.) pre-breeding lines: an insight into the source, features, discourse, and selection of novel pre-breeding lines
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B. C. Ajay, Pasupuleti Janila, S. K. Bera, Kirti Rani, M. D. Jasani, Rajeev K. Varshney, N. Manivannan, R. P. Vasanthi, Manish K. Pandey, K. L. Dobariya, T. Radhakrishnan, and J. H. Kamdar
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0106 biological sciences ,0301 basic medicine ,biology ,Linoleic acid ,Mutant ,Plant Science ,01 natural sciences ,Palmitic acid ,03 medical and health sciences ,chemistry.chemical_compound ,Oleic acid ,030104 developmental biology ,Fatty acid desaturase ,chemistry ,Genetics ,biology.protein ,Plant breeding ,Gene pool ,Food science ,Allele ,Agronomy and Crop Science ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
High oleic peanuts and derived food products offer longer shelf life benefits to the food processing industry in addition to multiple health benefits to the consumers. The two mutant alleles, ahFAD2A and ahFAD2B control composition of oleic, linoleic and palmitic acid content in peanut. A total of 563 peanut pre-breeding lines were tested for the presence ahFAD2A and ahFAD2B mutant alleles using allele specific markers. The ahFAD2A mutant allele was present in 82 lines, while none of these lines had ahFAD2B mutant allele. Among botanical types, ahFAD2A mutant allele was more frequent in lines with Virginia growth habit than Spanish bunch although no correlation of ahFAD2A mutant allele with high oleic acid content and growth habit could be established. Oleic and linoleic acid content in 82 pre-breeding lines ranged from 39.70 to 62.70% and 17.76 to 31.95%, respectively, with maximum oleic to linoleic acid ratio of 4. Oleic acid was found to be negatively correlated with linoleic and palmitic acid. Further, pre-breeding lines with ahFAD2A mutant allele, high oleic content and high oleic to linoleic ratio were investigated and novel lines were identified for resistance to late leaf spot, short duration, higher pod yield and other yield related traits. These novel pre-breeding lines can be used as a potential donor in peanut improvement programme and to diversify the primary gene pool including initiating further research on induction of fresh ahFAD2B mutant allele. more...
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- 2020
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14. Genome-based trait prediction in multi- environment breeding trials in groundnut
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Sudam C. Patil, Diego Jarquin, John M. Hickey, T. Radhakrishnan, Subramaniam Sundravadana, Ramesh S. Bhat, Sunil Chaudhari, Dhirendra Khare, Rajeev K. Varshney, Manish K. Pandey, José Crossa, and Pasupuleti Janila more...
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0106 biological sciences ,Arachis ,Genotype ,Population ,India ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,03 medical and health sciences ,Quantitative Trait, Heritable ,Animal science ,Oil content ,Genetics ,Plant breeding ,education ,Alleles ,Selection (genetic algorithm) ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Models, Genetic ,General Medicine ,biology.organism_classification ,Plant Breeding ,Phenotype ,Trait ,Original Article ,Gene-Environment Interaction ,Agronomy and Crop Science ,Genomic selection ,010606 plant biology & botany ,Biotechnology - Abstract
Key message Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Abstract Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K ‘Axiom_Arachis’ SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400–0.600) were obtained for pods/plant, shelling %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut. more...
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- 2020
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15. Reply to: Evaluating two different models of peanut’s origin
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Weijian Zhuang, Yixiong Zheng, Rajeev K. Varshney, Andrew H. Paterson, Huiwen Fu, Wenping Xie, Meng Yang, Zhang Chong, Chen Hua, Lihui Wang, Pengchuan Sun, Wenting Chu, and Xiyin Wang
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Evolutionary biology ,Genetics ,MEDLINE ,Fabaceae ,Biology ,Domestication - Published
- 2020
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16. Translational genomics for achieving higher genetic gains in groundnut
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Rakesh Kumar, Mei Yuan, Chogozie Victor Nwosu, Graeme C. Wright, Huifang Jiang, Issa Faye, Weijian Zhuang, S. K. Bera, Xingjun Wang, Boshou Liao, Rajeev K. Varshney, Arun K. Pandey, X Liang, Xiaoping Chen, Baozhu Guo, Manish K. Pandey, Ramesh S. Bhat, T. Radhakrishnan, and Xinyou Zhang more...
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0106 biological sciences ,Germplasm ,Quantitative Trait Loci ,Population ,Genomics ,Review ,Biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Genetics ,education ,Genotyping ,030304 developmental biology ,Molecular breeding ,Whole genome sequencing ,0303 health sciences ,education.field_of_study ,business.industry ,food and beverages ,Fabaceae ,General Medicine ,Plants, Genetically Modified ,Biotechnology ,Plant Breeding ,Genetics, Population ,Phenotype ,Backcrossing ,business ,Agronomy and Crop Science ,Genome, Plant ,010606 plant biology & botany - Abstract
Key message Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Abstract Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era. more...
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- 2020
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17. Crop genetics research in Asia: improving food security and nutrition
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Takao Komatsuda, Xianchun Xia, Mingliang Xu, Kai Shi, Rajeev K. Varshney, and Qifa Zhang
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Crops, Agricultural ,Epigenomics ,0106 biological sciences ,Asia ,Food security ,Oryza ,Genome-wide association study ,Genomics ,General Medicine ,Biology ,01 natural sciences ,Genome ,DNA sequencing ,Genetic architecture ,Food Security ,Evolutionary biology ,Genetics ,Agronomy and Crop Science ,Gene ,010606 plant biology & botany ,Biotechnology ,Reference genome - Abstract
Breakthroughs in genomics research in recent decades have fundamentally changed the landscape of crop science at a number of fronts: (1) High-quality reference genome sequences have become available for most of the crops which have provided the foundation for understanding the genome and for functional genomic studies. (2) Large numbers of genes have been identified and functionally characterized for many important agronomic traits, which have greatly enhanced the understanding of the regulatory mechanisms and the underlying biological processes for the making of the traits. (3) Large-scale resequencing of the diverse germplasms and genome-wide association studies (GWAS) have provided assessment about the extent of genome diversity, the genetic architecture, and association between the phenotype and DNA sequence polymorphisms in many crop species. (4) Systems of breeding technologies based on the advance in genomic studies, or genomic breeding, have now been developed including novel goals in response to the evolving demands of the consumers, upgraded definitions of traits to be improved, techniques for whole genome selection, and varietal designs for the implementation. more...
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- 2020
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18. High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea)
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Dongyang Xie, Ye Deng, Baozhu Guo, Weijian Zhuang, Gandeka Mamadou, Yuhua Chen, Zhang Chong, Chen Hua, Rajeev K. Varshney, Tiecheng Cai, Niaz Ali, and Shahid Ali Khan
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Genetic Markers ,0106 biological sciences ,Candidate gene ,Arachis ,Genotype ,Genetic Linkage ,Quantitative Trait Loci ,Aspergillus flavus ,Quantitative trait locus ,Plant disease resistance ,Polymorphism, Single Nucleotide ,01 natural sciences ,Aflatoxins ,Genetic linkage ,Genetics ,Gene ,Disease Resistance ,Oligonucleotide Array Sequence Analysis ,Plant Diseases ,biology ,Chromosome Mapping ,Computational Biology ,food and beverages ,General Medicine ,biology.organism_classification ,Plant disease ,WRKY protein domain ,Phenotype ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq. Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts. more...
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- 2020
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19. Publisher Correction: Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea
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Sonal Channale, Danamma Kalavikatte, John P. Thompson, Himabindu Kudapa, Prasad Bajaj, Rajeev K. Varshney, Rebecca S. Zwart, and Mahendar Thudi
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Multidisciplinary - Published
- 2022
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20. Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
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Xingguo Zhang, Manish K. Pandey, Xingli Ma, Baozhu Guo, Fangping Gong, Jianping Wang, Kunkun Zhao, Zhongfeng Li, Dongmei Yin, Rajeev K. Varshney, and Kai Zhao
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Arachis ,QH301-705.5 ,Mutant ,Cellular homeostasis ,ATAC-seq ,QH426-470 ,Biology ,3D structure ,Chromosomes ,Hi-C ,Gene Expression Regulation, Plant ,Genetics ,Transcriptional regulation ,Biology (General) ,Gene ,Regulation of gene expression ,Genome ,Research ,Wild type ,food and beverages ,Genomics ,Chromatin ,Gene regulation ,Biosynthetic Pathways ,Circadian Rhythm ,Cell biology ,Peanut ,Chromatin Immunoprecipitation Sequencing ,Gene expression - Abstract
Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants. more...
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- 2021
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21. Delineating investment opportunities for stakeholders in sorghum seed systems: a logit model perspective
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Justin Ringo, Geoffrey Muricho, Gerald Alex Lukurugu, Judith Ndossi, Essegbemon Akpo, Rajeev K. Varshney, Chris O. Ojiewo, Ronnie Vernooy, Lameck Nyaligwa Makoye, Ramadjita Tabo, and Eliud Kongola
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Ecology ,biology ,business.industry ,Distribution (economics) ,Sowing ,Sorghum ,biology.organism_classification ,Gross margin ,Agricultural science ,Agriculture ,Profitability index ,business ,Agronomy and Crop Science ,Productivity ,Hectare ,Food Science - Abstract
BackgroundSeed systems are considered as a vehicle through which the sustainable agricultural intensification can be achieved. However, most sub-Saharan African countries have been ineffective to provide sufficient incentives for stakeholders to consistently invest in the seed systems specifically for crops like sorghum. This study was therefore conducted to uncover investment opportunities for stakeholders in the sorghum seed systems to attain an impact-oriented seed production and delivery systems.ResultsThe study applied descriptive statistics, Logit regression model, and Gross margin to analyze possible areas for investments. Descriptive statistics analyzed the percentage of farmers using sorghum improved varieties and sources used to obtained improved variety seeds. Logit regression model was applied to analyze factors correlating with planting of improved seeds. Gross margin was applied to show profitability of growing improved sorghum seeds and grain. Findings revealed that 39.2% of the sampled farmers were growing improved sorghum variety seeds. Farmers obtained improved variety seeds from both informal (57.8%) and formal (42.2%) sources. Logit estimates indicate that variety preference, unavailability of seeds, resistance to diseases, and drought had significant correlation with planting of improved variety seeds. Seed companies and quality declared seed (QDS) producers earned high margin of 53,08,900 Tanzanian Shillings per hectare (TZS/ha, 1 USD = 2315 TZS during the period of data collection) and 33,94,709 TZS/ha, respectively. Farmers using improved variety seed earned higher margin (8,19,805 TZS/ha) than farmers who did not use improved variety seeds (3,17,373 TZS/ha)ConclusionsThe identified investment opportunities were increasing number of farmers using improved variety seeds that would drive increased production, distribution, and marketing of quality seed. The large number of farmers still sourcing seed from the informal channel provides avenue to reach out to these farmers through demand creation and wide variety popularization meeting farmer preferences. The huge margin seed producers make provides good incentive to drive private seed companies and individual seed entrepreneurs to make sustainable business out of sorghum seed. The policy implications for reviving sorghum production and productivity are further discussed. more...
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- 2021
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22. Identification of heterotic groups in South-Asian-bred hybrid parents of pearl millet
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Suresh Kumar Gupta, Vikas K. Singh, M. Boratkar, Kedar N. Rai, K. D. Mungra, K. Sudarshan Patil, Vaibhav Chaudhary, O. P. Yadav, Anil Kumar, Dev Vart Yadav, Ramesh Kumar, Abhishek Rathore, S. K. Gupta, Roma Rani Das, Rakesh K. Srivastava, Rajeev K. Varshney, H T Patil, Rajeev Gupta, and Lochan Sharma more...
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0106 biological sciences ,Heterotic string theory ,Veterinary medicine ,South asia ,Heterosis ,Crop yield ,General Medicine ,engineering.material ,Biology ,01 natural sciences ,Genetics ,engineering ,Grain yield ,Plant breeding ,Agronomy and Crop Science ,Pearl ,010606 plant biology & botany ,Biotechnology ,Hybrid - Abstract
Pearl millet breeding programs can use this heterotic group information on seed and restorer parents to generate new series of pearl millet hybrids having higher yields than the existing hybrids. Five hundred and eighty hybrid parents, 320 R- and 260 B-lines, derived from 6 pearl millet breeding programs in India, genotyped following RAD-GBS (about 0.9 million SNPs) clustered into 12 R- and 7 B-line groups. With few exceptions, hybrid parents of all the breeding programs were found distributed across all the marker-based groups suggesting good diversity in these programs. Three hundred and twenty hybrids generated using 37 (22 R and 15 B) representative parents, evaluated for grain yield at four locations in India, showed significant differences in yield, heterosis, and combining ability. Across all the hybrids, mean mid- and better-parent heterosis for grain yield was 84.0% and 60.5%, respectively. Groups G12 B × G12 R and G10 B × G12 R had highest heterosis of about 10% over best check hybrid Pioneer 86M86. The parents involved in heterotic hybrids were mainly from the groups G4R, G10B, G12B, G12R, and G13B. Based on the heterotic performance and combining ability of groups, 2 B-line (HGB-1 and HGB-2) and 2 R-line (HGR-1 and HGR-2) heterotic groups were identified. Hybrids from HGB-1 × HGR-1 and HGB-2 × HGR-1 showed grain yield heterosis of 10.6 and 9.3%, respectively, over best hybrid check. Results indicated that parental groups can be formed first by molecular markers, which may not predict the best hybrid combination, but it can reveal a practical value of assigning existing and new hybrid pearl millet parental lines into heterotic groups to develop high-yielding hybrids from the different heterotic groups. more...
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- 2020
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23. QTLian breeding for climate resilience in cereals: progress and prospects
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Mukesh Choudhary, Rajeev K. Varshney, Shabir H. Wani, Pardeep Kumar, Manish Roorkiwal, Pravin Kumar Bagaria, and Sujay Rakshit
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Crops, Agricultural ,0106 biological sciences ,0301 basic medicine ,Climate Change ,Quantitative Trait Loci ,Population ,Biology ,01 natural sciences ,03 medical and health sciences ,Stress, Physiological ,Genetics ,Humans ,Plant breeding ,education ,Abiotic component ,Molecular breeding ,education.field_of_study ,Food security ,Abiotic stress ,business.industry ,Agroforestry ,General Medicine ,Climate resilience ,Adaptation, Physiological ,Plant Breeding ,030104 developmental biology ,Agriculture ,Edible Grain ,business ,010606 plant biology & botany - Abstract
The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change. more...
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- 2019
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24. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication
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Pengchuan Sun, Annapurna Chitikineni, Shubiao Zhang, Jinpeng Wang, Jigao Yu, Haibao Tang, Shanshan Zhao, Niaz Ali, Zhang Chong, Chen Hua, Rong Long Pan, Andrew H. Paterson, Shihua Shan, Depeng Wang, Guohao He, Yuting Chen, Faqian Xiong, Zhenyi Wang, Kun Chen, Kangcheng Wu, Shahid Ali Khan, Jiang Hu, Xinguo Li, Ye Deng, Liangsheng Zhang, Meng Yang, Yongli Zhao, Baozhu Guo, Manish K. Pandey, Tiecheng Cai, Wenting Chu, Junpeng Fan, Yu Li, Ziliang Luo, Hansong Yan, Tao Zhuo, Mei Yuan, Vanika Garg, Chuanzhi Zhao, Prasad Bajaj, Xiyin Wang, Ruirong Zhuang, Xingjun Wang, Yuhao Zhao, Zifan Zhao, Dongyang Xie, Xingtan Zhang, Gandeka Mamadou, Li Zha, Yuhui Zhuang, Qinzheng Liu, Fan Liang, Wenping Xie, Qiang Yang, Chi Nga Chow, Congcong Wang, Jiaqing Yuan, Huasong Zou, Jianping Wang, Weijian Zhuang, Han Xia, Chunjuan Li, Tang Ronghua, Boshou Liao, Shengyi Liu, Ze Peng, Ray Ming, Weichang Yu, Weipeng Quan, Aamir W. Khan, Fanbo Meng, Xinyou Zhang, Wen Chi Chang, P. B. KaviKishor, Shuaiyin Wang, Yixiong Zheng, Jingjing Li, and Rajeev K. Varshney more...
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Arachis ,Karyotype ,Plant disease resistance ,Biology ,Plant Proteins, Dietary ,Genome ,Article ,Chromosomes, Plant ,Domestication ,Evolution, Molecular ,Polyploidy ,03 medical and health sciences ,0302 clinical medicine ,Polyploid ,Genetic variation ,Botany ,Genetics ,DNA sequencing ,Gene ,Disease Resistance ,Plant Diseases ,030304 developmental biology ,Ecotype ,Whole genome sequencing ,0303 health sciences ,Chromosome Mapping ,food and beverages ,Genomics ,Droughts ,Plant Breeding ,Seeds ,Peanut Oil ,Functional genomics ,Genome, Plant ,030217 neurology & neurosurgery - Abstract
High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement., High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut. more...
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- 2019
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25. Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops
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Manu Priya, P. V. Vara Prasad, Bindumadhava HanumanthaRao, Sarita K. Pandey, Sadhana Singh, Om P. Dhanker, Ramakrishnan M. Nair, Harsh Nayyar, Kadambot H. M. Siddique, and Rajeev K. Varshney
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0106 biological sciences ,Regulation of gene expression ,Abiotic stress ,fungi ,Drought tolerance ,food and beverages ,General Medicine ,Biology ,01 natural sciences ,Cell biology ,Late embryogenesis abundant proteins ,Heat shock protein ,Genetics ,Heat shock ,Adaptation ,Agronomy and Crop Science ,Transcription factor ,010606 plant biology & botany ,Biotechnology - Abstract
We describe here the recent developments about the involvement of diverse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of diverse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their individual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops. more...
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- 2019
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26. MAGIC lines in chickpea: development and exploitation of genetic diversity
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Biswajit Mondal, Srinivasan Samineni, Rajeev K. Varshney, Sobhan B. Sajja, Uttam Chand, Mahendar Thudi, and Pooran M. Gaur
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0106 biological sciences ,0301 basic medicine ,Germplasm ,education.field_of_study ,Genetic diversity ,Common line ,Population ,Plant Science ,Horticulture ,Biology ,Flowering time ,01 natural sciences ,Heat stress ,03 medical and health sciences ,030104 developmental biology ,Agronomy ,Genetics ,Grain yield ,education ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
In chickpea a multi-parent advanced generation intercross (MAGIC) population was developed using eight parents that are improved varieties and widely adaptable breeding lines. The main objective was to enhance the genetic diversity and bring novel alleles for developing superior chickpea varieties. The development scheme involved a sequence of 28 two-way, 14 four-way and 7 eight-way crosses, followed by bulking of final F1 plants. From F2 generation onwards single plants were grown as progenies and advanced to F8 by single seed descent method. The finally developed 1136 MAGIC lines were phenotyped under rainfed (RF) and irrigated (IR) conditions for 2 years (2013 and 2014) under normal season, and one year under heat stress (HS) condition (summer-2014) in field to estimate the genetic diversity created among these lines. Under RF-2014, RF-2013, IR-2014, IR-2013 and S-2014 seasons 46, 62, 83, 50 and 61 lines showed significantly higher grain yield than the best parent, respectively. Similarly, 23 and 19 common lines were identified under RF and IR conditions over two years and no common line was identified between RF/IR and HS conditions. Preliminary evaluation showed a large variation among MAGIC lines for flowering time (34–69 days), maturity (80–120 days), plant height (23.3–65 cm), grain yield (179–4554 kg/ha), harvest index (0.10–0.77) and 100 seed weight (10–45 g) under RF and IR conditions. Several genotypes with higher grain yield than the best check under heat stress were identified. These MAGIC lines provide a useful germplasm source with diverse allelic combinations to global chickpea community. more...
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- 2021
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27. Molecular mapping of dry root rot resistance genes in chickpea (Cicer arietinum L.)
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B. P. Mallikarjuna, Sobhan B. Sajja, Kannalli P. Viswanatha, Mamta Sharma, Pooran M. Gaur, Mahendar Thudi, Rajeev K. Varshney, Srinivasan Samineni, and Ashwini Karadi
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0106 biological sciences ,0301 basic medicine ,Candidate gene ,Plant Science ,Horticulture ,Plant disease resistance ,Biology ,Quantitative trait locus ,01 natural sciences ,Plant disease ,SNP genotyping ,03 medical and health sciences ,030104 developmental biology ,Inbred strain ,Genetic linkage ,Genetics ,Root rot ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Dry root rot (DRR) caused by Rhizoctonia bataticola [(Taub.) Butler] is an emerging disease of chickpea (Cicer arietinum L.) and a serious constraint to chickpea production in warm and arid regions. To identify the genomic regions conferring resistance to DRR, a total of 182 F9 derived Recombinant Inbred Lines (RILs) were developed from the cross between a susceptible line BG 212 and moderately resistant breeding line ICCV 08305. The parental lines and RILs were screened against Rb 6 isolate of R. bataticola using paper towel method under controlled environment at ICRISAT during 2016 and 2017. The RILs were genotyped with cost-effective SNP genotyping platform, Affymetrix® Axiom®CicerSNP array. As a result, a high-density genetic map with 13,110 SNP markers spanning 1224.11 cM with an average inter marker distance of 0.09 cM was developed. A single minor QTL (‘qDRR-8’) explaining 6.70% PVE with LOD scores 3.34 was identified on CaLG08 for DRR resistance which could be further explored for mining candidate genes and the linked SNP markers could be further validated for application in marker-assisted selection of DRR resistance in chickpea breeding programs. more...
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- 2021
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28. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
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David Edwards, Sam Reddy, Philipp E. Bayer, Theresa A. Musket, Trupti Joshi, Allen Sessions, Babu Valliyodan, Anne V. Brown, Tri D. Vuong, Ruth Wagner, Rex T. Nelson, Manish Roorkiwal, Rajeev K. Varshney, Juexin Wang, Paul I. Otyama, Xiaolei Wu, Dong Xu, Steven B. Cannon, Pradeep Marri, Gunvant Patil, Xin Liu, Yang Liu, Henry T. Nguyen, Qijian Song, and David Grant more...
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Crops, Agricultural ,0106 biological sciences ,Germplasm ,Statistics and Probability ,Data Descriptor ,Linkage disequilibrium ,Genotype ,Science ,Library and Information Sciences ,Polymorphism, Single Nucleotide ,01 natural sciences ,Plant breeding ,Linkage Disequilibrium ,Education ,03 medical and health sciences ,Genetic variation ,Selection, Genetic ,Domestication ,030304 developmental biology ,Genetics ,0303 health sciences ,Genetic diversity ,Geography ,biology ,food and beverages ,Fabaceae ,biology.organism_classification ,Computer Science Applications ,Genetic structure ,Soybeans ,Glycine soja ,Statistics, Probability and Uncertainty ,Plant sciences ,Genome, Plant ,010606 plant biology & botany ,Information Systems - Abstract
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions., Measurement(s) genetic variation • SNP • Linkage Disequilibrium Technology Type(s) DNA sequencing • bioinformatics analysis • computational phylogenetic analysis Sample Characteristic - Organism Glycine soja • Glycine max Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13568552 more...
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- 2021
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29. Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea
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Narendra Singh, Prasad Gandham, Vivek Thakur, Rachit K. Saxena, Abhishek Bohra, S. J. Satheesh Naik, Abhishek Rathore, and Rajeev K. Varshney
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0106 biological sciences ,0301 basic medicine ,Genetics ,Small RNA ,Apetala 2 ,Software maintainer ,Plant Science ,Biology ,01 natural sciences ,Deep sequencing ,03 medical and health sciences ,030104 developmental biology ,microRNA ,Gene expression ,Transcription factor ,Gene ,010606 plant biology & botany - Abstract
Exploitation of hybrid vigor using CMS technology has delivered nearly 50% yield gain in pigeonpea. Among various sterility-inducing cytoplasms (A1–A9) reported so far in pigeonpea, A2 and A4 are the two major sources that facilitate hybrid seed production. Recent evidence suggests involvement of micro RNA in vast array of biological processes including plant reproductive development. In pigeonpea, information about the miRNAs is insufficient. In view of this, we sequenced six small RNA libraries of CMS line UPAS 120A and isogenic fertile line UPAS 120B using Illumina technology. Results revealed 316 miRNAs including 248 known and 68 novel types. A total of 637 gene targets were predicted for known miRNAs, while 324 genes were associated with novel miRNAs. Degradome analysis revealed 77 gene targets of predicted miRNAs, which included a variety of transcription factors playing key roles in plant reproduction such as F-box family proteins, apetala 2, auxin response factors, ethylene-responsive factors, homeodomain-leucine zipper proteins etc. Differential expression of both known and novel miRNAs implied roles for both conserved as well as species-specific players. We also obtained several miRNA families such as miR156, miR159, miR167 that are known to influence crucial aspects of plant fertility. Gene ontology and pathway level analyses of the target genes showed their possible implications for crucial events during male reproductive development such as tapetal degeneration, pollen wall formation, retrograde signaling etc. To the best of our knowledge, present study is first to combine deep sequencing of small RNA and degradome for elucidating the role of miRNAs in flower and male reproductive development in pigeonpea. more...
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- 2021
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30. Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity
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Arindam Ghatak, Martin Brenner, Wolfram Weckwerth, Guntur Venkata Subbarao, Palak Chaturvedi, Gert Bachmann, Prasad Bajaj, Doris Engelmeier, Lena Fragner, Florian Schindler, and Rajeev K. Varshney
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0106 biological sciences ,0301 basic medicine ,Root growth ,Drought stress ,Soil Science ,Primary metabolites ,Biology ,Root exudates ,01 natural sciences ,Microbiology ,LC–MS ,Pearl millet ,03 medical and health sciences ,Genotype ,GC–MS ,Rhizosphere ,Secondary metabolites ,fungi ,Potential effect ,food and beverages ,030104 developmental biology ,Agronomy ,Microbial population biology ,Composition (visual arts) ,Nitrification ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative metabolic profiling of the exudates from sensitive and tolerant genotypes of pearl millet after a period of drought stress. We employed a combined platform of gas and liquid chromatography coupled to mass spectrometry to cover both primary and secondary metabolites. The results obtained demonstrate that both genotype and drought stress have a significant impact on the concentration and composition of root exudates. The complexity and function of these differential root exudates are discussed. To reveal the potential effect of root exudates on the soil microbial community after a period of drought stress, we also tested for biological nitrification inhibition (BNI) activity. The analysis revealed a genotype-dependent enhancement of BNI activity after a defined period of drought stress. In parallel, we observed a genotype-specific relation of elongated root growth and root exudation under drought stress. These data suggest that the drought stress-dependent change in root exudation can manipulate the microbial soil communities to adapt and survive under harsh conditions.The online version contains supplementary material available at 10.1007/s00374-021-01578-w. more...
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- 2021
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31. Genome-wide identification of meiotic recombination hot spots detected by SLAF in peanut (Arachis hypogaea L.)
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Tianyi Yu, Xiaoyuan Chi, Manish K. Pandey, Mei Yuan, Yin Liang, Xiaohua Wang, Shi Yanmao, Li Shuangling, Ping Xu, Hui Li, Ren Yan, Yan Wang, Xue Cao, and Rajeev K. Varshney
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Agricultural genetics ,0301 basic medicine ,Arachis ,DNA, Plant ,Genotype ,Science ,Quantitative Trait Loci ,Population ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Article ,Chromosomes, Plant ,Domestication ,03 medical and health sciences ,0302 clinical medicine ,Meiosis ,Homologous Recombination ,education ,Gene ,Genetics ,education.field_of_study ,Multidisciplinary ,Models, Genetic ,Haplotype ,food and beverages ,Chromosome Mapping ,Polyploidy in plants ,030104 developmental biology ,Natural population growth ,Medicine ,Homologous recombination ,Algorithms ,Genome, Plant ,030217 neurology & neurosurgery ,Recombination ,Microsatellite Repeats - Abstract
Recombination hot spots (RHP), caused by meiosis, are considered to play crucial roles in improvement and domestication of crop. Cultivated peanut is one of the most important rich-source of oil and protein crops. However, no direct scale of recombination events and RHP have been estimated for peanut. To examine the scale of recombination events and RHP in peanut, a RIL population with 200 lines and a natural population with 49 cultivars were evaluated. The precise integrated map comprises 4837 SLAF markers with genetic length of 2915.46 cM and density of 1.66 markers per cM in whole genome. An average of 30.0 crossover (2.06 cMMb−1) events was detected per RIL plant. The crossover events (CE) showed uneven distribution among B sub-genome (2.32) and A sub-genome (1.85). There were 4.34% and 7.86% of the genome contained large numbers of CE (> 50 cMMb−1) along chromosomes in F6 and natural population, respectively. High density of CE regions called RHP, showed negative relationship to marker haplotypes conservative region but positive to heatmap of recombination. The genes located within the RHP regions by GO categories showed the responding of environmental stimuli, which suggested that recombination plays a crucial role in peanut adaptation to changing environments more...
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- 2020
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32. Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping
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Jianbin Guo, Manish K. Pandey, Xiaoping Ren, Yong Lei, Li Huang, Huifang Jiang, Dongxin Huai, Xiaojing Zhou, Haiwen Chen, Huaiyong Luo, Boshou Liao, Yuning Chen, Bei Wu, Rajeev K. Varshney, Weigang Chen, and Nian Liu more...
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Genetic Markers ,0106 biological sciences ,0301 basic medicine ,China ,Arachis ,Genotype ,lcsh:QH426-470 ,Breeding program ,Oil content ,Population ,Locus (genetics) ,Association analysis ,Biology ,Geographic region ,01 natural sciences ,Linkage Disequilibrium ,03 medical and health sciences ,Genetics ,Allele ,Association mapping ,education ,Alleles ,Genetic Association Studies ,Phylogeny ,Genetics (clinical) ,Geographic difference ,Genetic association ,Principal Component Analysis ,education.field_of_study ,Chromosome Mapping ,food and beverages ,Plant Breeding ,lcsh:Genetics ,Genetics, Population ,Phenotype ,Peanut ,030104 developmental biology ,Vegetable oil ,Peanut Oil ,Research Article ,Microsatellite Repeats ,010606 plant biology & botany - Abstract
Background Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90–9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties. more...
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- 2020
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33. G × E interactions in QTL introgression lines of Spanish-type groundnut (Arachis hypogaea L.)
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K. Vemana, B.S. Yenagi, Manish K. Pandey, Murali T. Variath, S. Sundaravadana, H. L. Nadaf, N. Premalatha, Sudam C. Patil, P. P. Thirumalaisamy, J. Khatod, Rajeev K. Varshney, AL Rathnakumar, S. S. Patil, HB Lalwani, Milind P. Deshmukh, Pasupuleti Janila, P. Nagaraju, J. Suryawanshi, Surendra S. Manohar, Prasanna Rajesh, D. K. Kathmale, T. Radhakrishnan, K. S. S. Naik, Sunil Chaudhari, C. T. Kumbhar, and Narendra Kumar more...
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0106 biological sciences ,0301 basic medicine ,biology ,Introgression ,Plant Science ,Horticulture ,Quantitative trait locus ,Plant disease resistance ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Point of delivery ,Agronomy ,Genotype ,Backcrossing ,Genetics ,Leaf spot ,Agronomy and Crop Science ,Selection (genetic algorithm) ,010606 plant biology & botany - Abstract
Multi-environment testing at five locations for rust and late leaf spot (LLS) resistance with 41 introgressed lines (ILs) bred using marker-assisted backcross breeding in the genetic background Spanish-type groundnut varieties identified significant genotype, and genotype × environment interactions (GEI) for LLS disease resistance and yield parameters. Significant GEI effects suggest the need to identify location specific breeding lines to achieve gains in pod yield and LLS resistance. The observed variable LLS disease reaction among the ILs in part suggests influence of background genotype on the level of resistance. A breeding scheme with early generation selection using molecular markers followed by phenotyping for LLS, and multi-location testing of fixed breeding lines was optimized to enhance selection intensity and accuracy in groundnut breeding. The ILs, ICGVs 14431, 14436 and 14438 with pooled LLS score at 90 DAS of 3.5–3.7 were superior to respective recurrent parent for pod yield, with early maturing similar to recurrent parents. The pod yield advantage in ILs is attributed by more number of pods, besides resistance to LLS that contributes to better filling. more...
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- 2020
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34. Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant
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Liying Yan, Boshou Liao, Liyun Wan, Yong Lei, Rajeev K. Varshney, Manish K. Pandey, Xia Wan, Jiahai Fang, and Yue Liu
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Seed coat ,Candidate gene ,Arachis ,Mutant ,Cyclopentanes ,Plant Science ,Biology ,Genes, Plant ,Transcriptome ,Transcriptional regulation ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Suberin ,lcsh:Botany ,Brassinosteroids ,Metabolome ,Oxylipins ,Peanut (Arachis hypogaea L.) ,Gene ,Flavonoids ,Indoleacetic Acids ,Pigmentation ,Wild type ,food and beverages ,Hormone ,Phenotype ,lcsh:QK1-989 ,Biochemistry ,Flavonoid ,Research Article - Abstract
Background Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil. An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation. Result Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced plant hormones synthesis and signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and DFR by controlling hormone synthesis and signaling as well as the MBW complex. Conclusions The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality. more...
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- 2020
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35. Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
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Sailaja Bhogireddy, Rajeev K. Varshney, Renee S. Arias, Paxton Payton, Spurthi N. Nayak, Abishek Xavier, Vanika Garg, Nancy Layland, Naveen Puppala, and Manish K. Pandey
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0106 biological sciences ,0301 basic medicine ,Arachis ,Genotype ,lcsh:Medicine ,Single-nucleotide polymorphism ,Biology ,01 natural sciences ,Genome ,Article ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Stress, Physiological ,SNP ,lcsh:Science ,Gene ,Plant Proteins ,Genetics ,Multidisciplinary ,Abiotic ,Gene Expression Profiling ,lcsh:R ,High-Throughput Nucleotide Sequencing ,Droughts ,Gene expression profiling ,030104 developmental biology ,Plant stress responses ,lcsh:Q ,Ploidy ,010606 plant biology & botany - Abstract
Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNA-seq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes. more...
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- 2020
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36. Publisher Correction: A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea)
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Gaurav Agarwal, C. Corley Holbrook, Divya Choudhary, Baozhu Guo, Mei Yuan, Albert K. Culbreath, Xingjun Wang, Hui Wang, Rajeev K. Varshney, Manish K. Pandey, Xin Liu, Sandip M. Kale, and Josh Clevenger more...
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Horticulture ,Multidisciplinary ,Resistance (ecology) ,lcsh:R ,lcsh:Medicine ,lcsh:Q ,Biology ,Quantitative trait locus ,lcsh:Science ,Tomato spotted wilt virus ,Bin ,Recombination ,Arachis hypogaea - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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- 2020
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37. Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes
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Rajeev K. Varshney, Manish Roorkiwal, Shuai Sun, Prasad Bajaj, Annapurna Chitikineni, Mahendar Thudi, Narendra P. Singh, Xiao Du, Hari D. Upadhyaya, Aamir W. Khan, Yue Wang, Vanika Garg, Guangyi Fan, Wallace A. Cowling, José Crossa, Laurent Gentzbittel, Kai Peter Voss-Fels, Vinod Kumar Valluri, Pallavi Sinha, Vikas K. Singh, Cécile Ben, Abhishek Rathore, Ramu Punna, Muneendra K. Singh, Bunyamin Tar’an, Chellapilla Bharadwaj, Mohammad Yasin, Motisagar S. Pithia, Servejeet Singh, Khela Ram Soren, Himabindu Kudapa, Diego Jarquín, Philippe Cubry, Lee T. Hickey, Girish Prasad Dixit, Anne-Céline Thuillet, Aladdin Hamwieh, Shiv Kumar, Amit A. Deokar, Sushil K. Chaturvedi, Aleena Francis, Réka Howard, Debasis Chattopadhyay, David Edwards, Eric Lyons, Yves Vigouroux, Ben J. Hayes, Eric von Wettberg, Swapan K. Datta, Huanming Yang, Henry T. Nguyen, Jian Wang, Kadambot H. M. Siddique, Trilochan Mohapatra, Jeffrey L. Bennetzen, Xun Xu, and Xin Liu more...
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Multidisciplinary - Published
- 2022
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38. Genotyping-by-sequencing based genetic mapping reveals large number of epistatic interactions for stem rot resistance in groundnut
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P. P. Thirumalaisamy, Rajeev K. Varshney, Chandramohan Sangh, Manish K. Pandey, Sunil S. Gangurde, Pooja Soni, AL Rathnakumar, Annapurna Chitikineni, Sneha M. Dodia, Dayama Narandrakumar, Radhakrishnan Thankappan, Gyan P. Mishra, Jentilal R. Dobaria, Sumitra Chanda, and Binal Joshi more...
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0106 biological sciences ,Candidate gene ,Arachis ,Genotyping Techniques ,Genetic Linkage ,Quantitative Trait Loci ,Population ,Plant disease resistance ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Chromosomes, Plant ,Ascomycota ,Gene interaction ,Genetics ,Inbreeding ,education ,Disease Resistance ,Plant Diseases ,education.field_of_study ,Plant Stems ,Chromosome Mapping ,food and beverages ,Epistasis, Genetic ,Sequence Analysis, DNA ,General Medicine ,Genetic architecture ,Plant disease ,Phenotype ,Genetic Loci ,Stem rot ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Genetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance. Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, diverse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, linkage analysis and quantitative trait locus (QTL) mapping for resistance to stem rot disease was performed in a bi-parental recombinant inbred line population developed from TG37A (susceptible) × NRCG-CS85 (resistant) comprising of 270 individuals. Genotyping-by-sequencing approach was deployed to generate single nucleotide polymorphism (SNP) genotyping data leading to development of a genetic map with 585 SNP loci spanning map distance of 2430 cM. QTL analysis using multi-season phenotyping and genotyping data could not detect any major main-effect QTL but identified 44 major epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%. Large number interactions indicate the complexity of genetic architecture of resistance to stem rot disease. A QTL of physical map length 5.2 Mb identified on B04 comprising 170 different genes especially leucine reach repeats, zinc finger motifs and ethyleneresponsive factors, etc., was identified. The identified genomic regions and candidate genes will further validate and facilitate marker development to deploy GAB for developing stem rot disease resistance groundnut varieties. more...
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- 2018
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39. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.)
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Manish Roorkiwal, Manish K. Pandey, Manda Sriswathi, Shivali Sharma, Baozhu Guo, Krishna Shilpa, Pasupuleti Janila, Pawan Khera, Rajeev K. Varshney, Nalini Mallikarjuna, and Hari Kishan Sudini
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0106 biological sciences ,0301 basic medicine ,Arachis ,Genotype ,Quantitative Trait Loci ,Population ,Introgression ,Quantitative trait locus ,Biology ,01 natural sciences ,Domestication ,Genomic Imprinting ,03 medical and health sciences ,Genetics ,Plant Oils ,education ,Molecular Biology ,Alleles ,Disease Resistance ,Plant Diseases ,education.field_of_study ,Chromosome Mapping ,General Medicine ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Genetic marker ,Backcrossing ,Gene pool ,Genome, Plant ,Microsatellite Repeats ,010606 plant biology & botany - Abstract
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut. more...
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- 2018
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40. Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.)
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C. V. Sameer Kumar, Rachit K. Saxena, Rajeev K. Varshney, Kishan Patel, Kuldeep Tyagi, and Kulbhushan Saxena
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Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Plant Infertility ,Genotype ,Quantitative Trait Loci ,Population ,Inheritance Patterns ,Context (language use) ,Quantitative trait locus ,Biology ,Genes, Plant ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genetic analysis ,03 medical and health sciences ,Cajanus ,Gene mapping ,Genetics ,education ,Genotyping ,Genes, Dominant ,education.field_of_study ,Software maintainer ,Cytoplasmic male sterility ,Chromosome Mapping ,General Medicine ,Plant Breeding ,030104 developmental biology ,Pollen ,Original Article ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Key message We report molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea. We have also developed PCR-based markers amenable to low-cost genotyping to identify fertility restorer lines. Abstract Commercial hybrids in pigeonpea are based on A4 cytoplasmic male sterility (CMS) system, and their fertility restoration is one of the key prerequisites for breeding. In this context, an effort has been made to understand the genetics and identify quantitative trait loci (QTL) associated with restoration of fertility (Rf). One F2 population was developed by crossing CMS line (ICPA 2039) with fertility restorer line (ICPL 87119). Genetic analysis has shown involvement of two dominant genes in regulation of restoration of fertility. In parallel, the genotyping-by-sequencing (GBS) approach has generated ~ 33 Gb data on the F2 population. GBS data have provided 2457 single nucleotide polymorphism (SNPs) segregating across the mapping population. Based on these genotyping data, a genetic map has been developed with 306 SNPs covering a total length 981.9 cM. Further QTL analysis has provided the region flanked by S8_7664779 and S8_6474381 on CcLG08 harboured major QTL explained up to 28.5% phenotypic variation. Subsequently, sequence information within the major QTLs was compared between the maintainer and the restorer lines. From this sequence information, we have developed two PCR-based markers for identification of restorer lines from non-restorer lines and validated them on parental lines of hybrids as well as on another F2 mapping population. The results obtained in this study are expected to enhance the efficiency of selection for the identification of restorer lines in hybrid breeding and may reduce traditional time-consuming phenotyping activities. Electronic supplementary material The online version of this article (10.1007/s00122-018-3101-y) contains supplementary material, which is available to authorized users. more...
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- 2018
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41. A SWEET solution to rice blight
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Susan R. McCouch, Jonathan D. G. Jones, Ian D. Godwin, Trilochan Mohapatra, and Rajeev K. Varshney
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0303 health sciences ,biology ,fungi ,Biomedical Engineering ,food and beverages ,Bioengineering ,Plant disease resistance ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Plant disease ,Southeast asia ,03 medical and health sciences ,0302 clinical medicine ,Xanthomonas oryzae ,Agronomy ,Xanthomonas ,Crop loss ,Molecular Medicine ,Bacterial blight ,Blight ,030217 neurology & neurosurgery ,030304 developmental biology ,Biotechnology - Abstract
Bacterial blight is an important disease of rice that is particularly destructive in Southeast Asia and sub-Saharan Africa, exacerbated by the heavy rains of the monsoon seasons. Estimated crop loss due to bacterial blight may be as high as 75%, with millions of hectares of rice affected annually. In this issue, an international team of researchers describes the use of CRISPR editing to generate rice plants that are broadly resistant to the main pathogen that causes rice blight, Xanthomonas oryzae pv. oryzae (Xoo)1. To enhance the durability and management of resistance, the team has also developed a kit to trace the disease, and its virulence and resistance alleles2. more...
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- 2019
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42. Technological perspectives for plant breeding
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Lee T. Hickey, Jessica Rutkoski, Ian D. Godwin, and Rajeev K. Varshney
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Crops, Agricultural ,Gene Editing ,Genetic Markers ,0106 biological sciences ,Food security ,business.industry ,General Medicine ,Biology ,Plant biology ,01 natural sciences ,Data science ,Plant Breeding ,Agriculture ,Plant biochemistry ,Genetics ,ComputingMethodologies_GENERAL ,Plant breeding ,Selection, Genetic ,Genetic Engineering ,business ,Agronomy and Crop Science ,Genome, Plant ,Selection (genetic algorithm) ,010606 plant biology & botany ,Biotechnology - Abstract
New Breeding Technologies? For some, both inside and outside the scientific community, this phrase is synonymous with gene editing—or used exclusively to describe the application of CRISPR/Cas9 to plant improvement. Much as, historically, the term ‘biotech crops’ has been hijacked to only mean crop plants produced using genetic engineering. However, ‘breeding technologies’ refers not only to genetic modification using techniques of molecular biology, but also to a vast number of other techniques developed for breeding via the application of scientific advancements emanating from disciplines such as computer science, plant biology, statistics, automation, robotics and artificial intelligence. This concept is not new: in reality, technology has been a feature of crop improvement since early in the last century... more...
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- 2019
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43. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
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Jun Wang, Katrien M. Devos, Jianping Wang, Andrew H. Paterson, Cédric Mariac, Xinming Liang, Wenbin Chen, Dadakhalandar Doddamani, Sunil Gupta, Om Parkash Yadav, Rattan Yadav, Eric Lyons, Rajeev K. Varshney, Arindam Ghatak, Wolfram Weckwerth, C. Tom Hash, He Zhang, Mame Codou Gueye, Dev Paudel, Abhishek Rathore, Palak Chaturvedi, R. S. Mahala, Christian Dupuy, Xun Xu, Jeffrey L. Bennetzen, Guangyi Fan, Swapan K. Datta, Yusheng Zhao, Somashekhar Punnuri, Annapurna Chitikineni, Ndjido Ardo Kane, Mohan A. V. S. K. Katta, Falalou Hamidou, Francesca Sparvoli, Jason G. Wallace, Mahendar Thudi, Edward S. Buckler, Joann A. Conner, Prasad Bajaj, Xiyin Wang, Ramanjulu Sunkar, Peggy Ozias-Akins, Marie Couderc, Bharat P. Singh, Trilochan Mohapatra, Stefania Grando, Xin Liu, Bénédicte Rhoné, Vanika Garg, K. D. Mungra, Hari D. Upadhyaya, Chengcheng Shi, Peng Qi, Philippe Cubry, Yong Jiang, Hao Wang, Karen R. Harris-Shultz, Sabarinath Subramaniam, Yves Vigouroux, Jérémy Clotault, Cécile Berthouly-Salazar, Shifeng Cheng, Jochen C. Reif, Neetin Desai, Rakesh K. Srivastava, Institut des Mondes Africains (IMAF), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Numerical modeling and high performance computing for evolution problems in complex domains and heterogeneous media (NACHOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Unité de Mécanique (UME), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), State Key Laboratory of Fine Chemicals, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) more...
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0301 basic medicine ,genome sequence ,[SDV]Life Sciences [q-bio] ,adaptation ,Applied Microbiology and Biotechnology ,hybridism ,Conserved Sequence ,2. Zero hunger ,Agriculture ,Staple food ,genetic diversity ,Genomics ,hybridations ,Phenotype ,diversité génétique ,pennisetum glaucum ,Molecular Medicine ,Desert Climate ,pearl millet ,Genome, Plant ,Biotechnology ,Agricultural genetics ,Pennisetum ,[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory ,Drought tolerance ,Biomedical Engineering ,Bioengineering ,Biology ,Genes, Plant ,milieu aride ,Article ,domestication ,03 medical and health sciences ,Quantitative Trait, Heritable ,Mil (Cenchrus americanus) ,Genetic variation ,Plant breeding ,Domestication ,Millet (Cenchrus americanus) ,Genetic diversity ,Base Sequence ,Genetic Variation ,Molecular Sequence Annotation ,15. Life on land ,Arid ,arid environment ,Plant Breeding ,030104 developmental biology ,Agronomy ,Next-generation sequencing ,Hybridization, Genetic ,Genome-Wide Association Study - Abstract
Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users., Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users. more...
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- 2017
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44. Marker-assisted introgression of resistance to fusarium wilt race 2 in Pusa 256, an elite cultivar of desi chickpea
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Mahender Thudi, Rakhi Tomar, Sushil K. Chaturvedi, Rajeev K. Varshney, Nupur Malviya, Aditya Pratap, N. P. Singh, Neha Rajan, P. R. Saabale, and Umashanker Prajapati
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Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Fusarium ,Introgression ,01 natural sciences ,03 medical and health sciences ,Botany ,Genetics ,Cultivar ,Molecular Biology ,Pusa ,biology ,food and beverages ,General Medicine ,Background selection ,biology.organism_classification ,Cicer ,Fusarium wilt ,Horticulture ,030104 developmental biology ,Genetic marker ,Host-Pathogen Interactions ,Backcrossing ,010606 plant biology & botany - Abstract
Fusarium wilt caused by F. oxysporum f. sp. ciceris causes extensive damage to chickpea (Cicer arietinum L.) in many parts of the world. In the central part of India, pathogen race 2 (Foc 2) causes severe yield losses. We initiated molecular marker-assisted backcrossing (MABC) using desi cultivar, Vijay, as a donor to introgress resistance to this race (Foc2) in Pusa 256, another elite desi cultivar of chickpea. To confirm introgression of resistance for this race, foreground selection was undertaken using two SSR markers (TA 37 and TA110), with background selection to observe the recovery of recurrent parent genome using 45 SSRs accommodated in 8 multiplexes. F1 plants were confirmed with molecular markers and backcrossed with Pusa 256, followed by cycles of foreground and background selection at each stage to generate 161 plants in BC3F2 during the period 2009-2013. Similarly, 46 BC3F1 plants were also generated in another set during the same period. On the basis of foreground selection, 46 plants were found homozygotes in BC3F2. Among them, 17 plants recorded >91% background recovery with the highest recovery percentage of 96%. In BC3F1 also, 14 hybrid plants recorded a background recovery of >85% with the highest background recovery percentage of >94%. The identified plants were selfed to obtain 1341 BC3F3 and 2198 BC3F2 seeds which were screened phenotypically for resistance to fusarium wilt (race 2) besides doing marker analysis. Finally, 17 BC3F4 and 11 BC3F3 lines were obtained which led to identification of 5 highly resistant lines of Pusa 256 with Foc 2 gene introgressed in them. Development of these lines will help in horizontal as well as vertical expansion of chickpea in central part of India. more...
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- 2017
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45. Can a speed breeding approach accelerate genetic gain in pigeonpea?
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Lee T. Hickey, Rachit K. Saxena, Rajeev K. Varshney, and Kulbhushan Saxena
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0106 biological sciences ,0301 basic medicine ,biology ,food and beverages ,Plant Science ,Field tests ,Horticulture ,biology.organism_classification ,01 natural sciences ,Crop ,03 medical and health sciences ,Cajanus ,030104 developmental biology ,Agronomy ,Genetic gain ,Genetics ,Cultivar ,Plant breeding ,Genetic variability ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Pure line breeding is a resource-intensive activity that takes 10 years or more to develop a new cultivar. In some crops, conducting off-season nurseries has significantly reduced the length of the breeding cycle. This approach could not be exploited in pigeonpea [Cajanus cajan (L.) Millsp.], because traditionally it has been a photoperiod-sensitive crop that requires long periods of darkness to induce flowering. However, the recent success of breeding early maturing photoperiod-insensitive genotypes has opened up the possibility of adopting ‘speed breeding’ techniques to enable rapid generation turnover. This paper outlines a speed breeding approach that integrates the use of immature seed germination for rapid generation advancement and a “single pod descent” method of breeding. To accelerate line development, while conserving genetic variability, the approach permits four generations per year and can fast-track field evaluation of resulting homozygous lines. Therefore, the breeding strategy conserves resources and has potential to deliver new early maturing cultivars within a substantially reduced timeframe of 4–5 years. more...
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- 2019
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46. Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
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Tobias Kretzschmar, Joshua N. Cobb, Line Sandager, Erwin Tandayu, Annalhea Jarana, Rajeev K. Varshney, Patrik Stolt, Maria Ymber Reveche, Petra van Rogen, Juan David Arbelaez, and Enghwa Ng
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Genotyping ,Breeding program ,Rapid generation advancement ,Plant Science ,Breeding ,lcsh:Plant culture ,Biology ,Bottleneck ,Single nucleotide polymorphism (SNP) ,Genetics ,lcsh:SB1-1110 ,Plant breeding ,Seed DNA extraction ,lcsh:QH301-705.5 ,Panicle ,Rice (Oryza sativa L.) ,business.industry ,Methodology ,food and beverages ,Sowing ,Marker-assisted selection ,Forward breeding ,Biotechnology ,Fixation (population genetics) ,lcsh:Biology (General) ,Genetic gain ,Marker-assisted selection (MAS) ,business - Abstract
Background Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. Results Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. Conclusion This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development. Electronic supplementary material The online version of this article (10.1186/s13007-019-0464-2) contains supplementary material, which is available to authorized users. more...
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- 2019
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47. Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems
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Ram Baran Yadaw, Santosh Kumar, Arvind Kumar, Vikas K. Singh, Sushil Raj Subedi, M. P. Pandey, Surya Kant Ghimire, Nitika Sandhu, Rajeev K. Varshney, Pallavi Sinha, and S. P. Singh
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0301 basic medicine ,Edible Grain ,media_common.quotation_subject ,Quantitative Trait Loci ,Population ,lcsh:Medicine ,Plant Development ,Biology ,Quantitative trait locus ,Genome-wide association studies ,Plant Roots ,Polymorphism, Single Nucleotide ,Article ,Linkage Disequilibrium ,Adaptability ,03 medical and health sciences ,Quantitative Trait, Heritable ,0302 clinical medicine ,Nutrient ,Yield (wine) ,Cluster Analysis ,Plant breeding ,lcsh:Science ,education ,Genetic Association Studies ,media_common ,education.field_of_study ,Multidisciplinary ,lcsh:R ,Chromosome Mapping ,food and beverages ,Oryza ,Genomics ,Nutrients ,Phenotype ,Plant Breeding ,Genetics, Population ,030104 developmental biology ,Biological Variation, Population ,Agronomy ,Seedlings ,Seeds ,lcsh:Q ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR. more...
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- 2019
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48. Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition
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Santosh Kumar, M. P. Pandey, Surya Kant Ghimire, Ram Baran Yadaw, Vikas K. Singh, Nitika Sandhu, Pallavi Sinha, S. P. Singh, Rajeev K. Varshney, Arvind Kumar, and Sushil Raj Subedi
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Genetic Markers ,Marker-trait association ,0106 biological sciences ,Yield ,lcsh:QH426-470 ,lcsh:Biotechnology ,media_common.quotation_subject ,Genome-wide association study ,Root hair ,01 natural sciences ,Linkage Disequilibrium ,Adaptability ,03 medical and health sciences ,Nutrient ,lcsh:TP248.13-248.65 ,Yield (wine) ,Genetics ,Nutrient uptake ,030304 developmental biology ,media_common ,0303 health sciences ,biology ,food and beverages ,Oryza ,Genomics ,biology.organism_classification ,Adaptation, Physiological ,lcsh:Genetics ,Phenotype ,Root ,Agronomy ,Seedlings ,Seedling ,Trait ,Dry direct seeded ,Seeding ,Rice ,Genome-Wide Association Study ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system. Results Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10− 4, 0.0330 to 1.25 × 10− 4, and 0.0534 to 4.60 × 10− 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development. Conclusions Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR. Electronic supplementary material The online version of this article (10.1186/s12864-019-5840-9) contains supplementary material, which is available to authorized users. more...
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- 2019
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49. Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.)
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Yuning Chen, Nian Liu, Dongxin Huai, Hari K. Sudini, Weigang Chen, Rajeev K. Varshney, Xiaojing Zhou, Boshou Liao, Yanping Kang, Huifang Jiang, Xiaoping Ren, Manish K. Pandey, Bolun Yu, Li Huang, Huaiyong Luo, and Yong Lei more...
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Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Germplasm ,Veterinary medicine ,Aflatoxin ,Arachis ,lcsh:QH426-470 ,QTL ,Quantitative Trait Loci ,Resistance ,Population ,Food Contamination ,Aspergillus flavus ,Quantitative trait locus ,01 natural sciences ,03 medical and health sciences ,Aflatoxins ,Inbred strain ,Genetics ,Diagnostic marker ,education ,Genotyping ,Genetics (clinical) ,Recombination, Genetic ,education.field_of_study ,biology ,food and beverages ,Genomics ,biology.organism_classification ,lcsh:Genetics ,Phenotype ,Peanut ,030104 developmental biology ,Genome, Plant ,Research Article ,010606 plant biology & botany ,Food contaminant - Abstract
Background Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed infection and/or aflatoxin accumulation is the most effective and economic strategy for reducing aflatoxin risk in food chain. Breeding for resistance to aflatoxin in peanut is a challenging task for breeders because the genetic basis is still poorly understood. To identify the quantitative trait loci (QTLs) for resistance to aflatoxin contamination in peanut, a recombinant inbred line (RIL) population was developed from crossing Zhonghua 10 (susceptible) with ICG 12625 (resistant). The percent seed infection index (PSII), the contents of aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) of RILs were evaluated by a laboratory kernel inoculation assay. Results Two QTLs were identified for PSII including one major QTL with 11.32–13.00% phenotypic variance explained (PVE). A total of 12 QTLs for aflatoxin accumulation were detected by unconditional analysis, and four of them (qAFB1A07 and qAFB1B06.1 for AFB1, qAFB2A07 and qAFB2B06 for AFB2) exhibited major and stable effects across multiple environments with 9.32–21.02% PVE. Furthermore, not only qAFB1A07 and qAFB2A07 were co-localized in the same genetic interval on LG A07, but qAFB1B06.1 was also co-localized with qAFB2B06 on LG B06. Conditional QTL mapping also confirmed that there was a strong interaction between resistance to AFB1 and AFB2 accumulation. Genotyping of RILs revealed that qAFB1A07 and qAFB1B06.1 interacted additively to improve the resistance to both AFB1 and AFB2 accumulation. Additionally, validation of the two markers was performed in diversified germplasm collection and four accessions with resistance to aflatoxin accumulation were identified. Conclusions Single major QTL for resistance to PSII and two important co-localized intervals associated with major QTLs for resistance to AFB1 and AFB2. Combination of these intervals could improve the resistance to aflatoxin accumulation in peanut. SSR markers linked to these intervals were identified and validated. The identified QTLs and associated markers exhibit potential to be applied in improvement of resistance to aflatoxin contamination. Electronic supplementary material The online version of this article (10.1186/s12863-019-0734-z) contains supplementary material, which is available to authorized users. more...
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- 2019
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50. Inheritance of protein content and its relationships with seed size, grain yield and other traits in chickpea
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Pooran M. Gaur, Aravind K. Jukanti, Muneendra K. Singh, Sobhan B. Sajja, Rajeev K. Varshney, Suresh Kamatam, and Srinivasan Samineni
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0106 biological sciences ,Coat ,Low protein ,fungi ,food and beverages ,Pulse crop ,Plant physiology ,04 agricultural and veterinary sciences ,Plant Science ,Horticulture ,Biology ,Quantitative trait locus ,01 natural sciences ,Protein content ,Agronomy ,040103 agronomy & agriculture ,Genetics ,0401 agriculture, forestry, and fisheries ,Grain yield ,Cultivar ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Chickpea (Cicer arietinum L.), the second largest grown pulse crop of the world, is an important source of protein for millions of people, particularly in South Asia. Development of chickpea cultivars with further enhanced levels of protein is highly desired. This study was aimed at understanding the genetic control of protein content and its association with other traits so that suitable breeding strategies can be prepared for development of high protein content cultivars. A high protein (29.2 %) desi chickpea line ICC 5912 with pea-shaped small seed, grey seed coat and blue flower was crossed with a low protein (20.5 %) kabuli line ICC 17109 with owl’s head shaped large seed, beige seed coat, and white flower. The F2 population was evaluated under field conditions and observations were recorded on protein content and other traits on individual plants. The protein content of F2 segregants showed continuous distribution suggesting that it is a quantitative trait controlled by multiple genes. The blue flowered segregants had pea shaped seed with grey seed coat, while the white flowered segregants had owl’s head shaped seed with beige seed coat indicating pleiotropic effects of gene(s) on these traits. On an average, blue flowered segregants had smaller seed, lower grain yield per plant and higher protein content than the pink flowered and the white flowered segregants. The protein content was negatively correlated with seed size (r = −0.40) and grain yield per plant (r = −0.18). Thus, an increment in protein content is expected to have a negative effect on seed size and grain yield. However, careful selection of transgressive segregants with high protein content along with moderate seed size and utilizing diverse sources of high protein content will be usefull in developing chickpea cultivars with high protein content and high grain yield. more...
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- 2016
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