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Impact of Genomics on Chickpea Breeding

  • Srinivasan Samineni
  • Mahendar Thudi
  • Sobhan B. Sajja
  • Rajeev K. Varshney
  • Pooran M. GaurEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Chickpea is an economical source of vegetable protein for the poor living in the semi-arid regions globally. As a consequence of climate change and increasing climate variability, the incidences of drought and heat stresses and severity of some diseases, such as dry root rot and collar rot, have increased in chickpea crop, resulting in poor and unstable yields. By improoving the efficiency of crop breeding programs, climate resilient varieties with traits desired by the farmers, industries and consumers can be developed more rapidly. Excellent progress has been made in the development of genomic resources for chickpea in the recent past. Several national and international chickpea breeding programs have started utilizing these genomic resources and tools for genetic improvement of complex traits. One of such examples includes the introgression of “QTL-hotspot” containing quantitative trait loci (QTLs) for several drought tolerance-related traits, including root traits, through marker-assisted backcrossing (MABC) for enhancing drought tolerance in popular cultivars. Several drought-tolerant introgression lines with higher yield as compared to the popular cultivars have been identified. Multi-parent advanced generation intercross (MAGIC) populations developed from using 8 parents created large genetic diversity consequently several promising lines. Marker-assisted recurrent selection (MARS) has also been explored for yield improvement in chickpea. Development of diagnostic markers or the identification of candidate genes for several traits is essential for greater use of genomic resources in chickpea improvement.

References

  1. Ainsworth EA, Ort DR (2010) How do we improve crop production in a warming world? Plant Physiol 154:526–530CrossRefPubMedPubMedCentralGoogle Scholar
  2. Ali H, Shah TM, Iqbal N, Atta BM, Haq MA (2010) Mutagenic induction of double-podding trait in different genotypes of chickpea and their characterization by STMS marker. Plant Breed 129:116–119CrossRefGoogle Scholar
  3. Anbessa Y, Taran B, Warkentin TD, Tullu A, Vandenberg A (2009) Genetic analyses and conservation of QTL for Ascochyta blight resistance in chickpea (Cicer arietinum L.). Theor Appl Genet 4:757–765CrossRefGoogle Scholar
  4. Anuradha Ch, Gaur PM, Pande S, Gali KK, Ganesh M, Kumar J, Varshney RK (2011) Mapping QTL for resistance to botrytis grey mould in chickpea. Euphytica 182:1–9CrossRefGoogle Scholar
  5. Aryamanesh N, Nelson MN, Yan G, Clarke HJ, Siddique KHM (2010) Mapping a major gene for growth habit and QTLs for ascochyta blight resistance and flowering time in a population between chickpea and Cicer reticulatum. Euphytica 173:307–319Google Scholar
  6. Bernardo R, Charcosset A (2006) Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci 46:614–621CrossRefGoogle Scholar
  7. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Villeda HS, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718. http://science.sciencemag.org/content/325/5941/714
  8. Castro P, Pisto´n F, Madrid E, Milla`n T, Gil J, Rubio J (2010) Development of chickpea near-isogenic lines for Fusarium wilt. Theor Appl Genet 121:1519–1526Google Scholar
  9. Chandra S, Buhariwalla HK, Kashiwagi J, Harikrishna S, Sridevi KR, Krishnamurthy L, Serraj R, Crouch JH, (2004) Identifying QTL-linked markers in marker-deficient crops. In: Fisher T. (ed) Proceedings of the 4th International Crop Science Congress. Brisbane, Australia, 26 September–1 October 2004. The Regional Institute Ltd., Gosford, New South Wales, AustraliaGoogle Scholar
  10. Charcosset A, Moreau L (2004) Use of molecular markers for the development of new cultivars and the evaluation of genetic diversity. Euphytica 137:81–94CrossRefGoogle Scholar
  11. 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 109:733–739CrossRefPubMedGoogle Scholar
  12. Cho S, Kumar J, Shultz JL, Anupama K, Tefera F, Muehlbauer FJ (2002) Mapping genes for double podding and other morphological traits in chickpea. Euphytica 128:285–292CrossRefGoogle Scholar
  13. Cobos MJ, Ferna`ndez MJ, Rubio J, Kharrat M, Moreno MT, Gil J, Milla`n T (2005) A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli 9 Desi crosses: location of genes for resistance to Fusarium wilt race 0. Theor Appl Genet 110:1347–1353Google Scholar
  14. Devasirvatham V, Gaur PM, Mallikarjuna N, Raju TN, Trethowan RM, Tan DKY (2012) Effect of high temperature on the reproductive development of chickpea genotypes under controlled environments. Funct Plant Biol 39:1009–1018CrossRefGoogle Scholar
  15. FAOSTAT (2016) http://faostat3.fao.org/download/Q/QC/E. Accessed 11 Sept 2016
  16. Flandez-Galvez H, Ades R, Ford R, Pang E, Taylor P (2003a) QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (Cicer arietinum L.). Theor Appl Genet 107:1257–1265CrossRefPubMedGoogle Scholar
  17. 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 106:1447–1456CrossRefPubMedGoogle Scholar
  18. Gaur PM, Krishnamurthy L, Kashiwagi J (2008) Improving drought-avoidance root traits in chickpea (Cicer arietinum L.)—current status of research at ICRISAT. Plant Prod Sci 11:3–11CrossRefGoogle Scholar
  19. Gaur PM, Samineni S, Krishnamurthy L, Kumar S, Ghanem ME, Beebe S, Rao I, Chaturvedi SK, Basu PS, Nayyar H, Jayalakshmi V, Babbar A, Varshney RK (2015) High temperature tolerance in grain legumes. Legume Perspect 7:23–24Google Scholar
  20. Gaur PM, Samineni S, Tripathi S, Varshney RK, Gowda CLL (2016) Allelic relationships of flowering time genes in chickpea. Euphytica 203:295–308CrossRefGoogle Scholar
  21. Glaszmann JC, Kilian G, Upadhyaya HD, Varshney RK (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13:167–173CrossRefPubMedGoogle Scholar
  22. Gowda SJM, Radhika P, Mhase LB, Jamadagni BM, Gupta VS, Kadoo NY (2011) Mapping of QTLs governing agronomic and yield traits in chickpea. J Appl Genet 52:9–21CrossRefPubMedGoogle Scholar
  23. Halila I, Cobos MJ, Rubio J, Millán T, Kharrat M, Marrakchi M, Gil J (2009) Tagging and mapping a second resistance gene for Fusarium wilt race 0 in chickpea. Eur J Plant Pathol 124:87–92CrossRefGoogle Scholar
  24. Haware MP, Nene YL (1982) Races of Fusarium oxysporum f. sp. ciceris. Plant Dis 66:809–810CrossRefGoogle Scholar
  25. Ishii T, Yonezawa K (2007) Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: II. Strategies for selecting the objective homozygous plant. Crop Sci 47:1878–1886CrossRefGoogle Scholar
  26. Kanouni H, Taleei A, Peyghambari SA, Okhovat SM, Baum M, Abang M (2009) QTL analysis for ascochyta blight resistance in chickpea (Cicer arietinum L.) using microsatellite markers. J Agric Res 25:109–127Google Scholar
  27. Karim MA, Fracheboud Y, Stamp P (2000) Effect of high temperature on seedling growth and photosynthesis of tropical maize genotypes. J Agron Crop Sci 184:217–223CrossRefGoogle Scholar
  28. Kashiwagi J, Krishnamurthy L, Upadhyaya HD, Krishna H, Chandra S, Vadez V, Serraj R (2005) Genetic variability of drought-avoidance root traits in the mini-core germplasm collection of chickpea (Cicer arietinum L.). Euphytica 146:213–222CrossRefGoogle Scholar
  29. Krishnamurthy L, Gaur PM, Basu PS, Chaturvedi SK, Tripathi S, Vadez V, Rathore A, Varshney RK, Gowda CLL (2011) Large genetic variation for heat tolerance in the reference collection of chickpea (Cicer arietinum L.) germplasm. Plant Genet Resour 9:59–69CrossRefGoogle Scholar
  30. Kumar S, Kaushal N, Nayyar H, Gaur PM (2012) Abscisic acid induces heat tolerance in chickpea (Cicer arietinum L.) seedlings by facilitated accumulation of osmo protectants. Acta Physiol Plant 34:1651Google Scholar
  31. Lichtenzveig J, Bonfil DJ, Zhang HB, Shtienberg D, Abbo S (2006) Mapping quantitative trait loci in chickpea associated with time to flowering and resistance to Didymella rabiei the causal agent of Ascochyta blight. Theor Appl Genet 113:1357–1369CrossRefPubMedGoogle Scholar
  32. Madrid E, Chen W, Rajesh PN, Castro P, Millan T, Gil J (2013) Allele-specific amplification for the detection of Ascochyta blight resistance in chickpea. Euphytica 189:183–190CrossRefGoogle Scholar
  33. Mallikarjuna BP, Samineni S, Thudi M, Sajja SB, Khan AW, Patil A, Viswanatha KP, Varshney RK, Gaur PM (2017) Molecular mapping of flowering time major genes and QTLs in Chickpea (Cicer arietinum L.). Front Plan Sci 8Google Scholar
  34. Millán T, Clarke HJ, Siddique KHM, Buhariwalla HK, Gaur PM, Kumar J, Gill J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147:81–103CrossRefGoogle Scholar
  35. Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14:214–219CrossRefPubMedGoogle Scholar
  36. Nene YL, Haware MP, Reddy NMV, Philps JP, Castro EL, Kotasthane SR, Gupta O, Singh G, Shukia P, Sah RP (1989) Identification of broad based and stable resistance to wilt and root-rots in chickpea. Ind Phytopathol 42:499–505Google Scholar
  37. Pande S, Kishore GK, Upadhyaya HD, Rao JN (2006) Identification of sources of multiple disease resistance in mini-core collection of chickpea. Plant Dis 90:1214–1218CrossRefGoogle Scholar
  38. Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA 108:6893–6898CrossRefPubMedPubMedCentralGoogle Scholar
  39. Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KHM, 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 15:124CrossRefPubMedPubMedCentralGoogle Scholar
  40. Rajesh P, Tullu A, Gil J, Gupta V, Ranjekar P, Muehlbauer F (2002) Identification of an STMS marker for the double-podding gene in chickpea. Theor Appl Genet 105:604–607CrossRefPubMedGoogle Scholar
  41. Reddy MV, Singh KB (1984) Evaluation of a world collectionof chickpea germplasm accessions for resistance to ascochytablight. Plant Dis 68:900–901CrossRefGoogle Scholar
  42. Reynolds MP, Hays D, Chapman S (2010) Breeding for adaptation to heat and drought stress. In: Change Climate, Production Crop (eds) MP Reynolds. CABI, Oxfordshire, pp 71–91Google Scholar
  43. Samineni S, Kamatam S, Thudi S, Varshney RK, Gaur PM (2016) Vernalization response in chickpea is controlled by a major QTL. Euphytica 207:453–461CrossRefGoogle Scholar
  44. 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
  45. 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 Crops Res 88:115–127CrossRefGoogle Scholar
  46. Sharma KD, Chen W, Muehlbauer FJ (2005) Genetics of chickpea resistance to five races of usarium wilt and a concise set of race differentials for Fusarium oxysporum f. sp. ciceris. Plant Dis 89:385–390CrossRefGoogle Scholar
  47. Sharma KD, Muehlbauer FJ (2007) Fusarium wilt of chickpea: physiological specialization, genetics of resistance and resistance gene tagging. Euphytica 157:1–14CrossRefGoogle Scholar
  48. Sharma KD, Winter P, Kahl G, Muehlbauer FJ (2004) Molecular mapping of Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea. Theor Appl Genet 108:1243–1248CrossRefPubMedGoogle Scholar
  49. Singh G, Kapoor S (1985) Screening for combined resistance to botrytis gray mold and Ascochyta blight of chickpea. Int Chickpea Newsl 12:21–22Google Scholar
  50. Singh KB, Reddy MV (1990) Patterns of resistance and susceptibility to races of A. rabiei among germplasm accessions and breeding lines of chickpea. Plant Dis 74:127–129CrossRefGoogle Scholar
  51. Soltani A, Khooie FR, Ghassemi-Golezani K, Moghaddam M (2000) Thresholds for chickpea leaf expansion and transpiration response to soil water deficit. Field Crops Res 68:205–210CrossRefGoogle Scholar
  52. Stephens A, Lombardi M, Cogan NOI, Forster JW, Hobson K, Materne M, Kaur S (2014) Genetic marker discovery, interspecific linkage map construction and quantitative trait locus analysis of ascochyta blight resistance in chickpea (Cicer arietinum L.). Mol Breeding 33:297–313CrossRefGoogle Scholar
  53. Tekeoglu M, Rajesh PN, Muehlbauer FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 105:847–854CrossRefPubMedGoogle Scholar
  54. Tekeoglu M, Tullu A, Kaiser WJ, Muehlbauer FJ (2000) Inheritance and linkage of two genes that confer resistance to Fusarium wilt in chickpea. Crop Sci 40:1247–1251CrossRefGoogle Scholar
  55. Thudi M, Khan AW, Vinay Kumar, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK (2016) Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biol 16:10Google Scholar
  56. Udupa SM, Baum M (2003) Genetic dissection of patho type specific resistance to Ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theor Appl Genet 106:1196–1202CrossRefPubMedGoogle Scholar
  57. Upadhyaya HD, Dronavalli N, Gowda CLL, Singh S (2011) Identification and evaluation of chickpea germplasm for tolerance to heat stress. Crop Sci 51:2079–2094CrossRefGoogle Scholar
  58. Varshney RK, Glaszmann J-C, Leung H, Ribaut JM (2010) More genomic resources for less-studied crops. Trends Biotechnol 28:452–460CrossRefPubMedGoogle Scholar
  59. Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS, Viswanatha KP (2014a) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127:445–462Google Scholar
  60. Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK, Samineni S, Swapna N, Sharma M, Singh S, Kaur L, Pande S (2014b) 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 7:1Google Scholar
  61. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe A, Cannon S, Baek J, Rosen BD, Tar’an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Garcia NC, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel1 J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246Google Scholar
  62. Vaughan DA, Balász E, Heslop-Harrison JS (2007) From crop domestication to super-domestication. Ann Bot 100:893–901CrossRefPubMedPubMedCentralGoogle Scholar
  63. Wang J, Gan YT, Clarke F, McDonald CL (2006) Response of chickpea yield to high temperature stress during reproductive development. Crop Sci 46:2171–2178CrossRefGoogle Scholar
  64. Winter P, Benko-Iseppon AM, Hu¨ttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant VJ, Rajesh PN, Kahl G, Muehlbauer FJ (2000) A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum 9 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

  • Srinivasan Samineni
    • 1
  • Mahendar Thudi
    • 1
  • Sobhan B. Sajja
    • 1
  • Rajeev K. Varshney
    • 1
  • Pooran M. Gaur
    • 1
    Email author
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia

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