Advances in Chickpea Genomic Resources for Accelerating the Crop Improvement

  • Manish RoorkiwalEmail author
  • Ankit Jain
  • Mahendar Thudi
  • Rajeev K. Varshney
Part of the Compendium of Plant Genomes book series (CPG)


Chickpea plays a major role in food and nutritional security worldwide. Its productivity is severely affected by various biotic and abiotic stresses; hence development of stress resilience varieties that can yield higher under stress environment remains the call of the hour. Conventional breeding approaches clubbed with the genome information, commonly known as genomic-assisted breeding (GAB) have the potential to accelerate the crop improvement efforts. In order to deploy the GAB for crop improvement in chickpea, there was need to convert an orphan crop chickpea into the genomic resource-rich crop. Advent of sequencing technology has resulted in reduction of cost and led to development of huge genomic resources in chickpea. A variety of markers have been developed, used for various mapping studies including linkage mapping and association mapping and finally deployed for developing the superior varieties using GAB approached such as marker assisted backcrossing and genomic selection. The chapter reviews the journey of chickpea status from orphan crop with almost no marker resources to a genome resource-rich crop, which are being used for achieving the genetic gains at a momentum.


  1. Afonso-Grunz F, Molina C, Hoffmeier K, Rycak L, Kudapa H et al (2014) Genome-based analysis of the transcriptome from mature chickpea root nodules. Front Plant Sci 5:325CrossRefPubMedPubMedCentralGoogle Scholar
  2. Ahmad E, Gaur PM, Slinkard AE (1992) Isozyme polymorphism and phylogenetic interpretations in the genus Cicer L. Theor Appl Genet 83:620–627Google Scholar
  3. Ahmad F, Gaur PM, Croser J (2005) Chickpea (Cicer arietinum L.). In: Singh RJ, Jauhar PP (eds) Genetic resources, chromosome engineering, and crop improvement—grain legumes. vol 1. CRC Press, Boca Raton, pp 187–217Google Scholar
  4. Bajaj D, Das S, Upadhyaya HD, Ranjan R, Badoni S et al (2015) A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat color in chickpea. Front Plant Sci 6:979CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bakht J, Bano A, Dominy P (2006) The role of abscisic acid and low temperature in chickpea (Cicer arietinum) cold tolerance. II. Effects on plasma membrane structure and function. J Exp Bot 57:3707–3715CrossRefPubMedGoogle Scholar
  6. Banerjee H, Pai RA, Sharma RP (1999) Restriction fragment length polymorphism and random amplified polymorphic DNA analysis of chickpea accessions. Biologia Plant 42:197–208CrossRefGoogle Scholar
  7. Bharadwaj C, Chauhan SK, Yadav S, Satyavathi CT, Singh R et al (2011) Molecular marker-based linkage map of chickpea (Cicer arietinum) developed from desi × kabuli cross. Ind J Agric Sci 81:116–118Google Scholar
  8. Buhariwalla HK, Jayashree B, Crouch JH (2005) ESTs from chickpea roots with putative roles in drought tolerance. BMC Plant Biology 5:16CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chen WJ, Zhu T (2004) Networks of transcription factors with roles in environmental stress response. Trends in Plant Sci 9:591–596. doi: 10.1016/j.tplants.2004.10.007 CrossRefGoogle Scholar
  10. Cho S, Kumar J, Shultz JL, Anupama K, Tefera F et al (2002) Mapping genes for double podding and other morphological trait in chickpea. Euphytica 125:285–292CrossRefGoogle Scholar
  11. Choudhary S, Gaur R, Gupta S, Bhatia S (2012) EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor Appl Genet 124:1449–1462Google Scholar
  12. Cobos MJ, Fernández MJ, Rubio J, Kharrat M, Moreno MT et al (2005) A linkage map in chickpea (Cicer arietinum L.) in two populations from Kabuli × Desi crosses: location of a resistance gene for fusarium wilt race 0. Theor Appl Genet 110:1347–1353Google Scholar
  13. Collard BCY, Pang ECK, Ades PK, Taylor PWJ (2003) Preliminary investigation of QTLs associated with seedling resistance to Ascochyta blight from Cicer echinospermum, a wild relative of chickpea. Theor Appl Genet 107:719–729Google Scholar
  14. Croser JS, Ahmad F, Clarke HJ, Siddique KHM (2003) Utilisation of wild Cicer in chickpea improvement—progress, constraints, and prospects. Crop Pasture Sci 54:429–444CrossRefGoogle Scholar
  15. Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A et al (2014) Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 15:1CrossRefGoogle Scholar
  16. Garg R, Patel RK, Tyagi AK, Jain M (2011a) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53–63CrossRefPubMedPubMedCentralGoogle Scholar
  17. Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A et al (2011b) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol 156:1661–1678CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gaur PM, Slinkard AE (1990) Genetic control and linkage relations of additional isozyme markers in chick-pea. Theor Appl Genet 80:648–656Google Scholar
  19. Gaur PM, Stinkard AE (1990) Inheritance and linkage of isozyme coding genes in chickpea. J Heredity 81:455–461CrossRefGoogle Scholar
  20. Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V et al (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12:117CrossRefPubMedPubMedCentralGoogle Scholar
  21. Gaur R, Jeena G, Shah N, Gupta S, Pradhan S et al (2015) High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci Rep 5:13387CrossRefPubMedPubMedCentralGoogle Scholar
  22. Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P et al (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genet 122:1577–1589Google Scholar
  23. Gupta S, Kumar T, Verma S, Bharadwaj C, Bhatia S (2015) Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height. Mol Biol Rep 42:1571–1580CrossRefPubMedGoogle Scholar
  24. Gupta S, Nawaz K, Parween S, Roy R, Sahu K, et al (2016) Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement. DNA Res. doi:  10.1093/dnares/dsw042
  25. Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H et al (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 9:922–931CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA et al (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J 10:716–732CrossRefPubMedPubMedCentralGoogle Scholar
  27. Hüttel B, Winter P, Weising K, Choumane W, Weigand F et al (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217CrossRefPubMedGoogle Scholar
  28. Iruela M, Rubio J, Cubero JI, Gil J, Millán T (2002) Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theor Appl Genet 104:643–651Google Scholar
  29. Jaganathan D, Thudi M, Kale S, Azam S, Roorkiwal M et al (2015) Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea. Mol Genet Genomics 290:559–571CrossRefPubMedGoogle Scholar
  30. Jain M, Misra G, Patel RK, Priya P, Jhanwar S et al (2013) A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J 74:715–729CrossRefPubMedGoogle Scholar
  31. Jamalabadi JG, Saidi A, Karami E, Kharkesh M, Talebi R (2013) Molecular mapping and characterization of genes governing time to flowering, seed weight, and plant height in an intraspecific genetic linkage map of chickpea (Cicer arietinum). Biochem Genet 51:387–397CrossRefPubMedGoogle Scholar
  32. Jingade P, Ravikumar RL (2015) Development of molecular map and identification of QTLs linked to Fusarium wilt resistance in chickpea. J Genet 94:723–729CrossRefPubMedGoogle Scholar
  33. Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, et al (2015) Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 5, 15296Google Scholar
  34. Karami E, Talebi R, Kharkesh M, Saidi A (2015) A linkage map of chickpea (Cicer arietinum L.) based on population from ILC3279 × ILC588 crosses: location of genes for time to flowering, seed size and plant height. Genetika 47:253–263CrossRefGoogle Scholar
  35. Kazan K, Muehlbauer FJ (1991) Allozyme variation and phylogeny in annual species of Cicer (Leguminosae). Plant Syst Evol 175:11–21CrossRefGoogle Scholar
  36. Kazan KMFJ, Muehlbauer FJ, Weeden NE, Ladizinsky G (1993) Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theor Appl Genet 86:417–426Google Scholar
  37. Khajuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M et al (2015) Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea. PLoS ONE 10:e0125583CrossRefPubMedPubMedCentralGoogle Scholar
  38. Kottapalli P, Gaur PM, Katiyar SK, Crouch JH, Buhariwalla HK et al (2009) Mapping and validation of QTLs for resistance to an Indian isolate of Ascochyta blight pathogen in chickpea. Euphytica 165:79–88CrossRefGoogle Scholar
  39. Kudapa K, Azam S, Sharpe AG, Taran B, Li R et al (2014) Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications. PLoS ONE 9:e86039CrossRefPubMedPubMedCentralGoogle Scholar
  40. Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R et al (2015) Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front Plant Sci 6:162CrossRefPubMedPubMedCentralGoogle Scholar
  41. Kusmenoglu I, Muehlbauer FJ, Kazan K (1992) Inheritance of isozyme variation in ascochyta blight-resistant chickpea lines. Crop Sci 32:121–127CrossRefGoogle Scholar
  42. Labdi M, Robertson LD, Singh KB, Charrier A (1996) Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphism. Euphytica 88:181–188CrossRefGoogle Scholar
  43. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their application for generation of SSR markers for genome analysis of chickpea (Cicer arietinum L.). Theor Appl Genet 110:492–510Google Scholar
  44. McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK et al (2013) Agriculture: feeding the future. Nature 499:23–24CrossRefPubMedGoogle Scholar
  45. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome wide dense marker maps. Genetics 157:1819–1829PubMedPubMedCentralGoogle Scholar
  46. Millan T, Winter P, Jüngling R, Gil J, Rubio J et al (2010) A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations. Euphytica 175:175–189CrossRefGoogle Scholar
  47. Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney RK (2012) Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theor Appl Genet 125:625–645Google Scholar
  48. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK et al (2010) Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor Appl Genet 120:1415–1441Google Scholar
  49. Neumann K, Kobiljski B, Denčić S, Varshney RK, Börner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed 27:37–58CrossRefGoogle Scholar
  50. Nguyen TT, Taylor PWJ, Redden RJ, Ford R (2004) Genetic diversity estimates in Cicer using AFLP analysis. Plant Breed 123:173–179CrossRefGoogle Scholar
  51. Oram RN, Shaikh MAQ, Zaman KMS, Brown AHD (1987) Isozyme similarity and genetic differences in morphology between Hyprosola, A high yielding, high protein mutant of chickpea (Cicer arietinum L.) and its parental cultivar. Env Exp Bot 27:455–462CrossRefGoogle Scholar
  52. Palomino C, Fernández-Romero MD, Rubio J, Torres A, Moreno MT et al (2009) Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance. Theor Appl Genet 118:671–682Google Scholar
  53. Pandey MK, Roorkiwal M, Singh VK, Ramalingam A, Kudapa H et al (2016) Emerging genomic tools for legume breeding: current status and future prospects. Front Plant Sci 7:455. doi: 10.3389/fpls.2016.00455 PubMedPubMedCentralGoogle Scholar
  54. Parween S, Nawaz K, Roy R, Pole AK, Suresh BV, et al (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci Rep 5:12806.Google Scholar
  55. Pfaff T, Kahl G (2003) Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Mol Genet Genomics 269:243–251PubMedGoogle Scholar
  56. Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV et al (2015) Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines. BMC Plant Biol 15:124CrossRefPubMedPubMedCentralGoogle Scholar
  57. Radhika P, Gowda SJM, Kadoo NY, Mhase LB, Jamadagni BM et al (2007) Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115:209–216Google Scholar
  58. Roorkiwal M, Jain A, Kale SM, Doddamani D, Chitikineni A et al (2017) Development and evaluation of high density SNP array (Axiom®CicerSNP Array) for high resolution genetic mapping and breeding applications in chickpea. Plant Biotechnol J. doi: 10.1111/pbi.12836
  59. Roorkiwal M, Sawargaonkar SL, Chitikineni A, Thudi M, Saxena RK et al (2013) Single nucleotide polymorphism genotyping for breeding and genetics applications in chickpea and pigeonpea using the BeadXpress platform. Plant Genome 6:2CrossRefGoogle Scholar
  60. Roorkiwal M, Nayak SN, Thudi M, Upadhyaya HD, Brunel D et al (2014a) Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers. Front Plant Sci 5:248CrossRefPubMedPubMedCentralGoogle Scholar
  61. Roorkiwal M, Von Wettberg EJ, Upadhyaya HD, Warschefsky E, Rathore A et al (2014b) Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers. PLoS ONE 9:e102016CrossRefPubMedPubMedCentralGoogle Scholar
  62. Roorkiwal M, Rathore A, Das RR, Singh MK, Jain A et al (2016) Genome-enabled prediction models for yield related traits in chickpea. Front Plant Sci 7:1666CrossRefPubMedPubMedCentralGoogle Scholar
  63. Ruelland E, Cantrel C, Gawer M, Kader JC, Zachowski A (2002) Activation of phospholipases C and D is an early response to a cold exposure in Arabidopsis suspension cells. Plant Physiol 130:999–1007CrossRefPubMedPubMedCentralGoogle Scholar
  64. Ruperao P, Chan CK, Azam S, Karafiátová M, Hayashi S et al (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnol J 12:778–786CrossRefPubMedGoogle Scholar
  65. Sabbavarapu MM, Sharma M, Chamarthi SK, Swapna N, Rathore A et al (2013) Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.). Euphytica 193:121–133CrossRefGoogle Scholar
  66. Sant VJ, Patankar AG, Sarode ND, Mhase LB, Sainani MN et al (1999) Potential of DNA markers in detecting divergence and in analysing heterosis in Indian elite chickpea cultivars. Theor Appl Genet 98:1217–1225Google Scholar
  67. Santra DK, Tekeoglu M, Ratnaparkhe M, Kaiser WJ, Muehlbauer FJ (2000) Identification and mapping of QTLs conferring resistance to ascochyta blight in chickpea. Crop Sci 40:1606–1612CrossRefGoogle Scholar
  68. Serret MD, Udupa SM, Weigand F (1997) Assessment of genetic diversity of cultivated chickpea using microsatellite-derived RFLP markers; Implications for origin. Plant Breed 116:573–578CrossRefGoogle Scholar
  69. Shan F, Clarke HC, Plummer JA, Yan G, Siddique KHM (2005) Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms. Theor Appl Genet 110:381–391Google Scholar
  70. Simon CJ, Muehibauer FJ (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. J Heredity 88:115–119CrossRefGoogle Scholar
  71. Singh U (1985) Nutritional quality of chickpea (Cicer arietinum L.): current status and future research needs. Plant Foods for Human Nutr 35:339–351CrossRefGoogle Scholar
  72. Singh KB, Omar M, Saxena MC, Johansen C (1997) Screening for drought resistance in spring chickpea in the Mediterranean region. J Agronomy Crop Sci 178:227–235CrossRefGoogle Scholar
  73. Singh R, Prasad CD, Singhal V, Randhawa GJ (2003) Assessment of genetic diversity in chickpea cultivars using RAPD, AFLP and STMS markers. J Genet Breed 57:165–174Google Scholar
  74. Singh R, Sharma P, Varshney RK, Sharma SK, Singh NK (2008) Chickpea improvement: Role of wild species and genetic markers. Biotechnol Genet Eng Rev 25:267–314CrossRefPubMedGoogle Scholar
  75. Singh VK, Garg R, Jain M (2013) A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol 11:691–701CrossRefGoogle Scholar
  76. Srivastava R, Singh M, Bajaj D, Parida SK (2016) A high-resolution InDel (Insertion–Deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea. Front Plant Sci 7:1362PubMedPubMedCentralGoogle Scholar
  77. Stephens A, Lombardi M, Cogan NO, Forster JW, Hobson K et al (2013) Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of Ascochyta blight resistance in chickpea (Cicer arietinum L.). Mol Breed 33:297–313CrossRefGoogle Scholar
  78. Sudupak MA, Akkaya MS, Kence A (2004) Genetic relationships among perennial and annual Cicer species growing in Turkey assessed by AFLP fingerprinting. Theor Appl Genet 108:937–944Google Scholar
  79. Talebi R, Naji AM, Fayaz F (2008) Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism. Plant Soil Environ 54:447–452Google Scholar
  80. Tayyar RI, Waines JG (1996) Genetic relationships among annual species of Cicer (Fabaceae) using isozyme variation. Theor Appl Genet 92:245–254Google Scholar
  81. Tekeoglu M, Rajesh PN, Muehlbauer FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 105:847–854Google Scholar
  82. Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM et al (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6:e27275CrossRefPubMedPubMedCentralGoogle Scholar
  83. Thudi M, Li Y, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 11:3–11CrossRefPubMedGoogle Scholar
  84. Thudi M, Upadhyaya HD, Rathore A, Gaur PM, Krishnamurthy L et al (2014) Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches. PLoS ONE 9:e96758CrossRefPubMedPubMedCentralGoogle Scholar
  85. Thudi M, Chitikineni A, Liu X, He W, Roorkiwal M, et al (2016) Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.). Sci. Rep. 6:38636.Google Scholar
  86. Tullu A, Muehlbauer FJ, Simon CJ, Mayer MS, Kumar J et al (1998) Inheritance and linkage of a gene for resistance to race 4 of fusarium wilt and RAPD markers in chickpea. Euphytica 102:227–232CrossRefGoogle Scholar
  87. Turner NC, Begg JE (1978) Responses of pasture plants to water deficits. In: Wilson JR (ed) Plant relations in pastures, CSIRO Melbourne, pp. 50–66.Google Scholar
  88. Udupa SM, Sharma A, Sharma RP, Pai RA (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J Plant Biochem Biotechnol 2:83–86CrossRefGoogle Scholar
  89. Van Rheenen HA (1992) Biotechnology and chickpea breeding. Int Chickpea Newslett 26:14–17Google Scholar
  90. Varshney RK (2016) Exciting journey of 10 years from genomes to fields and markets: Some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut. Plant Sci 242:98–107CrossRefPubMedGoogle Scholar
  91. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630CrossRefPubMedGoogle Scholar
  92. Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007a) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649CrossRefGoogle Scholar
  93. Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD et al (2007b) Development of cost-effective SNP assays for chickpea genome analysis and breeding. J SAT Agric Res 3(1):1–3Google Scholar
  94. Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J et al (2009) A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10:523CrossRefPubMedPubMedCentralGoogle Scholar
  95. Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA et al (2012a) Can genomics boost productivity of orphan crops? Nat Biotechnol 30:1172–1176CrossRefPubMedGoogle Scholar
  96. Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK et al (2012b) Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J Biosci 37:811–820CrossRefPubMedGoogle Scholar
  97. Varshney RK, Song C, Saxena RK, Azam S, Yu S et al (2013a) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246CrossRefPubMedGoogle Scholar
  98. Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S et al (2013b) Fast-track introgression of “QTL-Hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. Plant Genome 6:3. doi: 10.3835/plantgenome2013.07.0022 Google Scholar
  99. Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J et al (2014a) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127:445–462Google Scholar
  100. Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y et al (2014b) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct Integrative Genomics 14:59–73CrossRefGoogle Scholar
  101. Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK et al (2014c) Marker-assisted backcrossing to introgress resistance to Fusarium wilt (FW) race 1 and Ascochyta blight (AB) in C 214, an elite cultivar of chickpea. Plant Genome 7:1. doi: 10.3835/plantgenome2013.10.0035 CrossRefGoogle Scholar
  102. Varshney RK, Kudapa H, Pazhamala L, Chitikineni A, Thudi M et al (2015) Translational genomics in agriculture: some examples in grain legumes. CRC Crit. Rev Plant Sci 34:169–194CrossRefGoogle Scholar
  103. Verma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, et al (2015) High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Sci Rep 5:17512Google Scholar
  104. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedPubMedCentralGoogle Scholar
  105. Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC et al (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 262:90–101CrossRefPubMedGoogle Scholar
  106. Winter P, Benko-Iseppon AM, Hüttel B, Ratnaparkhe M, Tullu A et al (2000) A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum × C. reticulatum cross; localization of resistance genes for fusarium wilt races 4 and 5. Theor Appl Genet 101:1155–1163Google Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Manish Roorkiwal
    • 1
    Email author
  • Ankit Jain
    • 1
  • Mahendar Thudi
    • 1
  • Rajeev K. Varshney
    • 1
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia

Personalised recommendations