Hostname: page-component-cd9895bd7-8ctnn Total loading time: 0 Render date: 2024-12-23T10:50:27.914Z Has data issue: false hasContentIssue false
  • English
  • Français

Genomic tools and germplasm diversity for chickpea improvement

Published online by Cambridge University Press:  14 January 2011

Hari D. Upadhyaya ,
Mahendar Thudi ,
Naresh Dronavalli ,
Neha Gujaria ,
Sube Singh ,
Shivali Sharma  and
Rajeev K. Varshney
Hari D. Upadhyaya
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Mahendar Thudi
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Naresh Dronavalli
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Neha Gujaria
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Sube Singh
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Shivali Sharma
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India
Rajeev K. Varshney*
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Hyderabad, AP, India Comparative and Applied Genomics (CAG), Generation Challenge Programme (GCP), CIMMYT, Int APDO Postal 6-641, 06600Mexico, DF, Mexico
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), diversity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Advent of the next generation sequencing technologies coupled with advances in bioinformatics offers the possibility of undertaking large-scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.

Keywords

Cicergenomic resourcesmini corereference setgermplasm repositoriesallelic diversitytrait-specific germplasm
Type
Research Article
Information
Plant Genetic Resources , Volume 9 , Issue 1 , April 2011 , pp. 45 - 58
Copyright
Copyright © NIAB 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abbo, S, Berger, J and Turner, NC (2003) Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Functional Plant Biology 30: 1081–1087.CrossRefGoogle ScholarPubMed
Abbo, S, Molina, C, Jungmann, R, Grusak, MA, Berkovitch, Z, Reifen, R, Kahl, G, Winter, P and Reifen, R (2005) Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 111: 185–195.CrossRefGoogle ScholarPubMed
Ahmad, F (1999) Random amplified polymorphic DNA (RAPD) analysis reveals genetic relationships among the annual Cicer species. Theoretical and Applied Genetics 98: 657–663.Google Scholar
Ahmad, F, Khan, AI, Awan, FS, Sadia, B, Sadaqat, HA and Bahadur, S (2010) Genetic diversity of chickpea (Cicer arietinum L.) germplasm in Pakistan as revealed by RAPD analysis. Genetics and Molecular Research 9: 1414–1420.CrossRefGoogle ScholarPubMed
Arumuganathan, K and Earle, ED (1991) Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9: 208–218.CrossRefGoogle Scholar
Berger, J, Abbo, S and Turner, NC (2003) Ecogeography of annual Cicer species: the poor state of the world collection. Crop Science 43: 1076–1090.CrossRefGoogle Scholar
Bhagyawant, SS and Srivastava, N (2008) Genetic fingerprinting of chickpea (Cicer arietinum L.) germplasm using ISSR markers and their relationships. African Journal of Biotechnology 7: 4428–4431.Google Scholar
Boominathan, P, Shukla, R, Kumar, A, Manna, D, Negi, D, Verma, PK and Chattopadhyay, D (2004) Long term transcript accumulation during the development of dehydration adaptation in Cicer arietinum. Plant Physiology 135: 1608–1620.CrossRefGoogle ScholarPubMed
Brown, AHD (1989) A case for core collections. In: Brown, AHD, Frankel, OH, Marshall, DR and Williams, JT (eds) The Use of Plant Genetic Resources. Cambridge: Cambridge University Press, pp. 136–156.Google Scholar
Buhariwalla, HK, Jayashree, B, Eshwar, K and Crouch, JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biology 5: 16.Google Scholar
Cho, S, Kumar, J, Schultz, JL, Anupama, K, Tefera, F and Muehlbauer, FJ (2002) Mapping genes for double podding and other morphological traits in chickpea. Euphytica 128: 285–292.CrossRefGoogle Scholar
Choudhary, S, Sethy, NK, Shokeen, B and Bhatia, S (2006) Development of sequence-tagged microsatellites site markers for chickpea (Cicer arietinum L.). Molecular Ecology Notes 6: 93–95.CrossRefGoogle Scholar
Choudhary, S, Sethy, NK, Shokeen, B and Bhatia, S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics 118: 591–608.Google Scholar
Choumane, W, Winter, P, Weigand, F and Kahl, G (2000) Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genus Cicer. Theoretical and Applied Genetics 101: 269–278.Google Scholar
Cobos, M, Rubio, J, Strange, RN, Moreno, MT, Gil, J and Millan, T (2006) A new QTL for Ascochyta blight resistance in an RIL population derived from an interspecific cross in chickpea. Euphytica 149: 105–111.CrossRefGoogle Scholar
Cobos, MJ, Fernandez, MJ, Rubio, J, Kharrat, M, Moreno, MT, Gil, J and Millan, T (2005) A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli × Desi crosses: location of genes for resistance to fusarium wilt race 0. Theoretical and Applied Genetics 110: 1347–1353.CrossRefGoogle ScholarPubMed
Collard, BCY, Pang, ECK, Ades, PK and Taylor, PWJ (2003) Preliminary investigation of QTLs associated with seedling resistance to ascochyta blight from Cicer echinospermum, a wild relative of chickpea. Theoretical and Applied Genetics 107: 719–729.Google Scholar
Coram, T and Pang, E (2005) Isolation and analysis of candidate ascochyta blight defense genes in chickpea, Part I. Generation and analysis of an expressed sequence tag (EST) library. Physiological and Molecular Plant Pathology 66: 192–200.CrossRefGoogle Scholar
Dwivedi, SL, Blair, MW, Upadhyaya, HD, Serraj, R, Balaji, J, Buhariwalla, HK, Ortiz, R and Crouch, JH (2005) Using genomics to exploit grain legume biodiversity in crop improvement. Plant Breeding Reviews 26: 171–357.Google Scholar
ESHA food data base(2010) The World's Healthiest Foods. www.whfoods.org. Salem, Oregon: ESHA Foundation.Google Scholar
FAO(2009) http://faostat.fao.org/site/567/desktopdefault.aspx?pageid = 567.Google Scholar
Flandez-Galvez, H, Ford, R, Pang, ECK and Taylor, PWJ (2003a) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theoretical and Applied Genetics 106: 1447–1456.CrossRefGoogle ScholarPubMed
Flandez-Galvez, H, Ades, PK, Ford, R, Pang, ECK and Taylor, PWJ (2003b) QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 107: 1257–1265.Google Scholar
Frankel, OH (1984) Genetic perspective of germplasm conservation. In: Arber, W, Limensee, K, Peacock, WJ and Stralinger, P (eds) Genetic Manipulations: Impact on Man and Society. Cambridge: Cambridge University Press, pp. 161–470.Google Scholar
Gaur, PM and Slinkard, AE (1990a) Genetic control and linkage relations of additional isozymes markers in chickpea. Theoretical and Applied Genetics 80: 648–653.CrossRefGoogle ScholarPubMed
Gaur, PM and Slinkard, AE (1990b) Inheritance and linkage of isozyme coding genes in chickpea. Journal of Heredity 81: 455–461.Google Scholar
Glaszmann, JC, Kilian, B, Upadhyaya, HD and Varshney, RK (2010) Accessing genetic diversity for crop improvement. Current Opinion in Plant Biology 13: 1–7.Google Scholar
Gowda, CLL, Upadhyaya, HD, Dronavalli, N and Sube, Singh (2010) Identification of large seeded high yielding stable kabuli chickpea (Cicer arietinum L.) germplasm lines for use in crop improvement. Crop Science 51: 198–209.CrossRefGoogle Scholar
Gupta, PK and Varshney, RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.CrossRefGoogle Scholar
Halward, TM and Wynne, JC (1991) Generation mean analysis for productivity in two diverse peanut crosses. Theoretical and Applied Genetics 82: 784–792.Google Scholar
Heslop-Harrison, JS (2002) Exploiting novel germplasm. Australian Journal of Agricultural Research 53: 873–879.Google Scholar
Hüttel, B, Winter, P, Weising, K, Choumane, W, Weigand, F and Kahl, G (1999) Sequence-tagged microsatellite markers for chickpea (Cicer arietinum L.). Genome 42: 210–217.CrossRefGoogle ScholarPubMed
Hyten, DL, Song, O, Fickus, EW, Quigley, CV, Lim, JS, Choi, IY, Hwang, EY, Pastor Corrales, M and Cregan, PB (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11: 475.Google Scholar
IBPGR, ICRISAT and ICARDA(1993) Descriptors for chickpea (Cicer arietinum L.). International Board for Plant Genetic Resources, Rome, Italy; International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India and International Center for Agriculture Research in the Dry Areas, Aleppo, Syria, p. 31.Google Scholar
Infantino, A, Porta-Puglia, A and Singh, KB (1996) Screening wild Cicer species for resistance to fusarium wilt. Plant Disease 80: 42–44.Google Scholar
Iruela, M, Rubio, J, Cubero, JI, Gil, J and Milan, T (2002) Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theoretical and Applied Genetics 104: 643–651.Google Scholar
Jannink, JL (2010) Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics 9: 166–177.Google Scholar
Javadi, F and Yamaguchi, H (2004) Interspecific relationships of the genus Cicer L. (Fabaceae) based on trnT-F sequences. Theoretical and Applied Genetics 109: 317–322.CrossRefGoogle ScholarPubMed
Kannenberg, LW and Falk, DE (1995) Models for activation of plant genetic resources for crop breeding programs. Canadian Journal of Plant Science 75: 45–53.CrossRefGoogle Scholar
Kashiwagi, J, Upadhyaya, HD and Krishnamurthy, L (2010) Significance and genetic diversity of SPAD chlorophyll meter reading (SCMR) in the chickpea (Cicer arietinum L.) germplasm in the semi-arid environments. Legumes Research 23: 99–105.Google Scholar
Kashiwagi, J, Krishnamurthy, L, Singh, S, Gaur, PM and Upadhyaya, HD (2006a) Variation of SPAD chlorophyll meter readings (SCMR) in the mini-core germplasm collection of chickpea. International Chickpea and Pigeonpea Newsletter 13: 16–18.Google Scholar
Kashiwagi, J, Krishnamurthy, L, Upadhyaya, HD, Krishna, H, Chandra, S, Vincent, Vadez and Serraj, R (2005) Genetic variability of drought avoidance root traits in the mini-core germplasm collection of chickpea (Cicer arietinum L.). Euphytica 146: 213–222.CrossRefGoogle Scholar
Kashiwagi, J, Krishnamurthy, L, Singh, S, Gaur, PM, Upadhyaya, HD, Panwar, JDS, Basu, PS, Ito, O and Tobita, S (2006b) Relationships between transpiration efficiency and carbon isotope discrimination in chickpea (C. arietinum L.). International Chickpea and Pigeonpea Newsletter 13: 19–21.Google Scholar
Kazan, K, Muehlbauer, FJ, Weeden, NE and Ladizinsky, G (1993) Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theoretical Applied Genetics 86: 417–426.Google Scholar
Khan, R, Khan, H, Farhatullah, and Harada, K (2010) Evaluation of microsatellite markers to discriminate induced mutation lines, hybrid lines and cultigens in chickpea (Cicer arietinum L.). Australian Journal of Crop Science 4: 301–308.Google Scholar
Knauft, DA and Gorbet, DW (1989) Genetic diversity among peanut cultivars. Crop Science 29: 1417–1422.CrossRefGoogle Scholar
Kottapalli, P, Gaur, PM, Katiyar, SK, Crouch, JH, Buhariwalla, HK, Pande, S and Gali, KK (2009) Mapping and validation of QTLs for resistance to an Indian isolate of ascochyta blight pathogen in chickpea. Euphytica 165: 79–88.Google Scholar
Krishnamurthy, L, Kashiwaji, J, Upadhyaya, HD and Serraj, R (2003) Genetic diversity of drought avoidance root traits in the mini core germplasm collection of chickpea. International Chickpea and Pigeonpea Newsletter 10: 21–24.Google Scholar
Kumar, S, Gupta, S and Singh, BB (2004) How wide is the genetic base of pulse crops? In: Ali, M, Singh, BB, Kumar, S and Dhar, V (eds) Pulses in New Perspective. Proceedings of the National Symposium on Crop Diversification and Natural Resources Management. Kanpur, India: ISPRD and IIPR, pp. 211–221.Google Scholar
Ladizinsky, G and Adler, A (1976) The origin of chickpea Cicer arietinum L. Euphytica 25: 211–217.Google Scholar
Lev-Yadun, S, Gopher, A and Abbo, S (2000) The cradle of agriculture. Science 288: 1602–1603.Google Scholar
Lichtenzveig, J, Scheuring, C, Dodge, J, Abbo, S and 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. Theoretical and Applied Genetics 110: 492–510.CrossRefGoogle ScholarPubMed
McIntosh, M and Miller, C (2001) A diet containing food rich in soluble and insoluble fiber improves glycemic control and reduces hyperlipidemia among patients with type 2 diabetes mellitus. Nutrition Reviews 59: 52–55.CrossRefGoogle Scholar
Millan, T, Winter, P, Jüngling, R, Gil, J, Rubio, J, Cho, S, Cobos, MJ, Iruela, M, Rajesh, PN, Tekeoglu, M, Kahl, G and Muehlbauer, FJ (2010) A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations. Euphytica 175: 175–189.CrossRefGoogle Scholar
Nasu, S, Suzuki, J, Ohta, R, Hasegawa, K, Yui, R, Kitazawa, N, Monna, L and Minobe, L (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP Markers. DNA Research 9: 163–171.Google Scholar
Nayak, SN, Zhu, H, Varghese, N, Choi, HK, Datta, S, Horres, R, Jüngling, R, Singh, J, Kavi Kishor, PB, Kahl, G, Winter, P, Cook, DR and Varshney, RK (2010) Integration of novel SSR and gene-based marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics 120: 1415–1441.CrossRefGoogle ScholarPubMed
Nguyen, TT, Taylor, PWJ, Redden, RJ and Ford, R (2004) Genetic diversity estimates in Cicer using AFLP analysis. Plant Breeding 123: 173–179.CrossRefGoogle Scholar
Pande, S, Kishore, GK, Upadhyaya, HD and Rao, JN (2006) Identification of multiple diseases resistance in mini-core collection of chickpea. Plant Disease 90: 1214–1218.Google Scholar
Pfaff, T and Kahl, G (2003) Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Molecular Genetics and Genomics 269: 243–251.Google Scholar
Pittaway, JK, Ahuja, KD, Cehun, M, Chronopoulos, A, Robertson, IK, Nestel, PJ and Ball, MJ (2006) Dietary supplementation with chickpeas for at least 5 weeks results in small but significant reductions in serum total and low-density lipoprotein cholesterols in adult women and men. Annals of Nutrition and Metabolism 50: 512–518.Google Scholar
Pusadeea, T, Jamjoda, S, Chiangb, Y-C, Rerkasema, B and Schaalc, BA (2008) Genetic structure and isolation by distance in a landrace of Thai rice. Proceedings of National Academy of Sciences 106: 13880–13885.Google Scholar
Qadir, SA, Datta, S, Singh, NP and Shiv, Kumar (2007) Development of highly polymorphic SSR markers for chickpea (Cicer arietinum L.) and their use in parental polymorphism. Indian Journal of Genetics 67: 329–333.Google Scholar
Queiroz, KS, de Oliveira, AC and Helbig, E (2002) Soaking the common bean in a domestic preparation reduced the contents of raffinose-type oligosaccharides but did not interfere with nutritive value. Journal of Nutritional Science and Vitaminology 48: 283–289.CrossRefGoogle Scholar
Radhika, P, Gowda, SJM, Kadoo, NY, Mhase, LB, Jamadagni, BM, Sainani, MN, Chandra, S and Gupta, VS (2007) Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theoretical and Applied Genetics 115: 209–216.Google Scholar
Rajesh, PN and Muehlbauer, FJ (2008) Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.). Euphytica 162: 291–300.Google Scholar
Rajesh, PN, Sant, VJ, Gupta, VS, Muehlbaur, FJ and Ranjekar, PK (2003) Genetic relationships among annual and perennial wild species of Cicer using inter simple sequence repeat (ISSR) polymorphism. Euphytica 129: 15–23.CrossRefGoogle Scholar
Rajesh, PN, Tullu, A, Gil, J, Gupta, VS, Ranjekar, PK and Muehlbauer, FJ (2002) Identification of an STMS marker for the double-podding gene in chickpea. Theoretical and Applied Genetics 105: 604–607.CrossRefGoogle ScholarPubMed
Rao, L, Usha Rani, P, Deshmukh, P, Kumar, P and Panguluri, S (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genetic Resources and Crop Evolution 54: 1235–1244.CrossRefGoogle Scholar
Romo, S, Labrador, E and Dopico, B (2004) Water stress-regulated gene expression in Cicer arietinum seedlings and plants. Journal of Plant Physiology and Biochemistry 39: 1017–1026.CrossRefGoogle Scholar
Santra, DK, Tekeoglu, M, Ratnaparkhe, ML, Kaiser, WJ and Muehlbauer, FJ (2000) Identification and mapping of QTLs conferring resistance to ascochyta blight in chickpea. Crop Science 40: 1606–1612.Google Scholar
Serraj, R, Krishanamurthy, L and Upadhyaya, HD (2004) Screening chickpea mini core germplasm for tolerance to soil salinity. International Chickpea and Pigeonpea Newsletter 11: 29–32.Google Scholar
Serret, MD, Udupa, SM and Weigand, F (2006) Assessment of genetic diversity of cultivated chickpea using microsatellite-derived RFLP markers: implications for origin. Plant Breeding 116: 573–578.Google Scholar
Sethy, NK, Shokeen, B and Bhatia, S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Molecular Ecology Notes 3: 428–430.Google Scholar
Sethy, NK, Choudhary, S, Shokeen, B and Bhatia, S (2006a) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theoretical and Applied Genetics 112: 347–357.Google Scholar
Sethy, NK, Shokeen, B, Edwards, KJ and Bhatia, S (2006b) Development of microsatellite markers and analysis of intra-specific genetic variability in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 112: 1416–1428.Google Scholar
Shah, TM, Hussan, MU, Haq, MA, Atta, BM, Alam, SS and Ali, H (2005) Evaluation of Cicer species for resistance to ascochyta blight. Pakistan Journal of Botany 37: 431–438.Google Scholar
Shan, F, Clarke, HC, Plummer, JA, Yan, G and Siddique, KHM (2005) Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms. Theoretical and Applied Genetics 110: 381–391.Google Scholar
Sharma, KD, Winter, P, Kahl, G and Muehlbauer, FJ (2004) Molecular mapping of Fusarium oxysporum f. sp. ciceris race 3 resistance gene in chickpea. Theoretical and Applied Genetics 108: 1243–1248.Google Scholar
Simon, CJ and Muehlbauer, FJ (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. Journal of Heredity 88: 115–119.CrossRefGoogle Scholar
Singh, G, Singh, K and Kapoor, S (1982) Screening for sources of resistance to Ascochyta blight of chickpea. International Chickpea Newsletter 6: 15–17.Google Scholar
Singh, R, Singhal, V and Randhawa, GJ (2008a) Molecular analysis of chickpea (Cicer arietinum L.) cultivars using AFLP and STMS markers. Journal of Plant Biochemistry and Biotechnology 17: 167–171.Google Scholar
Singh, R, Sharma, P, Varshney, RK, Sharma, SK and Singh, NK (2008b) Chickpea improvement: role of wild species and genetic markers. Biotechnology and Genetic Engineering Reviews 25: 267–314.CrossRefGoogle ScholarPubMed
Sudupak, MA (2004) Inter- and intra- species inter simple sequence repeat (ISSR) variation in the genus Cicer. Euphytica 135: 229–238.Google Scholar
Sudupak, MA, Akkaya, MS and Kence, A (2002) Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers. Theoretical and Applied Genetics 105: 1220–1228.Google Scholar
Sudupak, MA, Akkaya, MS and Kence, A (2004) Genetic relationships among perennial and annual Cicer species growing in Turkey assessed by AFLP fingerprinting. Theoretical and Applied Genetics 108: 937–944.CrossRefGoogle ScholarPubMed
Talebi, R, Naji, AM and Fayaz, F (2008a) Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism. Plant Soil and Environment 54: 447–452.CrossRefGoogle Scholar
Talebi, R, Jelodar, NAB, Mardi, M, Fayaz, F, Furman, BJ and Bagheri, AM (2009) Phylogenetic diversity and relationship among annual Cicer species using random amplified Polymorphic DNA markers. General and Applied Plant Physiology 35: 3–12.Google Scholar
Talebi, R, Fayaz, F, Mardi, M, Pirsyedi, SM and Naji, AM (2008b) Genetic relationships among chickpea (Cicer arietinum) elite lines on RAPD and Agronomic Markers. International Journal of Agriculture and Biology 10: 301–305.Google Scholar
Tayyar, RI and Waines, JG (1996) Genetic relationships among annual species of Cicer (Fabaceae) using isozymes variation. Theoretical and Applied Genetics 92: 245–254.CrossRefGoogle ScholarPubMed
Tekeoglu, M, Rajesh, PN and Muehlbauer, FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theoretical and Applied Genetics 105: 847–854.Google Scholar
Troyer, AF (1990) A retrospective view of corn genetic resources. Journal of Heredity 81: 17–24.Google Scholar
Udupa, SM and Baum, M (2003) Genetic dissection of pathotype specific resistance to ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theoretical and Applied Genetics 106: 1196–1202.Google Scholar
Udupa, SM, Sharma, A, Sharma, RP and Pai, RA (1993) Narrow genetic variability in Cicer arietinum as revealed by RFLP analysis. Journal of Plant Biochemistry and Biotechnology 2: 83–86.Google Scholar
Udupa, SM, Robertson, LD, Weigand, F, Baum, M and Hahl, G (1999) Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Molecular and General Genetics 261: 354–363.Google Scholar
Upadhyaya, HD (2003) Geographical patterns of variation for morphological and agronomic characteristics in the chickpea germplasm collection. Euphytica 132: 343–352.Google Scholar
Upadhyaya, HD (2008) Crop germplasm and wild relatives: a source of novel variation for crop improvement. Korean Journal of Crop Science 53: 12–15.Google Scholar
Upadhyaya, HD and Oritz, R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theoretical and Applied Genetics 102: 1292–1298.Google Scholar
Upadhyaya, HD, Bramel, PJ and Sube, Singh (2001) Development of a chickpea core collection using geographic distribution and quantitative traits. Crop Sciences 41: 206–210.Google Scholar
Upadhyaya, HD, Gowda, CLL, Buhariwalla, HK and Crouch, JH (2006a) Efficient use of crop germplasm resources: identifying useful germplasm for crop improvement through core and mini core collections and molecular marker approaches. Plant Genetics Resources Newsletters 4: 25–35.CrossRefGoogle Scholar
Upadhyaya, HD, Dwivedi, SL, Gowda, CLL and Sube, Singh (2007a) Identification of diverse germplasm lines for agronomic traits in a chickpea (Cicer arietinum L.) core collection for use in crop improvement. Field Crops Research 100: 320–326.Google Scholar
Upadhyaya, HD, Salimath, PM, Gowda, CLL and Sube, Singh (2007b) New early-maturing germplasm lines for utilization in chickpea improvement. Euphytica 157: 195–208.Google Scholar
Upadhyaya, HD, Pundir, RPS, Dwivedi, SL and Gowda, CLL (2009) Mini core collections for efficient utilization of plant genetic resources in crop improvement programs. Information Bulletin no. 78. Patancheru 502 324, Andhra Pradesh, India: International Crops Research Institute for the Semi-Arid Tropics, p. 52. ISBN 978-92-9066-519-9.Google Scholar
Upadhyaya, HD, Yadav, D, Dronavalli, N, Gowda, CLL and Singh, S (2010) Mini core germplasm collections for infusing genetic diversity in plant breeding programs. Electronic Journal of Plant Breeding 1: 1294–1309.Google Scholar
Upadhyaya, HD, Dwivedi, SL, Baum, M, Varshney, RK, Udupa, SM, Gowda, CLL, Hoisington, DA and Sube, Singh (2008) Genetic structure, diversity and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biology 8: 106.Google Scholar
Upadhyaya, HD, Furman, BJ, Dwivedi, SL, Udupa, SM, Gowda, CLL, Baum, M, Crouch, JH, Buhariwalla, HK and Sube, Singh (2006b) Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea. Plant Genetic Resources Newsletter 4: 13–19.Google Scholar
Vadez, V, Krishnamurthy, L, Serraj, R, Gaur, PM, Upadhyaya, HD, Hoisington, DA, Varshney, RK, Turner, NC and Siddique, KHM (2007) Large variation in salinity tolerance in chickpea is explained by differences in sensitivity at reproductive stage. Field Crops Research 104: 123–129.Google Scholar
van der Maesen, LJG (1972) Cicer L., A Monograph of the Genus with Special Reference to the Chickpea (Cicer arietinum L.), its Ecology and Distribution. Wageningen, The Netherlands: Mendelingen landbouwhogeschool, pp. 1–341.Google Scholar
Varshney, RK, Graner, A and Sorrells, ME (2005) Genomics-assisted breeding for crop improvement. Trends in Plant Science 10: 621–630.Google Scholar
Varshney, RK, Glaszmann, JC, Leung, H and Ribaut, JM (2010a) More genomic resources for less-studied crops. Trends in Biotechnology 28: 452–460.Google Scholar
Varshney, RK, Thudi, M, May, GD and Jackson, SA (2010b) Legume genomics and breeding. Plant Breeding Reviews 33: 257–304.Google Scholar
Varshney, RK, Nayak, SN, May, GD and Jackson, SA (2009c) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27: 522–530.Google Scholar
Varshney, RK, Close, TJ, Singh, NK, Hoisington, DA and Cook, DR (2009a) Orphan legume crops enter the genomics era! Current Opinions in Plant Biology 12: 202–210.Google Scholar
Varshney, RK, Hiremath, PJ, Lekha, PT, Kashiwagi, J, Jayasree, B, Deokar, AA, Vadez, V, Xiao, Y, Srinivasan, R, Gaur, PM, Siddique, KHM, Town, CD and Hoisington, DA (2009b) A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10: 523.Google Scholar
Varshney, RK, Nayak, S, Jayashree, B, Eshwar, K, Upadhyaya, HD and Hoisington, DA (2007) Development of cost-effecive SNP assays for chickpea genome analysis and breeding Journal of SAT Agriculture 3: 1. http://www.icrisat.org/Journal/chickpea_pigeonpea3.htm.Google Scholar
Vavilov, NI (1926) Studies on the origin of cultivated plants. Nature 118: 392–393.Google Scholar
Vavilov, NI (1951) The origin, variation immunity and breeding of cultivated plants. Chronica Botanica. 13-1/6:26-38, 75-78, 151 (1949-50). New York.Google Scholar
WIEWS-FAO(2009) World Information and Early Warning System on Plant Genetic Resources for Food and Agriculture. http://apps3.fao.org/wiews/wiews.jsp.Google Scholar
Williams, PC and Singh, U (1987) Nutritional quality and the evaluation of quality in breeding programmes. In: Saxena, MC and Singh, KB (eds) The Chickpea. Wallingford: CAB International, pp. 329–356.Google Scholar
Winter, P, Pfaff, T, Udupa, SM, Hüttel, B, Sharma, PC, Sahi, S, Arreguin-Espinoza, R, Weigand, F, Muehlbauer, FJ and Kahl, G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Molecular Genomics Genetics 262: 90–101.CrossRefGoogle ScholarPubMed
Winter, P, Benko-Iseppon, AM, Hüttel, B, Ratnaparkhe, M, Tullu, A, Sonnante, G, Pfaff, T, Tekeoglu, M, Santra, D, Sant, VJ, Rajesh, PN, Kahl, G and Muehlbauer, FJ (2000) A linkage map of 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. Theoretical and Applied Genetics 101: 1155–1163.Google Scholar
Wu, X, Ren, C, Joshi, T, Vuong, T, Xu, D and Nguyen, HT (2010) SNP discovery by high-throughput sequencing in soybean. BMC Genomics 11: 469.Google Scholar
Yadav, SS, Redden, R, Chen, W and Sharma, B (2007) Chickpea Breeding and Management. Oxfordshire, OX: CABI Publication, p. 638.Google Scholar
Yan, J, Shah, T, Warburton, ML, Buckler, ES, McMullen, MD and Crouch, JH (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4: e8451.Google Scholar
Zohary, D and Hopf, M (2000) Domestication of plants in the old world: The origin and spread of cultivated plants in west Asia, Europe and Nile valley, 3rd edn. Oxford, OX: Oxford University Press.Google Scholar
Supplementary material: PDF

Varshney Supplementary Material

Varshney Supplementary Tables

Download Varshney Supplementary Material(PDF)
PDF 41.8 KB