35 results on '"Mallana Gowdra Mallikarjuna"'
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2. Editorial: Application of network-theoretic approaches in biology
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Mallana Gowdra Mallikarjuna, Manish Kumar Pandey, Rinku Sharma, Josh Clevenger, and Sudeepto Bhattacharya
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gene regulatory network ,co-expression analyses ,network theoretic approaches ,biology ,protein–protein interaction ,systems biology ,Genetics ,QH426-470 - Published
- 2023
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3. Development of bread wheat (Triticum aestivum L) variety HD3411 following marker-assisted backcross breeding for drought tolerance
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Prashanth K. C. Kumar, Amasiddha Bellundagi, Hari Krishna, Mallana Gowdra Mallikarjuna, Ramya K. Thimmappa, Neha Rai, P. Shashikumara, Nivedita Sinha, Neelu Jain, Pradeep K. Singh, Gyanendra Pratap Singh, and Kumble Vinod Prabhu
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drought tolerance ,wheat ,MAS ,foreground selection ,background selection ,Genetics ,QH426-470 - Abstract
Marker-assisted backcross breeding enables selective insertion of targeted traits into the genome to improve yield, quality, and stress resistance in wheat. In the current investigation, we transferred four drought tolerance quantitative trait loci (QTLs) controlling traits, viz canopy temperature, normalized difference vegetative index, chlorophyll content, and grain yield from the drought-tolerant donor line, C306, into a popular high-yielding, drought-sensitive variety, HD2733. Marker-assisted selection coupled with stringent phenotypic screening was used to advance each generation. This study resulted in 23 improved lines carrying combinations of four drought tolerance QTLs with a range of 85.35%–95.79% background recovery. The backcross-derived lines gave a higher yield under moisture-deficit stress conditions compared with the recipient parent. They also showed higher phenotypic mean values for physiological traits and stability characteristics of HD2733. A promising genotype, HD3411, derived from this cross was identified for release after national multi-location coordinating trials under the All India Coordinated Wheat Improvement Project. Our study is a prime example of the advantages of precision breeding using integrating markers and phenotypic selection to develop new cultivars with desirable traits like drought tolerance.
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- 2023
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4. Comparative Assessment of Genetic Variability Realised in Doubled Haploids Induced from F1 and F2 Plants for Response to Fusarium Stalk Rot and Yield Traits in Maize (Zea mays L.)
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Budensab Mamtazbi Showkath Babu, Hirenallur Chandappa Lohithaswa, Gangadharaswamy Triveni, Mallana Gowdra Mallikarjuna, Nanjundappa Mallikarjuna, Devanagondi C. Balasundara, and Pandravada Anand
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maize ,Fusarium stalk rot (FSR) ,F1 ,F2 ,doubled haploids (DH) ,genetic variance ,Agriculture - Abstract
Doubled-haploid lines (DHs) are normally produced from F1 plants in maize (Zea mays L.). Several studies have found a low frequency of recombinants in doubled haploids produced from F1 plants that could limit the selection response. Hence, an attempt was made to produce doubled haploids from the F2 generation to verify whether one more round of meiotic recombination could lead to increased genetic variability and assess the response to selection. The F1 and F2 plants of two cross-combinations, VL1043 × CM212 and VL121096 × CM202, were subjected to doubled-haploid production and evaluated in terms of their reaction to Fusarium stalk rot and yield traits along with F2 individuals of the same two crosses. There was significant variation in the number of DHs produced when F1 and F2 plants were subjected to DH production in the cross VL121096 × CM202. Furthermore, substantial genetic variability was observed among the DHs produced from the F1 generation (DHF1s), F2 generation (DHF2s), and F2s for Fusarium stalk rot (FSR) resistance. The genetic variance was more extensive in DHF2 compared to DHF1 plants in the cross VL1043 × CM212. Extreme candidate plants (highly resistant, resistant, and highly susceptible) were found in the F2 generation with a more standardized range than in the DHs. In the DH populations, the close correspondence between the phenotypic coefficient of variability (PCV) and the genotypic coefficient of variability (GCV) indicated less influence from the environment compared to the F2 plants. The heritability estimates in the DHs were greater than in the F2 plants of the VL1043 × CM212 cross, while in the VL121096 × CM202 cross, the heritability was almost the same between the DHs and F2 plants due to the relatively small population size of the DHs. The positively skewed leptokurtic distribution of the DH populations indicated the role of fewer genes, with the majority of them exhibiting complementary epistasis with decreasing effects in response to FSR. The mean estimated yield and genotypic variance in the top crosses produced from randomly chosen DHF1 and DHF2 plants of the cross VL1043 × CM212 were similar in magnitude.
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- 2022
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5. Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi
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Shilpi Bansal, Mallana Gowdra Mallikarjuna, Alexander Balamurugan, S. Chandra Nayaka, and Ganesan Prakash
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Ascomycetes ,codon usage bias ,fungi ,compositional constraints ,host–pathogen interaction ,natural selection ,Biology (General) ,QH301-705.5 - Abstract
Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host–pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host–pathogen interactions through genome editing and functional genomics tools.
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- 2022
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6. RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize
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Kanika Arora, Kusuma Kumari Panda, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, and Nepolean Thirunavukkarasu
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Medicine ,Science - Abstract
Abstract Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition. Also, high up-regulation of expansins (42-fold), plant aspartic protease A3 (19-fold), polygalacturonases (16-fold), respiratory burst oxidase homolog (12-fold), and hydrolases (11-fold) explained the PCD of root cortical cells followed by the formation of aerenchyma tissue during waterlogging stress. We hypothesized that the oxygen transfer in waterlogged roots is promoted by a cross-talk of fermentative, metabolic, and glycolytic pathways that generate ATPs for PCD and aerenchyma formation in root cortical cells. SNPs were mapped to the DEGs regulating aerenchyma formation (12), ethylene-responsive factors (11), and glycolysis (4) under stress. RNAseq derived SNPs can be used in selection approaches to breed tolerant hybrids. Overall, this investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.
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- 2017
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7. Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.)
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Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu, Rinku Sharma, Kaliyugam Shiriga, Firoz Hossain, Jayant S Bhat, Amitha CR Mithra, Soma Sunder Marla, Kanchikeri Math Manjaiah, AR Rao, and Hari Shanker Gupta
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functional genomics ,homeostasis ,hormonal regulation ,iron ,maize ,malnutrition ,Botany ,QK1-989 - Abstract
Globally, one-third of the population is affected by iron (Fe) and zinc (Zn) deficiency, which is severe in developing and underdeveloped countries where cereal-based diets predominate. The genetic biofortification approach is the most sustainable and one of the cost-effective ways to address Fe and Zn malnutrition. Maize is a major source of nutrition in sub-Saharan Africa, South Asia and Latin America. Understanding systems’ biology and the identification of genes involved in Fe and Zn homeostasis facilitate the development of Fe- and Zn-enriched maize. We conducted a genome-wide transcriptome assay in maize inbred SKV616, under –Zn, –Fe and –Fe–Zn stresses. The results revealed the differential expression of several genes related to the mugineic acid pathway, metal transporters, photosynthesis, phytohormone and carbohydrate metabolism. We report here Fe and Zn deficiency-mediated changes in the transcriptome, root length, stomatal conductance, transpiration rate and reduced rate of photosynthesis. Furthermore, the presence of multiple regulatory elements and/or the co-factor nature of Fe and Zn in enzymes indicate their association with the differential expression and opposite regulation of several key gene(s). The differentially expressed candidate genes in the present investigation would help in breeding for Fe and Zn efficient and kernel Fe- and Zn-rich maize cultivars through gene editing, transgenics and molecular breeding.
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- 2020
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8. Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement
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Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri R. Rao, Prashant A. Jain, Prasanta K. Dash, and Nepolean Thirunavukkarasu
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CDPK ,differential expression ,drought ,3-D protein structure ,functional mechanism ,Chemistry ,QD1-999 - Abstract
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
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- 2017
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9. In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize
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Kanika Arora, Kusuma Kumari Panda, Shikha Mittal, Mallana Gowdra Mallikarjuna, and Nepolean Thirunavukkarasu
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Biology (General) ,QH301-705.5 - Abstract
Cell wall modification (CWM) promotes the formation of aerenchyma in roots under waterlogging conditions as an adaptive mechanism. Lysigenous aerenchyma formation in roots improves oxygen transfer in plants, which highlights the importance of CWM as a focal point in waterlogging stress tolerance. We investigated the structural and functional compositions of CWM genes and their expression patterns under waterlogging conditions in maize. Cell wall modification genes were identified for 3 known waterlogging-responsive cis -acting regulatory elements, namely, GC motif, anaerobic response elements, and G-box, and 2 unnamed elements. Structural motifs mapped in CWM genes were represented in genes regulating waterlogging stress-tolerant pathways, including fermentation, glycolysis, programmed cell death, and reactive oxygen species signaling. The highly aligned regions of characterized and uncharacterized CWM proteins revealed common structural domains amongst them. Membrane spanning regions present in the protein structures revealed transmembrane activity of CWM proteins in the plant cell wall. Cell wall modification proteins had interacted with ethylene-responsive pathway regulating genes (E3 ubiquitin ligases RNG finger and F-box) in a maize protein-protein interaction network. Cell wall modification genes had also coexpressed with energy metabolism, programmed cell death, and reactive oxygen species signaling, regulating genes in a single coexpression cluster. These configurations of CWM genes can be used to modify the protein expression in maize under waterlogging stress condition. Our study established the importance of CWM genes in waterlogging tolerance, and these genes can be used as candidates in introgression breeding and genome editing experiments to impart tolerance in maize hybrids.
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- 2017
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10. Variable Level of Dominance of Candidate Genes Controlling Drought Functional Traits in Maize Hybrids
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Ha Van Gioi, Mallana Gowdra Mallikarjuna, Mittal Shikha, Banduni Pooja, Shailendra K. Jha, Prasanta K. Dash, Arunkumar M. Basappa, Raveendra N. Gadag, Atmakuri Ramakrishna Rao, and Thirunavukkarasu Nepolean
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additive ,adaptive traits ,candidate genes ,dominance ,drought ,functional traits ,Plant culture ,SB1-1110 - Abstract
Breeding maize for drought tolerance necessitates the knowledge on tolerant genotypes, molecular basis of drought tolerance mechanism, action, and expression pattern of genes. Studying the expression pattern and gene action of candidate genes during drought stress in the hybrids will help in choosing target genes for drought tolerance breeding. In the present investigation, a set of five hybrids and their seven parents with a variable level of tolerance to drought stress was selected to study the magnitude and the direction of 52 drought-responsive candidate genes distributed across various biological functions, viz., stomatal regulation, root development, detoxification, hormone signaling, photosynthesis, and sugar metabolism. The tolerant parents, HKI1105 and CML425, and their hybrid, ADWLH2, were physiologically active under drought stress, since vital parameters viz., chlorophyll, root length and relative water content, were on par with the respective well-watered control. All the genes were up-regulated in ADWLH2, many were down-regulated in HM8 and HM9, and most were down-regulated in PMH1 and PMH3 in the shoots and roots. The nature of the gene action was controlled by the parental combination rather than the parent per se. The differentially expressed genes in all five hybrids explained a mostly non-additive gene action over additivity, which was skewed toward any of the parental lines. Tissue-specific gene action was also noticed in many of the genes. The non-additive gene action is driven by genetic diversity, allele polymorphism, events during gene regulation, and small RNAs under the stress condition. Differential regulation and cross-talk of genes controlling various biological functions explained the basis of drought tolerance in subtropical maize hybrids. The nature of the gene action and the direction of the expression play crucial roles in designing introgression and hybrid breeding programmes to breed drought tolerant maize hybrids.
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- 2017
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11. Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds
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Jayaraman Aravind, Sharma Rinku, Banduni Pooja, Mittal Shikha, Shiriga Kaliyugam, Mallana Gowdra Mallikarjuna, Arun Kumar, Atmakuri Ramakrishna Rao, and Thirunavukkarasu Nepolean
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drought ,gene expression ,maize ,miRNA ,mRNA ,post-transcriptional changes ,Plant culture ,SB1-1110 - Abstract
MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance. In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization. The largest number of members (14) was found in the zma-miR166 and zma-miR395 families, with several targets. However, zma-miR160, zma-miR390, zma-miR393, and zma-miR2275 each showed a single target. Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs. Many drought-related transcription factors, such as GAMYB, HD-Zip III, and NAC, were associated with the target mRNAs. Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372) were used to understand the miRNA-assisted regulation of target mRNA under drought stress. Approximately 35 and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively. The up-regulation of target mRNAs was as high as 14.2% in HKI-1532 but was only 2.38% in V-372. The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation, and Type IV- opposite regulation. HKI-1532 displayed 46 Type I, 13 Type II, and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151). A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance. Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids.
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- 2017
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12. Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize
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Thirunavukkarasu Nepolean, Mittal Shikha, Arora Kanika, Atmakuri Ramakrishna Rao, Mallana Gowdra Mallikarjuna, and Hari Shanker Gupta
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drought ,genomic selection ,transcription factor ,SNP ,parametric ,non-parametric ,Plant culture ,SB1-1110 - Abstract
Traditional breeding strategies for selecting superior genotypes depending on phenotypic traits have proven to be of limited success, as this direct selection is hindered by low heritability, genetic interactions such as epistasis, environmental-genotype interactions, and polygenic effects. With the advent of new genomic tools, breeders have paved a way for selecting superior breeds. Genomic selection (GS) has emerged as one of the most important approaches for predicting genotype performance. Here, we tested the breeding values of 240 maize subtropical lines phenotyped for drought at different environments using 29,619 cured SNPs. Prediction accuracies of seven genomic selection models (ridge regression, LASSO, elastic net, random forest, reproducing kernel Hilbert space, Bayes A and Bayes B) were tested for their agronomic traits. Though prediction accuracies of Bayes B, Bayes A and RKHS were comparable, Bayes B outperformed the other models by predicting highest Pearson correlation coefficient in all three environments. From Bayes B, a set of the top 1053 significant SNPs with higher marker effects was selected across all datasets to validate the genes and QTLs. Out of these 1053 SNPs, 77 SNPs associated with 10 drought-responsive transcription factors. These transcription factors were associated with different physiological and molecular functions (stomatal closure, root development, hormonal signaling and photosynthesis). Of several models, Bayes B has been shown to have the highest level of prediction accuracy for our data sets. Our experiments also highlighted several SNPs based on their performance and relative importance to drought tolerance. The result of our experiments is important for the selection of superior genotypes and candidate genes for breeding drought-tolerant maize hybrids.
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- 2017
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13. Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
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Nepolean Thirunavukkarasu, Rinku Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Firoz Hossain, and Hari Shanker Gupta
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Genetics ,QH426-470 - Abstract
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
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- 2017
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14. Correction: Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones.
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Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu, Firoz Hossain, Jayant S Bhat, Shailendra K Jha, Abhishek Rathore, Pawan Kumar Agrawal, Arunava Pattanayak, Sokka S Reddy, Satish Kumar Gularia, Anju Mahendru Singh, Kanchikeri Math Manjaiah, and Hari Shanker Gupta
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Medicine ,Science - Published
- 2015
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15. Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones.
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Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu, Firoz Hossain, Jayant S Bhat, Shailendra K Jha, Abhishek Rathore, Pawan Kumar Agrawal, Arunava Pattanayak, Sokka S Reddy, Satish Kumar Gularia, Anju Mahendru Singh, Kanchikeri Math Manjaiah, and Hari Shanker Gupta
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Medicine ,Science - Abstract
Deficiency of iron and zinc causes micronutrient malnutrition or hidden hunger, which severely affects ~25% of global population. Genetic biofortification of maize has emerged as cost effective and sustainable approach in addressing malnourishment of iron and zinc deficiency. Therefore, understanding the genetic variation and stability of kernel micronutrients and grain yield of the maize inbreds is a prerequisite in breeding micronutrient-rich high yielding hybrids to alleviate micronutrient malnutrition. We report here, the genetic variability and stability of the kernel micronutrients concentration and grain yield in a set of 50 maize inbred panel selected from the national and the international centres that were raised at six different maize growing regions of India. Phenotyping of kernels using inductively coupled plasma mass spectrometry (ICP-MS) revealed considerable variability for kernel minerals concentration (iron: 18.88 to 47.65 mg kg(-1); zinc: 5.41 to 30.85 mg kg(-1); manganese: 3.30 to 17.73 mg kg(-1); copper: 0.53 to 5.48 mg kg(-1)) and grain yield (826.6 to 5413 kg ha(-1)). Significant positive correlation was observed between kernel iron and zinc within (r = 0.37 to r = 0.52, p < 0.05) and across locations (r = 0.44, p < 0.01). Variance components of the additive main effects and multiplicative interactions (AMMI) model showed significant genotype and genotype × environment interaction for kernel minerals concentration and grain yield. Most of the variation was contributed by genotype main effect for kernel iron (39.6%), manganese (41.34%) and copper (41.12%), and environment main effects for both kernel zinc (40.5%) and grain yield (37.0%). Genotype main effect plus genotype-by-environment interaction (GGE) biplot identified several mega environments for kernel minerals and grain yield. Comparison of stability parameters revealed AMMI stability value (ASV) as the better representative of the AMMI stability parameters. Dynamic stability parameter GGE distance (GGED) showed strong and positive correlation with both mean kernel concentrations and grain yield. Inbreds (CM-501, SKV-775, HUZM-185) identified from the present investigation will be useful in developing micronutrient-rich as well as stable maize hybrids without compromising grain yield.
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- 2015
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16. Unravelling structural, functional, evolutionary and genetic basis of SWEET transporters regulating abiotic stress tolerance in maize
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P.N. Vinodh Kumar, Mallana Gowdra Mallikarjuna, Shailendra Kumar Jha, Anima Mahato, Shambhu Krishan Lal, Yathish K.R., Hirenallur Chandappa Lohithaswa, and Viswanathan Chinnusamy
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Structural Biology ,General Medicine ,Molecular Biology ,Biochemistry - Abstract
Sugars Will Eventually be Exported Transporters (SWEETs) are the novel sugar transporters widely distributed among living systems. SWEETs play a crucial role in various bio-physiological processes, viz., plant developmental, nectar secretion, pollen development, and regulation of biotic and abiotic stresses, in addition to their prime sugar-transporting activity. Thus, in-depth structural, evolutionary, and functional characterization of maize SWEET transporters was performed for their utility in maize improvement. The mining of SWEET genes in the latest maize genome release (v.5) showed an uneven distribution of 20 ZmSWEETs. The comprehensive structural analyses and docking of ZmSWEETs with four sugars, viz., fructose, galactose, glucose, and sucrose, revealed frequent amino acid residues forming hydrogen (asparagine, valine, serine) and hydrophobic (tryptophan, glycine, and phenylalanine) interactions. Evolutionary analyses of SWEETs showed a mixed lineage with 50-100 % commonality of ortho-groups and -sequences evolved under strong purifying selection (Ka/Ks 0.5). The duplication analysis showed non-functionalization (ZmSWEET18 in B73) and neo- and sub-functionalization (ZmSWEET3, ZmSWEET6, ZmSWEET9, ZmSWEET19, and ZmSWEET20) events in maize. Functional analyses of ZmSWEET genes through co-expression, in silico expression and qRT-PCR assays showed the relevance of ZmSWEETs expression in regulating drought, heat, and waterlogging stress tolerances in maize. The first ever ZmSWEET-regulatory network revealed 286 direct (ZmSWEET-TF: 140 ZmSWEET-miRNA: 146) and 1226 indirect (TF-TF: 597; TF-miRNA: 629) edges. The present investigation has given new insights into the complex transcriptional and post-transcriptional regulation and the regulatory and functional relevance of ZmSWEETs in assigning stress tolerance in maize.
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- 2022
17. Corrigendum to 'Unravelling structural, functional, evolutionary and genetic basis of SWEET transporters regulating abiotic stress tolerance in maize' [Int. J. Biol. Macromol. 229 (2023) 539–560]
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P.N. Vinodh Kumar, Mallana Gowdra Mallikarjuna, Shailendra Kumar Jha, Anima Mahato, Shambhu Krishan Lal, K.R. Yathish, Hirenallur Chandappa Lohithaswa, and Viswanathan Chinnusamy
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Structural Biology ,General Medicine ,Molecular Biology ,Biochemistry - Published
- 2023
18. Characterization and validation of hypothetical virulence factors in recently sequenced genomes of Magnaporthe species
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Shilpi Bansal, Mallana Gowdra Mallikarjuna, Bhaskar Reddy, Alexander Balamurugan, V. Mohan Murali Achary, Malireddy K. Reddy, Aundy Kumar, and Ganesan Prakash
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Genetics ,Plant Science - Published
- 2023
19. Genome-Wide Association Studies and Genomic Selection for Nutrient Use Efficiency in Cereals
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Bingi Pujari Mallikarjuna, Niveditha Shettigar, Dattatraya Hegde Radhika, E. Lamalakshmi Devi, Jayant S. Bhat, B. S. Patil, Hirenallur Chandappa Lohithaswa, and Mallana Gowdra Mallikarjuna
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- 2022
20. Next-Generation Breeding Approaches for Stress Resilience in Cereals: Current Status and Future Prospects
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Mallana Gowdra Mallikarjuna, Palanisamy Veeraya, Rakhi Tomar, Shailendra Jha, S. Chandra Nayaka, H. C. Lohithaswa, and Viswanathan Chinnusamy
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- 2022
21. Genomic and Bioinformatic Resources for Next-Generation Breeding Approaches Towards Enhanced Stress Tolerance in Cereals
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Rinku Sharma, Mallana Gowdra Mallikarjuna, K. R. Yathish, Chikkappa G. Karjagi, and H. C. Lohithaswa
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- 2022
22. Genomic Selection for Enhanced Stress Tolerance in Maize
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Hirenallur Chandappa Lohithaswa, Sowmya Muntagodu Shreekanth, Santhosh Kumari Banakara, K. V. Sripathy, and Mallana Gowdra Mallikarjuna
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- 2022
23. Evolutionary and functional characterisation of glutathione peroxidases showed splicing mediated stress responses in Maize
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Mallana Gowdra Mallikarjuna, Rinku Sharma, Palanisamy Veeraya, Akshita Tyagi, Atmakuri Ramakrishna Rao, Lohithaswa Hirenallur Chandappa, and Viswanathan Chinnusamy
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Glutathione Peroxidase ,Physiology ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetics ,Plant Science ,Hydrogen Peroxide ,Zea mays ,Droughts - Abstract
Maize (Zea mays L) is an important cereal with extensive adaptability and multifaceted usages. However, various abiotic and biotic stresses limit the productivity of maize across the globe. Exposure of plant to stresses disturb the balance between reactive oxygen species (ROS) production and scavenging, which subsequently increases cellular damage and death of plants. Tolerant genotypes have evolved higher output of scavenging antioxidative defence compounds (ADCs) during stresses as one of the protective mechanisms. The glutathione peroxidases (GPXs) are the broad class of ADCs family. The plant GPXs catalyse the reduction of hydrogen peroxide (H
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- 2021
24. Genetic Enhancement of Heat Tolerance in Maize Through Conventional and Modern Strategies
- Author
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Firoz Hossain, Chikkappa G. Karjagi, Akshita Tyagi, Jayant S. Bhat, Mallana Gowdra Mallikarjuna, Palanisamy Veeraya, and H. C. Lohithaswa
- Subjects
Heat tolerance - Published
- 2020
25. Next-Generation Plant Breeding Approaches for Stress Resilience in Cereal Crops
- Author
-
Mallana Gowdra Mallikarjuna, S. Chandra Nayaka, Tanushri Kaul, Mallana Gowdra Mallikarjuna, S. Chandra Nayaka, and Tanushri Kaul
- Subjects
- Grain--Breeding, Grain--Genetic engineering
- Abstract
This edited book highlights the gravity and efficacy of next-generation breeding tools for the enhancement of stress-resilience in cereals, especially in the context of climate change, pests, diseases, and abiotic stresses. The content of the book helps in understanding the application of emerging genetic concepts and neoteric genomic approaches in cereal breeding. It collates all the latest information about enhancing the stress resilience in cereal crops for overcoming food security issues. Cereals have predominantly been used as a staple food since time immemorial and contribute more than 50% of the caloric requirement of the global population. However, in cereals, the yield losses due to various stresses are very high, considering the crop growth stage and stress sensitivity. Therefore, to feed and nourish the generations in the era of climate change, it is imperative to develop stress-resilient cereal cultivars. This book explores newly developed next-generation breeding tools, viz., genome-wide association studies, genomic prediction, genome editing, and accelerated generation advancement methodologies, which revealed promising outcomes by enhancing the stress resilience in cereals with yield potential. This book is useful for postgraduate students specializing in plant breeding, plant stress physiology, plant genomics, agriculture, and agronomy. It is of immense value to scientific community involved in teaching, research, and extension activities related to cereal cultivation.
- Published
- 2022
26. RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize
- Author
-
Shikha Mittal, Mallana Gowdra Mallikarjuna, Kusuma Kumari Panda, Prasanta K. Dash, Nepolean Thirunavukkarasu, Atmakuri Ramakrishna Rao, and Kanika Arora
- Subjects
0106 biological sciences ,0301 basic medicine ,Programmed cell death ,Aspartic Acid Proteases ,Science ,Biology ,Genes, Plant ,01 natural sciences ,Polymorphism, Single Nucleotide ,Zea mays ,Article ,Aerenchyma ,Aerenchyma formation ,Transcriptome ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Stress, Physiological ,Hexokinase ,Gene ,Plant Proteins ,Regulation of gene expression ,Genetics ,Multidisciplinary ,beta-Fructofuranosidase ,NADPH Oxidases ,food and beverages ,Adaptation, Physiological ,Cell biology ,Oxygen ,030104 developmental biology ,Polygalacturonase ,chemistry ,Medicine ,010606 plant biology & botany ,Waterlogging (agriculture) - Abstract
Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition. Also, high up-regulation of expansins (42-fold), plant aspartic protease A3 (19-fold), polygalacturonases (16-fold), respiratory burst oxidase homolog (12-fold), and hydrolases (11-fold) explained the PCD of root cortical cells followed by the formation of aerenchyma tissue during waterlogging stress. We hypothesized that the oxygen transfer in waterlogged roots is promoted by a cross-talk of fermentative, metabolic, and glycolytic pathways that generate ATPs for PCD and aerenchyma formation in root cortical cells. SNPs were mapped to the DEGs regulating aerenchyma formation (12), ethylene-responsive factors (11), and glycolysis (4) under stress. RNAseq derived SNPs can be used in selection approaches to breed tolerant hybrids. Overall, this investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.
- Published
- 2017
27. Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
- Author
-
Sweta Mohan, Nepolean Thirunavukkarasu, Shikha Mittal, Atmakuri Ramakrishna Rao, Firoz Hossain, Mallana Gowdra Mallikarjuna, Nidhi Singh, Prasanta K. Dash, Rinku Sharma, Swati Mittal, Kaliyugam Shiriga, and Hari S. Gupta
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Article Subject ,lcsh:QH426-470 ,Drought tolerance ,Pharmaceutical Science ,Transporter ,Lipid metabolism ,Biology ,01 natural sciences ,Biochemistry ,Transcriptome ,lcsh:Genetics ,03 medical and health sciences ,030104 developmental biology ,Phosphoprotein ,Genotype ,Molecular Biology ,Transcription factor ,Gene ,Research Article ,010606 plant biology & botany - Abstract
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
- Published
- 2017
28. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize
- Author
-
Mallana Gowdra Mallikarjuna, Prashant Jain, Pooja Banduni, Nepolean Thirunavukkarasu, Prasanta K. Dash, Shikha Mittal, and Atmakuri Ramakrishna Rao
- Subjects
0106 biological sciences ,0301 basic medicine ,Drought tolerance ,drought ,Biology ,maize ,01 natural sciences ,lcsh:Chemistry ,03 medical and health sciences ,Gene interaction ,transcription factors ,Gene expression ,Gene duplication ,Gene ,Transcription factor ,Original Research ,Genetics ,Regulation of gene expression ,Phylogenetic tree ,gene interaction ,fungi ,food and beverages ,General Chemistry ,Chemistry ,030104 developmental biology ,lcsh:QD1-999 ,gene expression ,010606 plant biology & botany - Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
- Published
- 2018
29. Genetics and Applied Genomics of Quality Protein Maize for Food and Nutritional Security
- Author
-
Hari S. Gupta, Pawan Kumar Agrawal, and Mallana Gowdra Mallikarjuna
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Calorie ,media_common.quotation_subject ,food and beverages ,Genomics ,Biology ,medicine.disease ,01 natural sciences ,Crop ,03 medical and health sciences ,Malnutrition ,030104 developmental biology ,Elderly persons ,medicine ,Quality (business) ,Cultivar ,Hectare ,010606 plant biology & botany ,media_common - Abstract
Maize (Zea mays L.) is an important food and feed crop of the world. Together with rice and wheat, it provides around 40% of the food calories to more than 4.5 billion people in 94 developing countries. It also provides nearly 50% of the dietary protein for humans. In Africa and some of the Asian countries, almost 90% of maize grown is for human consumption and may account for 80–90% of the energy intake. In India, it is the third most important food crop after rice and wheat, both in terms of area and production. India is the fifth largest producer of maize in the world contributing 3% of the total global production. Protein malnutrition is widespread in the developing and underdeveloped countries, where 780 million people are affected by the same. Maize is the leading cereal in terms of production and accounts for 15% of proteins and 20% of calories requirement of the world. Protein malnutrition is caused by lack of access to adequate quantity and better quality protein intake and usually affects children and elderly persons. Maize, however, lacks adequate amounts of the essential amino acids, namely, lysine and tryptophan. Decades of efforts by maize researchers lead to the development of nutritionally superior maize cultivar popularly called as quality protein maize (QPM), which has twice the amount of lysine and tryptophan, thus making its quality as good as casein of milk. The o2 allele along with modifiers for tryptophan and lysine content and grain hardness made QPM agronomically suitable for cultivations. Intensive efforts were made by many workers to understand the genetics, molecular mechanism of QPM modifiers and applied these genomics knowledge to developed MAS-based QPM inbreds and commercial hybrids. All those studies and concerted efforts led to development and utilization of QPM. The area under QPM globally is more than 9.0 million hectares. Several reports were available on positive impact of QPM on children and adults. It has also been demonstrated in poultry and piggery, resulting in increased egg production and egg quality parameters and body mass. The area under QPM and consumption of QPM can be increased significantly by providing policy supports for QPM.
- Published
- 2018
30. Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement
- Author
-
Nepolean Thirunavukkarasu, Prasanta K. Dash, Shikha Mittal, Prashant Jain, Atmakuri Ramakrishna Rao, and Mallana Gowdra Mallikarjuna
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,Drought tolerance ,drought ,01 natural sciences ,differential expression ,lcsh:Chemistry ,03 medical and health sciences ,Protein structure ,CDPK ,Arabidopsis ,Gene ,Original Research ,Genetics ,3-D protein structure ,Phylogenetic tree ,biology ,functional mechanism ,Intron ,food and beverages ,General Chemistry ,Sorghum ,biology.organism_classification ,Chemistry ,030104 developmental biology ,lcsh:QD1-999 ,010606 plant biology & botany - Abstract
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
- Published
- 2017
31. Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones
- Author
-
Anju Singh, Sokka S. Reddy, Jayant S. Bhat, Abhishek Rathore, Hari S. Gupta, Mallana Gowdra Mallikarjuna, Pawan Kumar Agrawal, K.M. Manjaiah, Firoz Hossain, Shailendra K. Jha, Nepolean Thirunavukkarasu, Arunava Pattanayak, and Satish Kumar Gularia
- Subjects
Edible Grain ,Biplot ,Biofortification ,chemistry.chemical_element ,lcsh:Medicine ,Zinc ,Zea mays ,Mass Spectrometry ,Zinc deficiency (plant disorder) ,Plant breeding ,lcsh:Science ,Ecosystem ,Mathematics ,Multidisciplinary ,biology ,lcsh:R ,food and beverages ,Correction ,Ammi ,Micronutrient ,biology.organism_classification ,Trace Elements ,Phenotype ,Agronomy ,chemistry ,lcsh:Q ,Research Article - Abstract
Deficiency of iron and zinc causes micronutrient malnutrition or hidden hunger, which severely affects ~25% of global population. Genetic biofortification of maize has emerged as cost effective and sustainable approach in addressing malnourishment of iron and zinc deficiency. Therefore, understanding the genetic variation and stability of kernel micronutrients and grain yield of the maize inbreds is a prerequisite in breeding micronutrient-rich high yielding hybrids to alleviate micronutrient malnutrition. We report here, the genetic variability and stability of the kernel micronutrients concentration and grain yield in a set of 50 maize inbred panel selected from the national and the international centres that were raised at six different maize growing regions of India. Phenotyping of kernels using inductively coupled plasma mass spectrometry (ICP-MS) revealed considerable variability for kernel minerals concentration (iron: 18.88 to 47.65 mg kg(-1); zinc: 5.41 to 30.85 mg kg(-1); manganese: 3.30 to 17.73 mg kg(-1); copper: 0.53 to 5.48 mg kg(-1)) and grain yield (826.6 to 5413 kg ha(-1)). Significant positive correlation was observed between kernel iron and zinc within (r = 0.37 to r = 0.52, p < 0.05) and across locations (r = 0.44, p < 0.01). Variance components of the additive main effects and multiplicative interactions (AMMI) model showed significant genotype and genotype × environment interaction for kernel minerals concentration and grain yield. Most of the variation was contributed by genotype main effect for kernel iron (39.6%), manganese (41.34%) and copper (41.12%), and environment main effects for both kernel zinc (40.5%) and grain yield (37.0%). Genotype main effect plus genotype-by-environment interaction (GGE) biplot identified several mega environments for kernel minerals and grain yield. Comparison of stability parameters revealed AMMI stability value (ASV) as the better representative of the AMMI stability parameters. Dynamic stability parameter GGE distance (GGED) showed strong and positive correlation with both mean kernel concentrations and grain yield. Inbreds (CM-501, SKV-775, HUZM-185) identified from the present investigation will be useful in developing micronutrient-rich as well as stable maize hybrids without compromising grain yield.
- Published
- 2015
32. Understanding Genetic and Molecular Bases of Fe and Zn Accumulation Towards Development of Micronutrient-Enriched Maize
- Author
-
Mallana Gowdra Mallikarjuna, Firoz Hossain, M. Vignesh, Hari S. Gupta, and T. Nepolean
- Subjects
Micronutrient deficiency ,business.industry ,Biofortification ,food and beverages ,Staple food ,Biology ,medicine.disease ,Micronutrient ,Biotechnology ,Crop ,Malnutrition ,Agronomy ,Genetic variation ,medicine ,Plant breeding ,business - Abstract
Micronutrient malnutrition is a global problem afflicting billions of people worldwide. The effects are more prevalent in developing countries where people rely upon cereal-based diets that are inherently deficient in micronutrients. Micronutrients are required in less quantity but play critical role in the growth and development of humans. Since human body cannot synthesize micronutrients, they must be made available through diet. Among micronutrients, deficiency of iron (Fe) and zinc (Zn) has profound effects and require urgent attention. Development of micronutrient-rich staple plant foods through plant breeding, a process referred to as “biofortification,” holds promise for sustainable food-based solutions to combat micronutrient deficiency. Maize is the third most important crop of the world, serving as staple food to billions of people in sub-Saharan Africa, Latin America and Asia. The development of Fe- and Zn-rich maize cultivar(s) would therefore have positive effects on health and well-being of humans. Wide variability has been reported for Fe and Zn in maize, which can be explored for genetic improvement of the trait. Genetics of Fe and Zn has been well elucidated, and genes/QTLs governing high Fe and Zn accumulation in maize have been identified. Moreover, by targeting the genes involved in Fe and Zn uptake, transportation and translocation, concentration of the same can be increased in the maize endosperm. Further, manipulating genes for promoter and antinutritional factors, bioavailability of Fe and Zn can be enhanced. Quality protein maize (QPM) genotype reported to have higher concentration of Fe and Zn provides opportunity to develop multinutrient-rich maize through a systematic breeding approach. We discussed here available genetic variation for Fe and Zn and their interactions with environments, relationship among micronutrients and grain yield, summary of research efforts with specific emphasis on mechanism of uptake and translocation, genetic and molecular basis of Fe and Zn accumulation, and the strategies that can be explored to breed for high Fe and Zn maize.
- Published
- 2014
33. In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize
- Author
-
Nepolean Thirunavukkarasu, Kanika Arora, Shikha Mittal, Kusuma Kumari Panda, and Mallana Gowdra Mallikarjuna
- Subjects
0301 basic medicine ,cell wall modification ,In silico ,Biology ,maize ,Biochemistry ,Candidate genes ,Aerenchyma formation ,Aerenchyma ,Cell wall ,03 medical and health sciences ,Structural motif ,Cwm ,lcsh:QH301-705.5 ,Molecular Biology ,Gene ,Cell wall modification ,Original Research ,waterlogging tolerance ,Applied Mathematics ,Computer Science Applications ,Cell biology ,Computational Mathematics ,030104 developmental biology ,lcsh:Biology (General) ,plant stress - Abstract
Cell wall modification (CWM) promotes the formation of aerenchyma in roots under waterlogging conditions as an adaptive mechanism. Lysigenous aerenchyma formation in roots improves oxygen transfer in plants, which highlights the importance of CWM as a focal point in waterlogging stress tolerance. We investigated the structural and functional compositions of CWM genes and their expression patterns under waterlogging conditions in maize. Cell wall modification genes were identified for 3 known waterlogging-responsive cis-acting regulatory elements, namely, GC motif, anaerobic response elements, and G-box, and 2 unnamed elements. Structural motifs mapped in CWM genes were represented in genes regulating waterlogging stress-tolerant pathways, including fermentation, glycolysis, programmed cell death, and reactive oxygen species signaling. The highly aligned regions of characterized and uncharacterized CWM proteins revealed common structural domains amongst them. Membrane spanning regions present in the protein structures revealed transmembrane activity of CWM proteins in the plant cell wall. Cell wall modification proteins had interacted with ethylene-responsive pathway regulating genes (E3 ubiquitin ligases RNG finger and F-box) in a maize protein-protein interaction network. Cell wall modification genes had also coexpressed with energy metabolism, programmed cell death, and reactive oxygen species signaling, regulating genes in a single coexpression cluster. These configurations of CWM genes can be used to modify the protein expression in maize under waterlogging stress condition. Our study established the importance of CWM genes in waterlogging tolerance, and these genes can be used as candidates in introgression breeding and genome editing experiments to impart tolerance in maize hybrids.
- Published
- 2017
34. Genetic variability and correlation of kernel micronutrients among exotic quality protein maize inbreds and their utility in breeding programme
- Author
-
Anju Singh, Firoz Hossain, K.M. Manjaiah, T. Nepolean, Mallana Gowdra Mallikarjuna, and Himanshu Gupta
- Subjects
Genetic diversity ,Micronutrient deficiency ,business.industry ,Biofortification ,food and beverages ,Plant Science ,Biology ,Micronutrient ,Biotechnology ,Crop ,Agronomy ,Genetic variation ,Genetics ,Genetic variability ,business ,Hybrid - Abstract
Micronutrient malnutrition is a widespread problem known to affect millions of children and women. However, the adverse effects of micronutrient deficiency can be overcome through self-targeting, cost-effective and sustainable genetic biofortification approach, which is mainly based on staple food crops. Since maize has emerged as a prominent future crop especially for India, developing maize hybrids that are rich in kernel micronutrients will help in reducing the problems of micronutrient malnutrition. Here, we report variability of kernel Fe and Zn in 120 exotic Quality Protein Maize (QPM) inbreds and kernel Mn and Cu in a representative subset of 68 lines. A wide range of genetic variation was found among genotypes for all the kernel micronutrients: Fe (16.6–83.4 ppm), Zn (16.4–53.2 ppm), Mn (1.7–34.8 ppm) and Cu (0.5–9.5 ppm). Higher mean for kernel Fe and Zn in QPM inbreds suggests possible influence of opaque2 gene and/or modifiers present in them. Significant and positive correlation was observed among kernel Fe, Zn, Mn and Cu. Genetic diversity based on all four micronutrients grouped 68 lines into three major clusters with a mean coefficient of genetic dissimilarity of 2.46. Parental combinations were selected from different heterotic pools and maturity groups to develop high-yielding hybrids enriched with micronutrients.
- Published
- 2014
35. Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize
- Author
-
Thirunavukkarasu Nepolean, Mittal Shikha, Arora Kanika, Atmakuri Ramakrishna Rao, Mallana Gowdra Mallikarjuna, and Hari Shanker Gupta
- Subjects
0106 biological sciences ,0301 basic medicine ,Drought tolerance ,SNP ,Plant Science ,drought ,parametric ,lcsh:Plant culture ,Quantitative trait locus ,Biology ,01 natural sciences ,genomic selection ,03 medical and health sciences ,Bayes' theorem ,Gene interaction ,Lasso (statistics) ,semi-parametric ,non-parametric ,lcsh:SB1-1110 ,transcription factor ,Original Research ,Genetics ,Phenotypic trait ,Heritability ,030104 developmental biology ,Epistasis ,010606 plant biology & botany - Abstract
Traditional breeding strategies for selecting superior genotypes depending on phenotypic traits have proven to be of limited success, as this direct selection is hindered by low heritability, genetic interactions such as epistasis, environmental-genotype interactions, and polygenic effects. With the advent of new genomic tools, breeders have paved a way for selecting superior breeds. Genomic selection (GS) has emerged as one of the most important approaches for predicting genotype performance. Here, we tested the breeding values of 240 maize subtropical lines phenotyped for drought at different environments using 29,619 cured SNPs. Prediction accuracies of seven genomic selection models (ridge regression, LASSO, elastic net, random forest, reproducing kernel Hilbert space, Bayes A and Bayes B) were tested for their agronomic traits. Though prediction accuracies of Bayes B, Bayes A and RKHS were comparable, Bayes B outperformed the other models by predicting highest Pearson correlation coefficient in all three environments. From Bayes B, a set of the top 1053 significant SNPs with higher marker effects was selected across all datasets to validate the genes and QTLs. Out of these 1053 SNPs, 77 SNPs associated with ten drought-responsive transcription factors. These transcription factors were associated with different physiological and molecular functions (stomatal closure, root development, hormonal signaling and photosynthesis). Of several models, Bayes B has been shown to have the highest level of prediction accuracy for our data sets. Our experiments also highlighted several SNPs based on their performance and relative importance to drought tolerance. The result of our experiments is important for the selection of superior genotypes and candidate genes for breeding drought-tolerant maize hybrids.
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