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Climate change is significantly impacting agricultural production worldwide. Peanuts provide food and nutritional security to millions of people across the globe because of its high nutritive values. Drought and heat stress alone or in combination cause substantial yield losses to peanut production. The stress, in addition, adversely impact nutritional quality. Peanuts exposed to drought stress at reproductive stage are prone to aflatoxin contamination, which imposes a restriction on use of peanuts as health food and also adversely impact peanut trade. A comprehensive understanding of the impact of drought and heat stress at physiological and molecular levels may accelerate the development of stress tolerant productive peanut cultivars adapted to a given production system. Significant progress has been achieved towards the characterization of germplasm for drought and heat stress tolerance, unlocking the physiological and molecular basis of stress tolerance, identifying significant marker-trait associations as well major QTLs and candidate genes associated with drought tolerance, which after validation may be deployed to initiate marker-assisted breeding for abiotic stress adaptation in peanut. The proof of concept about the use of transgenic technology to add value to peanuts has been demonstrated. Advances in phenomics and artificial intelligence to accelerate the timely and cost-effective collection of phenotyping data in large germplasm/breeding populations have also been discussed. Greater focus is needed to accelerate research on heat stress tolerance in peanut. A suits of technological innovations are now available in the breeders toolbox to enhance productivity and nutritional quality of peanuts in harsh environments. A holistic breeding approach that considers drought and heat-tolerant traits to simultaneously address both stresses could be a successful strategy to produce climate-resilient peanut genotypes with improved nutritional quality.

Blast [Magnaporthe grisea (Herbert) Barr] is an economically important disease in Asian pearl millet production ecologies. The recurrent occurrence of blast in the past one decade has caused enormous strain on grain and forage production. Identification of resistance genes is an important step to develop durable varieties. The present study is the first attempt to use RNA-Seq to investigate the transcript dynamics in a pearl millet inbred ICMB 93333, which had a unique differential reaction to two isolates—Pg 45 (avirulent) and Pg 174 (virulent) of M. grisea. The inbred was inoculated by both isolates and samples taken at six different time intervals for genome-wide RNA-Seq experiment. The transcriptome results revealed the differential expression of more than 2,300 genes. The time-specific comparison showed activation or repression of specific genes in various pathways. Genes and transcriptions factors related to pathogenesis-related proteins, reactive oxygen species generating and its scavenging genes, cell wall defense, primary and secondary metabolic pathways, and signaling pathways were identified by comparing the host-plant compatible and incompatible interactions. The genes identified from this experiment could be useful to understand the host-plant resistance and design novel strategies to manage blast disease in pearl millet.

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Aflatoxin production by isolates of Aspergillus flavus varies, ranging from highly toxigenic to completely atoxigenic. Several mechanisms have been identified which regulate aflatoxin production including medium carbon source and oxidative stress. In recent studies, aflatoxin production has been implicated in partially ameliorating oxidative stress in A. flavus. To better understand the role of aflatoxin production in oxidative stress responses, a selection of toxigenic and atoxigenic isolates of A. flavus with moderate to high oxidative stress tolerance were exposed to increasing concentrations of H2O2 in both aflatoxin-conducive and non-conducive media. Mycelial mats were collected for global transcriptome sequencing followed by differential expression, functional prediction, and weighted co-expression analyses. Oxidative stress and medium carbon source had a significant effect on the expression of several secondary metabolite gene clusters including those for aflatoxin, aflatrem, aflavarin, cyclopiazonic acid, and kojic acid. Atoxigenic biological control isolates showed less differential expression under stress than other atoxigenic isolates suggesting expression profiles may be useful in screening. Increasing stress also resulted in regulation of SakA/Hog1 and MpkA MAP kinase signalling pathways pointing to their potential roles in regulating oxidative stress responses. Their expression was also influenced by medium carbon source. These results suggest that aflatoxin production along with that of other mycotoxins may occur as part of a concerted coping mechanism for oxidative stress and its effects in the environment. This mechanism is also regulated by availability of simple sugars and glycolytic compounds for their biosynthesis.

Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.

Hypergravity is a condition where the force of gravity exceeds that on the surface of the Earth and can be simulated by centrifugation. Previously, a significant increase in root growth phenotype was observed when wheat seeds were exposed to hypergravity (10 g for 12 h). In the present study, we investigated the molecular basis of this change through root transcriptome. The data revealed a total of 3765 up-regulated and 2102 down-regulated transcripts in response to hypergravity. GO enrichment analysis revealed hormonal responses, cell division, and cell-wall-related terms were significantly enriched in hypergravity. The increased isoform level expression of transcripts involved in auxin biosynthesis, transport, and signaling was observed. Further, enhanced expression of cell division transcripts and down-regulation of cell number regulator genes suggests rapid cell division. Overexpression of cellulose and hemicellulose biosynthesis transcripts suggests demand for cell-wall constituents. Collectively, this study identified candidate genes associated with hypergravity-induced enhanced root growth.

A total of 60 genotypes of peanut comprising 46 genotypes selected from ICRISAT mini core collection and 14 elite cultivars with differing kernel color and size were used to profile the nutritional parameters such as proximates (moisture, fat, ash, crude protein, crude fiber, carbohydrate content) and nutraceuticals (total polyphenol content and total antioxidant activity). The genotypes showed varied kernel color ranging from white to purple. Kernel skin color was quantified using colorimetry, and the color parameters were expressed as CIELAB color parameters. In total, nine morphological traits, six yield related traits, eight nutritional traits and eleven color parameters were observed across 60 genotypes. The sixty genotypes were grouped into ten clusters based on the color strength. Among them, Cluster-III with dark red seeds had the maximum fat content and total polyphenol content (TPC). Cluster-VI with light pink colored seeds had high antioxidant activity (AOA) and Cluster-X with white colored seeds had highest moisture and crude protein content. Color strength (K/S) was found to be positively correlated with TPC. Another color parameter, redness/greenness (a*) was found to be positively correlated with AOA. However, seed size was positively correlated with the crude protein content, but not with any other nutritional traits under study. The population studies based on the genotypic data indicated two distinct groups pertaining to botanical types of peanut. The marker-trait association (MTA) using single marker analysis indicated 75 major MTAs for most of the nutritional traits except for moisture content. The markers associated with nutritional parameters and other important yield related traits can further be utilized for genomics-assisted breeding for nutrient-rich peanuts.

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.

The colonization of maize (Zea mays L.) and peanut (Arachis hypogaea L.) by the fungal pathogen Aspergillus flavus results in the contamination of kernels with carcinogenic mycotoxins known as aflatoxins leading to economic losses and potential health threats to humans. The regulation of aflatoxin biosynthesis in various Aspergillus spp. has been extensively studied, and has been shown to be related to oxidative stress responses. Given that environmental stresses such as drought and heat stress result in the accumulation of reactive oxygen species (ROS) within host plant tissues, host-derived ROS may play an important role in cross-kingdom communication between host plants and A. flavus. Recent technological advances in plant breeding have provided the tools necessary to study and apply knowledge derived from metabolomic, proteomic, and transcriptomic studies in the context of productive breeding populations. Here, we review the current understanding of the potential roles of environmental stress, ROS, and aflatoxin in the interaction between A. flavus and its host plants, and the current status in molecular breeding and marker discovery for resistance to A. flavus colonization and aflatoxin contamination in maize and peanut. We will also propose future directions and a working model for continuing research efforts linking environmental stress tolerance and aflatoxin contamination resistance in maize and peanut.

An effort was made in the present study to identify the main effect and epistatic quantitative trait locus (QTL) for the morphological and yield-related traits in peanut. A recombinant inbred line (RIL) population derived from TAG 24 × GPBD 4 was phenotyped in seven environments at two locations. QTL analysis with available genetic map identified 62 main-effect QTLs (M-QTLs) for ten morphological and yield-related traits with the phenotypic variance explained (PVE) of 3.84–15.06%. Six major QTLs (PVE > 10%) were detected for PLHT, PPP, YPP, and SLNG. Stable M-QTLs appearing in at least two environments were detected for PLHT, LLN, YPP, YKGH, and HSW. Five M-QTLs governed two traits each, and 16 genomic regions showed co-localization of two to four M-QTLs. Intriguingly, a major QTL reported to be linked to rust resistance showed pleiotropic effect for yield-attributing traits like YPP (15.06%, PVE) and SLNG (13.40%, PVE). Of the 24 epistatic interactions identified across the traits, five interactions involved six M-QTLs. Three interactions were additive × additive and remaining two involved QTL × environment (QE) interactions. Only one major M-QTL governing PLHT showed epistatic interaction. Overall, this study identified the major M-QTLs for the important productivity traits and also described the lack of epistatic interactions for majority of them so that they can be conveniently employed in peanut breeding.

To identify marker–trait associations (MTAs) for yield and quality traits in peanut, genic and nongenic Arachis hypogaea transposable element (AhTE) markers were employed in a population consisting of independent mutants from several parents. The population was field-evaluated during the rainy seasons of 2014 and 2015, and genotyped with 110 AhTE markers to check the polymorphisms for AhMITE1 transposition. The gene diversity index ranged from 0.00 to 0.50 with average of 0.35, indicating low to moderate genetic diversity in the population. Diversity analysis indicated the grouping of mutants derived from each parent in respective subgroups. Marker–trait association analysis for 110 markers and 40 traits resulted in 132 highly significant MTAs, represented by 58 AhTE markers for 39 traits. Nutritional traits recorded the highest number of MTAs (38), followed by agronomic traits (35), productivity traits (31), foliar disease resistance (23), and taxonomic traits (5). Seventeen MTAs with phenotypic variance explained (PVE) value above 50 % were observed for resistance to late leaf spot (LLS) and rust, plant height, and pod width. The genic and nongenic AhTE markers associated with the above traits were analyzed for their genomic location and functional annotation so that the significance of these loci can be analyzed in the future.

The Saccharum L. genus includes important crops that are utilized for sugar and fuel production. The World Collection of Sugarcane and Related Grasses (World Collection) in Miami, FL contains diverse and potentially useful germplasm for this and related genera; however, this collection has been underutilized because little is known about the traits of its accessions. Our objectives were to phenotypically characterize the World Collection and select a representative core collection that could then be studied intensively. In total, eight morphological traits of the World Collection were evaluated three times in 1 year. A core of 300 accessions that included each species in the World Collection was selected by using the Maximization Strategy in MStrat software. The core had a higher diversity rating than random selections of 300 accessions. The Shannon–Weaver Diversity Index scores of the core and whole collection were similar indicating that the majority of the diversity was captured by the core collection. The ranges and medians between the core and World Collection were similar; only two of the trait medians were not significant at P = 0.05 using the non-parametric Wilcoxon method and the coincidence rate (CR % = 96.2) was high (>80) indicating that extreme values were retained. Thus, the phenotypic diversity of these traits in the World Collection was well represented by the core collection. Agronomic studies on the core should be useful for characterizing the World Collection and genes for useful traits should be available in the core collection.

Key message Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Abstract Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea. Electronic supplementary material The online version of this article (doi:10.1007/s00122-013-2230-6) contains supplementary material, which is available to authorized users.

Advances in availability of genomic resources coupled with genetic resources have accelerated the process of developing better understanding of cytogenetics and genetics of peanut using modern technologies. The cytogenetic studies provided greater insights on chromosomal structures and behaviour of different Arachis species along with their genetic relationship with each other. Researchers are moving faster now in using single nucleotide polymorphism (SNP) markers in their genetic studies as simple sequence repeats (SSRs) did not provide optimum genome density for genetic mapping studies in peanut. Due to availability of reference genome of diploid progenitors, resequencing of some genotypes and soon to be available tetraploid genome, a high-density genotyping array with 58 K SNPs is now available for conducting high-resolution mapping in peanut. ICRISAT has developed next generation genetic mapping populations such as multi-parent advanced generation intercross (MAGIC) and nested association mapping (NAM) populations for conducting high-resolution trait mapping for multiple traits in one go. Affordability of sequencing also encouraged initiation of sequence-based trait mapping such as QTL-seq for dissecting foliar disease resistance trait. Few successful examples are available in peanut regarding development of diagnostic markers and their deployment in breeding to develop improved genotypes, which may see a significant increase in coming years for developing appropriate genomics tools for breeding in peanut.

Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. To understand the genome of the cultivated peanut, it is prerequisite to know the genome organization of its diploid progenitors, A-genome—Arachis duranensis and B-genome—A. ipaensis. Two genome sequencing projects conducted sequencing and analysis of the genomes of diploid ancestors: (1) International Peanut Genome Initiative (IPGI) reported the sequencing of both A- and B-genomes; while (2) Diploid Progenitor Peanut Arachis Genome Sequencing Consortium (DPPAGSC) reported the sequencing of A-genome. IPGI study showed that these genomes are similar to cultivated peanut’s A- and B-subgenomes and used them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut’s subgenomes thus providing evidence about direct descendant of the B subgenome in cultivated peanut. The DPPAGSC study, on the other hand, provided new insights into geocarpy, oil biosynthesis, and allergens in addition to providing information about evolution and polyploidization. These genome sequencing efforts have improved the understanding about the complex peanut genome and genome architecture which will play a very important role in peanut applied genomics and breeding.

The infection of maize and peanut with Aspergillus flavus and subsequent contamination with aflatoxin pose a threat to global food safety and human health, and is exacerbated by drought stress. Drought stress-responding compounds such as reactive oxygen species (ROS) are associated with fungal stress responsive signaling and secondary metabolite production, and can stimulate the production of aflatoxin by A. flavus in vitro. These secondary metabolites have been shown to possess diverse functions in soil-borne fungi including antibiosis, competitive inhibition of other microbes, and abiotic stress alleviation. Previously, we observed that isolates of A. flavus showed differences in oxidative stress tolerance which correlated with their aflatoxin production capabilities. In order to better understand these isolate-specific oxidative stress responses, we examined the transcriptional responses of field isolates of A. flavus with varying levels of aflatoxin production (NRRL3357, AF13, and Tox4) to H2O2-induced oxidative stress using an RNA sequencing approach. These isolates were cultured in an aflatoxin-production conducive medium amended with various levels of H2O2. Whole transcriptomes were sequenced using an Illumina HiSeq platform with an average of 40.43 million filtered paired-end reads generated for each sample. The obtained transcriptomes were then used for differential expression, gene ontology, pathway, and co-expression analyses. Isolates which produced higher levels of aflatoxin tended to exhibit fewer differentially expressed genes than isolates with lower levels of production. Genes found to be differentially expressed in response to increasing oxidative stress included antioxidant enzymes, primary metabolism components, antibiosis-related genes, and secondary metabolite biosynthetic components specifically for aflatoxin, aflatrem, and kojic acid. The expression of fungal development-related genes including aminobenzoate degradation genes and conidiation regulators were found to be regulated in response to increasing stress. Aflatoxin biosynthetic genes and antioxidant enzyme genes were also found to be co-expressed and highly correlated with fungal biomass under stress. This suggests that these secondary metabolites may be produced as part of coordinated oxidative stress responses in A. flavus along with antioxidant enzyme gene expression and developmental regulation.

Peanut (Arachis hypogaea; 2n = 4x = 40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis., Genome-wide single nucleotide polymorphisms (SNPs), identified among diploid and tetraploid Arachis species and used to construct an Affymetrix 60K SNP array, provided insight into diversity across US runner-type peanut cultivars and the US mini - core collection. The frequency of fixed marker polymorphisms and identification of preferentially selected haplotypes will inform future peanut breeding to enhance diversity.

Contamination of crops with aflatoxin is a serious global threat to food safety. Aflatoxin production by Aspergillus flavus is exacerbated by drought stress in the field and by oxidative stress in vitro. We examined transcriptomes of three toxigenic and three atoxigenic isolates of A. flavus in aflatoxin conducive and non-conducive media with varying levels of H2O2 to investigate the relationship of secondary metabolite production, carbon source, and oxidative stress. We found that toxigenic and atoxigenic isolates employ distinct mechanisms to remediate oxidative damage, and that carbon source affected the isolates’ expression profiles. Iron metabolism, monooxygenases, and secondary metabolism appeared to participate in isolate oxidative responses. The results suggest that aflatoxin and aflatrem biosynthesis may remediate oxidative stress by consuming excess oxygen and that kojic acid production may limit iron-mediated, non-enzymatic generation of reactive oxygen species. Together, secondary metabolite production may enhance A. flavus stress tolerance, and may be reduced by enhancing host plant tissue antioxidant capacity though genetic improvement by breeding selection.

Fusarium species are dominant within the sorghum grain mold complex. Some species of Fusarium involved in grain mold complex produce mycotoxins, such as fumonisins. An attempt was made to identify Fusarium spp. associated with grain mold complex in major sorghum-growing areas in India through AFLP-based grouping of the isolates and to further confirm the species by sequencing part of α-Elongation factor gene and comparing the sequences with that available in the NCBI database. The dendrogram generated from the AFLP data clustered the isolates into 5 groups. Five species of Fusarium--F. proliferatum, F. thapsinum, F. equiseti, F. andiyazi and F. sacchari were identified based on sequence similarity of α-Elongation factor gene of the test isolates with those in the NCBI database. Fusarium thapsinum was identified as predominant species in Fusarium--grain mold complex in India and F. proliferatum as highly toxigenic for fumonisins production. Analysis of molecular variance (AMOVA) revealed 54% of the variation in the AFLP patterns of 63 isolates was due to the differences between Fusarium species, and 46% was due to differences between the strains within a species.

Contact: fax: +91 40 30713074/30713075. E-mail address: r.k.varshney@cgiar.org; International audience; The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.

A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1-7 seasons and 1-3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2

The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for example, early generation selection, enrichment of complex F(1)s, choice of donor parent in backcrossing, recovery of recurrent parent genotype in backcrossing, linkage block analysis and selection. Other main areas of applications of molecular markers in plant breeding include germplasm characterization/fingerprinting, determining seed purity, systematic sampling of germplasm, and phylogenetic analysis. Molecular markers, thus, have proved powerful tools in replacing the bioassays and there are now many examples available to show the efficacy of such markers. We have illustrated some basic concepts and methodology of applying molecular markers for enhancing the selection efficiency in plant breeding. Some successful examples of product developments of molecular breeding have also been presented.

Using next-generation sequencing technologies it is possible to resequence entire plant genomes or sample entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing individual genomes, we envision the sequencing of hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations. In this review, we outline some important areas such as the large-scale development of molecular markers for linkage mapping, association mapping, wide crosses and alien introgression, epigenetic modifications, transcript profiling, population genetics and de novo genome/organellar genome assembly for which these technologies are expected to advance crop genetics and breeding, leading to crop improvement.

The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for example, early generation selection, enrichment of complex F(1)s, choice of donor parent in backcrossing, recovery of recurrent parent genotype in backcrossing, linkage block analysis and selection. Other main areas of applications of molecular markers in plant breeding include germplasm characterization/fingerprinting, determining seed purity, systematic sampling of germplasm, and phylogenetic analysis. Molecular markers, thus, have proved powerful tools in replacing the bioassays and there are now many examples available to show the efficacy of such markers. We have illustrated some basic concepts and methodology of applying molecular markers for enhancing the selection efficiency in plant breeding. Some successful examples of product developments of molecular breeding have also been presented.

Background There is a need for software scripts and modules for format parsing, data manipulation, statistical analysis and annotation especially for tasks related to marker identification from sequence data and sequence diversity analysis. Results Here we present several new Perl scripts and a module for sequence data diversity analysis. To enable the use of these software with other public domain tools, we also make available PISE (Pasteur Institute Software Environment) wrappers for these Perl scripts and module. This enables the user to generate pipelines for automated analysis, since PISE is a web interface generator for bioinformatics programmes. Conclusion A new set of modules and scripts for diversity statistic calculation, format parsing and data manipulation are available with PISE wrappers that enable pipelining of these scripts with commonly used contig assembly and sequence feature prediction software, to answer specific sequence diversity related questions.