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Chickpea Genomics

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Biotechnologies of Crop Improvement, Volume 3

Abstract

As precise phenotyping is essential and the cost of generating phenotyping data at every generation is very expensive, recent advances in genomics technologies and the availability of a wide range of genotyping platforms have made the cost of genotyping much less expensive compared with phenotyping. The recent developments in sequencing technologies have manifold increased the repertoire of various types of markers that are available in chickpea including SSRs, SNPs, DArTs, hundreds of thousands transcript reads and BAC-end sequences saturated genetic maps, QTL maps as well as physical maps, and the sequencing of both kabuli and desi type has greatly helped in using marker-assisted technologies to be applied in plant breeding. Germplasm resequencing for identification of genome-wide SNPs and their subsequent utilization in genomic selection has the potential to break the yield barrier being experienced in chickpea and many other crops. Genomic-assisted breeding for marker-assisted backcrossing (MABC) for introgressing QTL region, marker-assisted recurrent selection, gene pyramiding, marker-assisted selection (MAS), and genomic selection can now be taken up in chickpea. The conventional plant breeding should take these tools to make greater genetic gains, increase selection potential, and have faster breeding cycles so that the genetic improvement gains are increased in chickpea.

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References

  • Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25(12):1263–1274

    Article  PubMed  CAS  Google Scholar 

  • Alderborn A, Kristofferson A, Hammerling U (2000) Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 10(8):1249–1258

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Allen DJ, Lenné JM (1998) The pathology of food and pasture legumes. CAB International, New York

    Google Scholar 

  • Anuradha C, Gaur PM, Pande S, Gali KK, Ganesh M, Kumar J, Varshney RK (2011) Mapping QTL for resistance to botrytis grey mould in chickpea. Euphytica 182(1):1–9

    Article  CAS  Google Scholar 

  • Araus JL, Slafer GA, Reynolds MP, Royo C (2002) Plant breeding and drought in C3 cereals: what should we breed for? Ann Bot 89(7):925–940

    Article  PubMed  PubMed Central  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9(3):208–218

    Article  CAS  Google Scholar 

  • Bernardo R, Charcosset A (2006) Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci 46(2):614–621

    Article  Google Scholar 

  • Bharadwaj C, Chauhan SK, Rajguru G, Srivastava R, Satyavathi T, C Yadav S, Rizvi AH, Kumar J, Solanki RK (2010) Diversity analysis of chickpea (Cicer arietinum) cultivars using STMS markers. J Agri Sci 9:947

    Google Scholar 

  • Bharadwaj C, Tripathi S, Varshney R, Kumar J (2011) Deployment of molecular markers for developing high yielding wilt resistance chickpea genotypes. In: Theme 2: 2.5: Integrated crop breeding. Poster Abstracts. 2011. General Research Meeting, Generation Challenge Programme. 21–25 September, 2011, Hyderabad, India. P13

    Google Scholar 

  • Bharadwaj C, Srivastava R, Chauhan SK, Satyavathi CT, Kumar J, Faruqui A, Yadav S, Rizvi AH, Kumar T (2013) Molecular diversity and phylogeny in geographical collection of chickpea (Cicer sp.) accessions. J Genet 92(2):94–100

    Article  Google Scholar 

  • Bhardwaj C, Chauhan SK, Yadav S, Satyavathi TC, Singh R, Kumar J, Srivastava R, Rajguru G (2002) Molecular marker based linkage map of chickpea (Cicer arietinum) developed from desi× kabuli cross 81(2):116–118

    Google Scholar 

  • Biedenkapp H, Borgmeyer U, Sippel AE, Klempnauer KH (1988) Viral myb oncogene encodes a sequence-specific DNA-binding activity. Nature 335(6193):835–837

    Article  PubMed  CAS  Google Scholar 

  • Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13(3):513–523

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 5(1):16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chandra, S., Buhariwalla, H. K., Kashiwagi, J., Harikrishna, S., Sridevi, K. R., Krishnamurthy, L., Serraj, R., Crouch, J. H. Identifying QTL-linked markers in marker-deficient crops T. Fisher (Ed.), Proceedings of the 4th international crop science congress, Brisbane, Australia, 26 September–1 October 2004 2006

    Google Scholar 

  • Charmet G, Robert N, Perretant MR, Gay G, Sourdille P, Groos C, Bernard S, Bernard M (2001) Marker assisted recurrent selection for cumulating QTLs for bread-making related traits. Euphytica 119:89–93. https://doi.org/10.1023/A:1017577918541

    Article  CAS  Google Scholar 

  • Ching A, Rafalski A (2002) Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis. Cell Mol Biol Lett 7(2B):803–810

    PubMed  CAS  Google Scholar 

  • Cho S, Chen W, Muehlbauer FJ (2004) Pathotype-specific genetic factors in chickpea (Cicer arietinum L.) for quantitative resistance to ascochyta blight. Theor Appl Genet 109(4):733–739

    Article  PubMed  Google Scholar 

  • Choudhary P, Khanna SM, Jain PK (2012a) Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers. Genet Molecul Res 11(2):891–905

    Article  CAS  Google Scholar 

  • Choudhary S, Gaur R, Gupta S, Bhatia S (2012b) EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor Appl Genet 124(8):1449–1462

    Article  PubMed  CAS  Google Scholar 

  • Choudhary P, Khanna SM, Jain PK, Bharadwaj C, Kumar J, Lakhera PC, Srinivasan R (2013) Molecular characterization of primary gene pool of chickpea based on ISSR markers. Biochem Genet 51(3–4):306–322

    Article  PubMed  CAS  Google Scholar 

  • Chourey PS, Taliercio EW, Kane EJ (1991) Tissue-specific expression and anaerobically induced posttranscriptional modulation of sucrose synthase genes in Sorghum bicolor M. Plant Physiol 96(2):485–490

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Clarke HJ, Siddique KHM (2004) Response of chickpea genotypes to low temperature stress during reproductive development. Field Crop Res 90(2–3):323–334

    Article  Google Scholar 

  • Close TJ (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97(4):795–803

    Article  CAS  Google Scholar 

  • 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(4):719–729

    Article  PubMed  CAS  Google Scholar 

  • Cotsaftis O, Plett D, Johnson AA, Walia H, Wilson C, Ismail AM, Close TJ, Tester M, Baumann U (2011) Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. Mol Plant 4(1):25–41

    Article  PubMed  CAS  Google Scholar 

  • Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11(1):163

    Article  PubMed  PubMed Central  Google Scholar 

  • Croser JS, Clarke HJ, Siddique KHM, Khan TN (2003) Low-temperature stress: implications for chickpea (Cicer arietinum L.) improvement. Crit Rev Plant Sci 22(2):185–219

    Article  Google Scholar 

  • Delmer DP, Amor Y (1995) Cellulose biosynthesis. Plant Cell 7(7):987

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deokar AA, Kondawar V, Jain PK, Karuppayil SM, Raju NL, Vadez V, Varshney RK, Srinivasan R (2011) Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and-susceptible genotypes of chickpea under terminal drought stress. BMC Plant Biol 11(1):70

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dure L, Crouch M, Harada J, Ho THD, Mundy J, Quatrano R, Thomas T, Sung ZR (1989) Common amino acid sequence domains among the LEA proteins of higher plants. Plant Mol Biol 12(5):475–486

    Article  PubMed  CAS  Google Scholar 

  • Eggen A (2012) The development and application of genomic selection as a new breeding paradigm. Anim Front 2(1):10–15

    Article  Google Scholar 

  • Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L (2003) Highly parallel SNP genotyping. In: January (ed) Cold Spring Harbor symposia on quantitative biology, vol 68. Cold Spring Harbor Laboratory Press, New York, pp 69–78

    Google Scholar 

  • Flandez-Galvez H, Ades PK, Ford R, Pang ECK, Taylor PWJ (2003a) QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (Cicer arietinum L.). Theor Appl Genet 107(7):1257–1265

    Article  PubMed  CAS  Google Scholar 

  • Flandez-Galvez H, Ford R, Pang ECK, Taylor PWJ (2003b) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theor Appl Genet 106(8):1447–1456

    Article  PubMed  CAS  Google Scholar 

  • Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18(1):53–63

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M (2016) Transcriptome analyses reveal genotype-and developmental stage-specific molecular responses to drought and salinity stresses in chickpea. Sci Rep 6:19228

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gaur PM, Krishnamurthy L, Kashiwagi J (2008) Improving drought-avoidance root traits in chickpea (Cicer arietinum L.)-current status of research at ICRISAT. Plant Product Sci 11(1):3–11

    Article  Google Scholar 

  • Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12(1):117

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gaur PM, Thudi M, Samineni S, Varshney RK (2014) Advances in chickpea genomics. In: Legumes in the Omic Era. Springer, New York, pp 73–94

    Chapter  Google Scholar 

  • Geigenberger P, Stitt M (1993) Sucrose synthase catalyses a readily reversible reaction in vivo in developing potato tubers and other plant tissues. Planta 189(3):329–339

    Article  PubMed  CAS  Google Scholar 

  • Geigenberger P, Krause KP, Hill LM, Reimholz R, MacRae E, Quick WP, Sonnewald U, Stitt M (1995) The regulation of sucrose synthesis in leaver and tubers of potato plants. In: International Symposium on sucrose metabolism. American Society Plant Physiologists

    Google Scholar 

  • Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13(2):167–173

    Article  PubMed  CAS  Google Scholar 

  • Grenier, C., Châtel, M., Ospina, Y., Cao, T.V., Guimaraes, E.P., Martinez, C., Tohmé, J., Courtois, B. and Ahmadi, N., (2012). Population Improvement Through Recurrent Selection in Rice Prospect for Maker Assisted Recurrent Selection and Genome-Wide Selection W011

    Google Scholar 

  • Grishkevich V, Yanai I (2013) The genomic determinants of genotype× environment interactions in gene expression. Trends Genet 29(8):479–487

    Article  PubMed  CAS  Google Scholar 

  • Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Prakash AB, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genet 122(8):1577–1589

    Article  PubMed  PubMed Central  Google Scholar 

  • 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(11):1571–1580

    Article  PubMed  CAS  Google Scholar 

  • Haileselasie TH, Teferii G (2012) The effect of salinity stress on germination of chickpea (Cicer arietinum L.) land race of Tigray. Curr Res J Biol Sci 4(5):578–583

    CAS  Google Scholar 

  • Haware, M. P., Tripathi, H. S., Rathi, Y. P. S., Lenne, J. M., & Jayanthi, S. (1997). Integrated management of Botrytis gray mold of chickpea: cultural, chemical, biological, and resistance options. In Recent advances in research on botrytis gray mold of chickpea: summary proceedings of the Third Working Group Meeting to Discuss Collaborative Research on Botrytis Gray Mold of Chickpea, 15–17 Apr 1996, Pantnagar, Uttar Pradesh, India. Patancheru 502 324, Andhra Pradesh: International Crops Research Institute for the Semi-Arid Tropics. 68 pp (p. 9). ISBN 92–9066–373-1. Order code CPE 112

    Google Scholar 

  • Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, BhanuPrakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L (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(8):922–931

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kishor K (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(6):716–732

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10(2):156–161

    Article  PubMed  CAS  Google Scholar 

  • Huang JC, Lin SM, Wang CS (2000) A pollen-specific and desiccation-associated transcript in Lilium longiflorum during development and stress. Plant Cell Physiol 41(4):477–485

    Article  PubMed  CAS  Google Scholar 

  • Huber SC, Huber JL (1996) Role and regulation of sucrose-phosphate synthase in higher plants. Annu Rev Plant Biol 47(1):431–444

    Article  CAS  Google Scholar 

  • Hüttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42(2):210–217

    Article  PubMed  Google Scholar 

  • Ingram J, Chandler JW, Gallagher L, Salamini F, Bartels D (1997) Analysis of cDNA clones encoding sucrose-phosphate synthase in relation to sugar interconversions associated with dehydration in the resurrection plant Craterostigma plantagineum Hochst. Plant Physiol 115(1):113–121

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Iruela M, Rubio J, Cubero JI, Gil J, Millan T (2002) Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theor Appl Genet 104(4):643–651

    Article  PubMed  CAS  Google Scholar 

  • Iusem ND, Bartholomew DM, Hitz WD, Scolnik PA (1993) Tomato (Lycopersicon esculentum) transcript induced by water deficit and ripening. Plant Physiol 102(4):1353

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jain D, Chattopadhyay D (2010) Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance. BMC Plant Biol 10(1):24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jeanneau M, Gerentes D, Foueillassar X, Zivy M, Vidal J, Toppan A, Perez P (2002) Improvement of drought tolerance in maize: towards the functional validation of the Zm-Asr1 gene and increase of water use efficiency by over-expressing C4–PEPC. Biochimie 84(11):1127–1135

    Article  PubMed  CAS  Google Scholar 

  • Johnson R (2003) Marker-assisted selection. In: Plant breeding reviews: part 1: long-term selection: maize, 24, pp 293–309

    Google Scholar 

  • Kahl G, Molina C, Udupa SM, Rotter B, Horres R, Jungmann R, Belarmino LC, L'Taief B, Drevon J, Baum M, Winter P (2007) Super SAGE: exploring the stress transcriptome in chickpea. In: Plant and animal genome XV conference, pp 13–17

    Google Scholar 

  • Kalifa Y, Gilad A, Konrad Z, Zaccai M, Scolnik PA, Dudy BZ (2004) The water-and salt-stress-regulated Asr1 (abscisic acid stress ripening) gene encodes a zinc-dependent DNA-binding protein. Biochem J 381(2):373–378

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Konsam S, Chellapilla B, Ram G, Chellapilla TS, Jain PK (2014) Molecular diversity of chickpea ('Cicer arietinum'L.) genotypes differing in their Raffinose family oligosaccharides viz., raffinose and stachyose content as revealed through SSR markers. Aust J Crop Sci 8(8):1175

    CAS  Google Scholar 

  • Krishnamurthy L, Kashiwagi J, Tobita S, Ito O, Upadhyaya HD, Gowda CL, Gaur PM, Sheshshayee MS, Singh S, Vadez V, Varshney RK (2013a) Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm. Funct Plant Biol 40(12):1350–1361

    Article  CAS  PubMed  Google Scholar 

  • Krishnamurthy L, Kashiwagi J, Upadhyaya HD, Gowda CLL, Gaur PM, Singh S, Purushothaman R, Varshney RK (2013b) Partitioning coefficient—a trait that contributes to drought tolerance in chickpea. Field Crop Res 149:354–365

    Article  Google Scholar 

  • Kumar S, Hamwieh A, Manickavelu A, Kumar J, Sharma TR, Baum M (2014) Advances in lentil genomics. In: Legumes in the omic era. Springer, New York, pp 111–130

    Chapter  Google Scholar 

  • Ladizinsky G, Adler A (1976) Genetic relationships among the annual species of Cicer L. Theor Appl Genet 48(4):197–203

    Article  PubMed  CAS  Google Scholar 

  • Lenka SK, Katiyar A, Chinnusamy V, Bansal KC (2011) Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J 9(3):315–327

    Article  PubMed  CAS  Google Scholar 

  • Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110(3):492–510

    Article  PubMed  CAS  Google Scholar 

  • Maqbool MA, Aslam M, Ali H, Shah TM (2016) Evaluation of advanced chickpea (Cicer arietinum L.) accessions based on drought tolerance indices and SSR markers against different water treatments. Pak. J Bot 48(4):1421–1429

    CAS  Google Scholar 

  • Maskin L, Gudesblat GE, Moreno JE, Carrari FO, Frankel N, Sambade A, Rossi M, Iusem ND (2001) Differential expression of the members of the Asr gene family in tomato (Lycopersicon esculentum). Plant Sci 161(4):739–746

    Article  CAS  Google Scholar 

  • Masle J, Gilmore SR, Farquhar GD (2005) The ERECTA gene regulates plant transpiration efficiency in Arabidopsis. Nature 436(7052):866

    Article  PubMed  CAS  Google Scholar 

  • Matsumura H, Ito A, Saitoh H, Winter P, Kahl G, Reuter M, Krüger DH, Terauchi R (2005) SuperSAGE. Cell Microbiol 7(1):1–18

    Google Scholar 

  • Meena HP, Kumar J, Upadhyaya HD, Bharadwaj C, Chauhan SK, Verma AK, Rizvi AH (2010) Chickpea mini core germplasm collection as rich sources of diversity for crop improvement. J SAT Agric Res 8:1–5

    Google Scholar 

  • Millan T, Rubio J, Iruela M, Daly K, Cubero JI, Gil J (2003) Markers associated with Ascochyta blight resistance in chickpea and their potential in marker-assisted selection. Field Crop Res 84(3):373–384

    Article  Google Scholar 

  • Millan T, Clarke HJ, Siddique KH, Buhariwalla HK, Gaur PM, Kumar J, Gil J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147(1–2):81–103

    Article  Google Scholar 

  • Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9(1):553

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, JŘngling R, Singh J, Kishor PK, Sivaramakrishnan S, Hoisington DA (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(7):1415–1441

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nayyar H, Bains T, Kumar S (2005) Low temperature induced floral abortion in chickpea: relationship to abscisic acid and cryoprotectants in reproductive organs. Environ Exp Bot 53(1):39–47

    Article  CAS  Google Scholar 

  • Neeraj K, Bharadwaj C, Satyavathi CT, Madan P, Tapan K, Tripti S, Jain PK, Patil BS, Soren KR (2016) Yield correlation of chickpea (Cicer arietinum L.) genotypes based on physiological and morphological traits for salt tolerance. Int J Trop Agric 34(3):693–699

    Google Scholar 

  • Nene YL, Reddy MV (1987) Chickpea diseases and their control. In: Chickpea diseases and their control, pp 233–270

    Google Scholar 

  • Nguyen TT, Taylor PWJ, Redden RJ, Ford R (2004) Genetic diversity estimates in Cicer using AFLP analysis. Plant Breed 123(2):173–179

    Article  CAS  Google Scholar 

  • Oukarroum A, Schansker G, Strasser RJ (2009) Drought stress effects on photosystem I content and photosystem II thermotolerance analyzed using Chl a fluorescence kinetics in barley varieties differing in their drought tolerance. Physiol Plant 137(2):188–199

    Article  PubMed  CAS  Google Scholar 

  • Pande S, Singh G, Rao JN, Bakr MA, Chaurasia PCP, Joshi S, Johansen C, Singh SD, Kumar J, Rahman MM, Gowda CL (2001) Integrated management of botrytis gray mold of chickpea. International Crops Research Institute for the Semi-Arid Tropics, India

    Google Scholar 

  • Petřivalský M, Brauner F, Luhová L, Gagneul D, Šebela M (2007) Aminoaldehyde dehydrogenase activity during wound healing of mechanically injured pea seedlings. J Plant Physiol 164(11):1410–1418

    Article  PubMed  CAS  Google Scholar 

  • Pratap A, Chaturvedi SK, Tomar R, Rajan N, Malviya N, Thudi M, Saabale PR, Prajapati U, Varshney RK, Singh NP (2017) Marker-assisted introgression of resistance to fusarium wilt race 2 in Pusa 256, an elite cultivar of desi chickpea. Mol Gen Genomics 292(6):1237–1245

    Article  CAS  Google Scholar 

  • Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KH, Colmer TD, Turner NC, Varshney RK, Vadez V (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(1):124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Qadir SA, Datta S, Singh NP, Kumar S (2007) Development of highly polymorphic SSR markers for chickpea (Cicer arietinum L.) and their use in parental polymorphism. Indian J Genet Plant Breed 67(4):329–333

    CAS  Google Scholar 

  • Radhika P, Gowda SJM, Kadoo NY, Mhase LB, Jamadagni BM, Sainani MN, Chandra S, Gupta VS (2007) Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115(2):209–216

    Article  PubMed  CAS  Google Scholar 

  • Rajesh PN, Muehlbauer FJ (2008) Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.). Euphytica 162(2):291–300

    Article  CAS  Google Scholar 

  • Rakshit S, Winter P, Tekeoglu M, Muñoz JJ, Pfaff T, Benko-Iseppon AM, Muehlbauer FJ, Kahl G (2003) DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.). Euphytica 132(1):23–30

    Article  CAS  Google Scholar 

  • Rao LS, Rani PU, Deshmukh PS, Kumar PA, Panguluri SK (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genet Resour Crop Evol 54(6):1235–1244

    Article  CAS  Google Scholar 

  • Robertson, L. D., Singh, K. B., & Ocampo, B. (1995). A catalog of annual wild

    Google Scholar 

  • Rodi CP, Darnhofer-Patel B, Stanssens P, Zabeau M, van den Boom D (2002) A strategy for the rapid discovery of disease markers using the MassARRAY system. BioTechniques 32:S62–S69

    Google Scholar 

  • Roorkiwal M, Sharma PC (2012) Sequence similarity based identification of abiotic stress responsive genes in chickpea. Bioinformation 8(2):92

    Article  PubMed  PubMed Central  Google Scholar 

  • Rosenzweig C, Parry ML (1994) Potential impact of climate change on world food supply. Nature 367(6459):133–138

    Article  Google Scholar 

  • Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci 103(49):18656–18661

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Rudrabhatla P, Rajasekharan R (2004) Functional characterization of peanut serine/threonine/tyrosine protein kinase: molecular docking and inhibition kinetics with tyrosine kinase inhibitors. Biochemistry 43(38):12123–12132

    Article  PubMed  CAS  Google Scholar 

  • Sam RE, Theodore MC, Marlin DE, Robert SR, Jason K (2009).(2007) Molecular markers in a commercial breeding program. Crop Sci 47(S3):154–163

    Google Scholar 

  • Savithri KS, Ganapathy PS, Sinha SK (1980) Sensitivity to low temperature in pollen germination and fruit-set in Cicer arietinum L. J Exp Bot 31(2):475–481

    Article  Google Scholar 

  • Saxena NP, Johansen C, Sethi SC, Talwar HS, Krishnamurthy L (1988) Improving harvest index in chickpea through incorporation of cold tolerance. Int Chickpea Newsletter 19:17–19

    Google Scholar 

  • Schefers JM, Weigel KA (2012) Genomic selection in dairy cattle: integration of DNA testing into breeding programs. Anim Front 2(1):4–9

    Article  Google Scholar 

  • Schneider A, Salamini F, Gebhardt C (1997) Expression patterns and promoter activity of the cold-regulated gene ci21A of potato. Plant Physiol 113(2):335–345

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sefera T, Abebie B, Gaur PM, Assefa K, Varshney RK (2011) Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers. Crop Pasture Sci 62(2):177–187

    Article  Google Scholar 

  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31(3):79–292

    Article  Google Scholar 

  • Serraj R, Krishnamurthy L, Kashiwagi J, Kumar J, Chandra S, Crouch JH (2004) Variation in root traits of chickpea (Cicer arietinum L.) grown under terminal drought. Field Crop Res 88(2–3):115–127

    Article  Google Scholar 

  • Sethy NK, Shokeen B, Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Mol Ecol Resour 3(3):428–430

    Article  CAS  Google Scholar 

  • Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112(8):1416–1428

    Article  PubMed  CAS  Google Scholar 

  • Sharma KD, Muehlbauer FJ (2007) Fusarium wilt of chickpea: physiological specialization, genetics of resistance and resistance gene tagging. Euphytica 157(1–2):1–14

    Article  CAS  Google Scholar 

  • Sharma KD, Nayyar H (2014) Cold stress alters transcription in meiotic anthers of cold tolerant chickpea (Cicer arietinum L.). BMC Res Notes 7(1):717

    Article  PubMed  PubMed Central  Google Scholar 

  • Shpak ED, Berthiaume CT, Hill EJ, Torii KU (2004) Synergistic interaction of three ERECTA-family receptor-like kinases controls Arabidopsis organ growth and flower development by promoting cell proliferation. Development 131(7):1491–1501

    Article  PubMed  CAS  Google Scholar 

  • Singh KB (1993) Problems and prospects of stress resistance breeding in chickpea

    Google Scholar 

  • Singh S (2014) PM Gaur, SK Chaturvedi, NP Singh, and JS Sandhu. Broadening the genetic base of grain legumes, 51

    Google Scholar 

  • Singh KB, Malhotra RS, Saxena MC (1995) Additional sources of tolerance to cold in cultivated and wild Cicer species. Crop Sci 35(5):1491–1497

    Article  Google Scholar 

  • Soren KR, Patil PG, Das A, Bohra A, Datta S, Chaturvedi SK, Nadarajan N (2012) Advances in pulses genomic research. Indian Institute of Pulses Research, Kanpur, p 25

    Google Scholar 

  • Sreenivasulu N, Kishor PK, Varshney RK, Altschmied L (2002) Mining functional information from cereal genomes–the utility of expressed sequence tags. Curr Sci:965–973

    Google Scholar 

  • Srinivasan A, Johansen C, Saxena NP (1998) Cold tolerance during early reproductive growth of chickpea (Cicer arietinum L.): characterization of stress and genetic variation in pod set1. Field Crop Res 57(2):181–193

    Article  Google Scholar 

  • Supriya S, Bharadwaj C, Vinay S, Neeraj K, Kv B, Patil BS, Soren KR, Chaturvedi SK, Manish R, Chauhan SK, Rajeev V (2017) Morpho-physiological grouping of chickpea (Cicerarietinum L.) genotypes on the basis of their response to drought stress. Int J Trop Agric 35(1):5–13

    Google Scholar 

  • Tapan K, Bharadwaj C, Rizvi AH, Ashutosh S, Shailesh T, Afroz A, Chauhan SK (2015) Chickpea landraces: a valuable and divergent source for drought tolerance. Int J Tropical Agri 33(2 (part II)):633–638

    Google Scholar 

  • Tekeoglu M, Santra DK, Kaiser WJ, Muehlbauer FJ (2000) Ascochyta blight resistance inheritance in three chickpea recombinant inbred line populations. Crop Sci 40(5):1251–1256

    Article  Google Scholar 

  • Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD (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(11):e27275

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thudi M, Gaur PM, Krishnamurthy L, Mir RR, Kudapa H, Fikre A, Kimurto P, Tripathi S, Soren KR, Mulwa R, Bharadwaj C (2014) Genomics-assisted breeding for drought tolerance in chickpea. Funct Plant Biol 41(11):1178–1190

    Article  CAS  PubMed  Google Scholar 

  • Turner NC, Colmer TD, Quealy J, Pushpavalli R, Krishnamurthy L, Kaur J, Singh G, Siddique KH, Vadez V (2013) Salinity tolerance and ion accumulation in chickpea (Cicer arietinum L.) subjected to salt stress. Plant Soil 365(1–2):347–361

    Article  CAS  Google Scholar 

  • Udupa SM, Baum M (2003) Genetic dissection of pathotype-specific resistance to ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theor Appl Genet 106(7):1196–1202

    Article  PubMed  CAS  Google Scholar 

  • Udupa SM, Weigand F, Saxena MC, Kahl G (1998) Genotyping with RAPD and microsatellite markers resolves pathotype diversity in the ascochyta blight pathogen of chickpea. Theor Appl Genet 97(1–2):299–307

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102(8):1292–1298

    Article  Google Scholar 

  • Upadhyaya HD, Dwivedi SL, Baum M, Varshney RK, Udupa SM, Gowda CL, Hoisington D, Singh S (2008) Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol 8(1):106

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Upadhyaya HD, Kashiwagi J, Varshney RK, Gaur PM, Saxena KB, Krishnamurthy L, Gowda CLL, Pundir RPS, Chaturvedi SK, Basu PS, Singh IP (2012) Phenotyping chickpeas and pigeonpeas for adaptation to drought. Front Physiol 3:179

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vadez V, Krishnamurthy L, Serraj R, Gaur PM, Upadhyaya HD, Hoisington DA, Varshney RK, Turner NC, Siddique KHM (2007) Large variation in salinity tolerance in chickpea is explained by differences in sensitivity at the reproductive stage. Field Crop Res 104(1–3):123–129

    Article  Google Scholar 

  • Vadez V, Krishnamurthy L, Thudi M, Anuradha C, Colmer TD, Turner NC et al (2012) Assessment of ICCV 2× JG 62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTL for seed yield and yield components. Mol Breed 30(1):9–21

    Article  Google Scholar 

  • Valente F, Gauthier F, Bardol N, Blanc G, Joets J, Charcosset A, Moreau L (2013) OptiMAS: a decision support tool for marker-assisted assembly of diverse alleles. J Hered 104(4):586–590

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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 242:98–107

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10(12):621–630

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Hoisington DA, Upadhyaya HD, Gaur PM, Nigam SN, Saxena K, Vadez V, Sethy NK, Bhatia S, Aruna R, Gowda MC (2007) Molecular genetics and breeding of grain legume crops for the semi-arid tropics. In: Genomics-assisted crop improvement. Springer, Dordrecht, pp 207–241

    Chapter  Google Scholar 

  • Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009a) Orphan legume crops enter the genomics era! Curr Opin Plant Biol 12(2):202–210

    Article  PubMed  Google Scholar 

  • Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KH (2009b) A comprehensive resource of drought-and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10(1):523

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Varshney RK, Glaszmann JC, Leung H, Ribaut JM (2010) More genomic resources for less-studied crops. Trends Biotechnol 28(9):452–460

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P (2012) Can genomics boost productivity of orphan crops? Nat Biotechnol 30(12):1172

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB (2013a) Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 31(8):1120–1134

    Article  PubMed  Google Scholar 

  • Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T (2013b) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31(3):240

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013c) 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)

    Google Scholar 

  • Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK, Srinivasan S, Swapna N, Sharma M, Pande S, Singh S, Kaur L (2014a) Marker-assisted backcrossing to introgress resistance to Fusarium wilt race 1 and Ascochyta blight in C 214, an elite cultivar of chickpea. The plant genome 7(1)

    Google Scholar 

  • Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A (2014b) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127(2):445–462

    Article  PubMed  CAS  Google Scholar 

  • Verma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, Bhatia S (2015) High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using genotyping-by-sequencing (GBS). Sci Rep 5:17512

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet MGG 262(1):90–101

    Article  PubMed  CAS  Google Scholar 

  • Xu Y (2010) Molecular dissection of complex traits: practice. In: Molecular plant breeding, pp 249–285

    Chapter  Google Scholar 

  • Yadav S, Bharadwaj C, Chauhan SK, Rizvi AH, Kumar J, Satyavathi CT (2011) Analysis of genetic diversity in Cicerspecies using molecular markers. Indian J Genet Plant Breed 71(3):272–275

    Google Scholar 

  • Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, Longin FH, Ranc N, Reif JC (2012) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124(4):769–776

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India

    C. Bharadwaj, Supriya Sachdeva, Rajesh Kumar Singh & B. S. Patil

  2. Centre of Excellence in Genomics, ICRISAT, Patancheru, India

    Manish Roorkiwal & Rajeev Varshney

  3. ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Sushil Chaturvedi

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  1. C. Bharadwaj
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  3. Rajesh Kumar Singh
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  4. B. S. Patil
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  1. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India

    Satbir Singh Gosal

  2. Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India

    Shabir Hussain Wani

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Bharadwaj, C. et al. (2018). Chickpea Genomics. In: Gosal, S., Wani, S. (eds) Biotechnologies of Crop Improvement, Volume 3. Springer, Cham. https://doi.org/10.1007/978-3-319-94746-4_13

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