Browsing by Author "Varshney, Rajeev K."

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A 1000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics
(Springer, 2007) Stein, Nils; Prasad, Manoj; Scholz, Uwe; Thiel, Thomas; Zhang, Hangning; Wolf, Markus; Kota, Raja; Varshney, Rajeev K.; Perovic, Dragan; Grosse, Ivo; Graner, Andreas
An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identiWcation of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.
Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects
(Frontiers Media S.A., 2015) Kole, Chittaranjan; Muthamilarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J.; Cockram, James; Oliveira, Antonio Costa de; Pace, Ciro De; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W.; Iorizzo, Massimo; Ismail, Abdelbagi M.; Marshall, Athole; Mayes, Sean; Nguyen, Henry T.; Ogbonnaya, Francis C.; Ortiz, Rodomiro; Paterson, Andrew H.; Simon, Philipp W.; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K.; Wullschleger, Stan D.; Yano, Masahiro; Prasad, Manoj
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)
(Springer Science, 2011) Gujaria, Neha; Kumar, Ashish; Dauthal, Preeti; Dubey, Anuja; Hiremath, Pavana; Bhanu Prakash, A.; Farmer, Andrew; Bhide, Mangla; Shah, Trushar; Gaur, Pooran M.; Upadhyaya, Hari D.; Bhatia, Sabhyata; Cook, Douglas R.; May, Greg D.; Varshney, Rajeev K.
A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics.
Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas
(John Wiley & Sons, 2023) Jan, Sofora; Kumar, Sandeep; Yousuf, Munaza; Shafi, Safoora; Majid, Ronak; Khan, M. Anwar; Jeelani, Fehim; Shikari, Asif Bashir; Kaur, Satinder; Kumar, Sundeep; Kalia, Sanjay; Singh, Kuldeep; Prasad, Manoj; Varshney, Rajeev K.; Mir, Reyazul Rouf
Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021–2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H202), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
(Springer Nature Publishing AG, 2019) Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal-Bertioli, Soraya C. M.; Ren, Longhui; Farmer, Andrew D.; Pandey, Manish K.; Samoluk, Sergio S.; Abernathy, Brian; Agarwal, Gaurav; Ballén-Taborda, Carolina; Cameron, Connor; Campbell , Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; Baidouri, Moaine El; Guo, Baozhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher G.; Mirouze, Marie; Moretzsohn, Márcio C.; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, Erez L.; Michelmore, Richard; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K. S.; Scheffler, Brian E.; Grimwood, Jane; Ozias-Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz , Jeremy
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
(Springer, 2014) Varshney, Rajeev K.; Mir, Reyazul Rouf; Bhatia, Sabhyata; Thudi, Mahendar; Hu, Yuqin; Azam, Sarwar; Zhang, Yong; Jaganathan, Deepa; You, Frank M.; Gao, Jinliang; Riera-Lizarazu, Oscar; Luo, Ming-Cheng
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species
(Elsevier B.V., 2009) Nayak, Spurthi N.; Balaji, Jayashree; Upadhyaya, Hari D.; Hash, C. Tom; Kavi Kishor, P.B.; Chattopadhyay, Debasis; Rodriquez, Lina Marıa; Blair, Matthew W.; Baum, Michael; McNally, Kenneth; This, Dominique; Hoisington, David A.; Varshney, Rajeev K.
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.
Molecular genetics and breeding of grain legume crops for the semi-arid tropics
(Springer, 2007) Varshney, Rajeev K.; Hoisington, David A.; Upadhyaya, Hari D.; Gaur, Pooran M.; Nigam, Shyam N.; Saxena, Kulbhushan; Vadez, Vincent; Sethy, Niroj K.; Bhatia, Sabhyata; Aruna, Rupakula; Gowda, M. V. Channabyre; Singh, Nagendra K.
Grain legumes are important crops for providing key components in the diets of resource-poor people of the semi-arid tropic (SAT) regions of the world. Although there are several grain legume crops grown in SAT, the present chapter deals with three important legumes i.e. groundnut or peanut (Arachis hypogaea), chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). Production of these legume crops are challenged by serious abiotic stresses e.g. drought, salinity as well as several fungal, viral and nematode diseases. To tackle these constraints through molecular breeding, some efforts have been initiated to develop genomic resources e.g. molecular markers, molecular genetic maps, expressed sequence tags (ESTs), macro-/micro- arrays, bacterial artificial chromosomes (BACs), etc. These genomic resources together with recently developed genetic and genomics strategies e.g. functional molecular markers, linkage-disequilibrium (LD) based association mapping, functional and comparative genomics offer the possibility of accelerating molecular breeding for abiotic and biotic stress tolerances in the legume crops. However, low level of polymorphism present in the cultivated genepools of these legume crops, imprecise phenotyping of the germplasm and the higher costs of development and application of genomic tools are critical factors in utilizing genomics in breeding of these legume crops.
Molecular genetics and genomics of abiotic stress responses
(Frontiers Media S.A., 2014) Garg, Rohini; Varshney, Rajeev K.; Jain, Mukesh
Abiotic stresses are the major causes that limit productivity of crop plants worldwide. Plants have developed intricate machinery to respond and adapt over these adverse environmental conditions both at physiological and molecular levels. Due to increasing abiotic stress constraints, plant biotechnologists and breeders need to devise and employ new approaches to improve abiotic stress tolerance in crop plants. Although the current research has divulged several key genes, gene regulatory networks and quantitative trait loci (QTLs) that mediate plant responses to various abiotic stresses, the comprehensive understanding of this complex trait is still not available. With an objective to understand the plant response/adaptation to various abiotic stresses, a special issue was planned for the journal. The current research topic “Abiotic Stress: Molecular Genetics and Genomics” has a combination of primary research articles, perspective, opinion and review work, written by authorities in their respective fields. These articles provide novel insights and detailed overviews on the current knowledge into different aspects of plant responses and adaptation to abiotic stresses.
Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea
(Nature Publishing Group, 2016) Garg, Rohini; Shankar, Rama; Thakkar, Bijal; Kudapa, Himabindu; Krishnamurthy, Lakshmanan; Mantri, Nitin; Varshney, Rajeev K.; Bhatia, Sabhyata; Jain, Mukesh
Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies
(Frontiers Media S.A., 2024) Danakumara, Thippeswamy; Kumar, Neeraj; Patil, Basavanagouda Siddanagouda; Kumar, Tapan; Bharadwaj, Chellapilla; Jain, Pradeep Kumar; Nimmy, Manduparambil Subramanian; Joshi, Nilesh; Parida, Swarup Kumar; Bindra, Shayla; Kole, Chittaranjan; Varshney, Rajeev K.
Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.