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Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations

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Abstract

A composite intraspecific linkage map of chickpea was developed by integrating individual maps developed from two F8:9 RIL populations with one common parent. Different molecular markers viz. RAPD, ISSR, RGA, SSR and ASAP were analyzed along with three yield related traits: double podding, seeds per pod and seed weight. A total of 273 markers and 186 RILs were used to generate the map with eight linkage groups at a LOD score of ≥3.0 and maximum recombination fraction of 0.4. The map spanned 739.6 cM with 230 markers at an average distance of 3.2 cM between markers. The predominantly used SSR markers facilitated identification of homologous linkage groups from the previously published interspecific linkage map of chickpea and confirmed conservation of the SSR markers across the two maps as well as the variation in terms of marker distance and order. The double podding gene was tagged by the markers NCPGR33 and UBC249z at 2.0 and 1.1 cM, respectively. Whereas, seeds per pod, was tagged by the markers TA2x and UBC465 at 0.1 and 1.8 cM, respectively. Eight QTLs were identified that influence seed weight. The joint map approach allowed mapping a large number of markers with a moderate coverage of the chickpea genome and few linkage gaps.

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References

  • Abbo S, Molina C, Jungmann R, Grusak M, Berkovitch Z, Reifen R, Kahl G, Winter P, Reifen R (2005) Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.). Theor Appl Genet 111:185–195

    Article  PubMed  CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Castiglioni P, Ajmone P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theor Appl Genet 99:425–431

    Article  CAS  Google Scholar 

  • Chen X, Line R, Leung H (1998) Genome scanning for resistance-gene analogs in rice, barley and wheat by high-resolution electrophoresis. Theor Appl Genet 97:345–355

    Article  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Cho S, Kumar J, Shultz J, Anupama K, Tefera F, Muehlbauer F (2002) Mapping genes for double podding and other morphological traits in chickpea. Euphytica 128:285–292

    Article  CAS  Google Scholar 

  • Choudhary S, Sethy N, Shokeen B, Bhatia S (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes 6:93–95

    Article  CAS  Google Scholar 

  • Cobos M, Fernandez M, Rubio J, Kharrat M, Moreno M, Gil T, 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. Theor Appl Genet 110:1347–1353

    Article  PubMed  CAS  Google Scholar 

  • Ellis T, Turner L, Hellens R, Lee D, Harker C, Enard C, Domoney C, Davies D (1992) Linkage maps in pea. Genetics 130:649–663

    PubMed  CAS  Google Scholar 

  • Eujayl I, Sledge M, Wang L, May G, Chekhovskiy K, Zwonitzer J, Mian M (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Gaur P, Slinkard A (1990) Inheritance and linkage of isozyme coding genes in chickpea. J Hered 81:455–461

    CAS  Google Scholar 

  • Hays A, Maroof S (2000) Targeted resistance gene mapping in soybean using modified AFLPs. Theor Appl Genet 100:1279–1283

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Kanazin V, Marek F, Shoemaker R (1996) Resistance gene analogs are conserved and clustered in soybean. Proc Natl Acad Sci USA 93:11746–11750

    Article  PubMed  CAS  Google Scholar 

  • Kazan K, Muehlbauer F, Weeden N, Ladizinsky G (1993) Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theor Appl Genet 86:417–426

    Article  CAS  Google Scholar 

  • Kleinhofs A, Kilian A, Saghai-Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp S, Liu B, Sorrells M, Heun M, Fanckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712

    Article  CAS  Google Scholar 

  • Kosambi D (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Kumar J, Srivastava R, Ganesh M (2000) Penetrance and expressivity of the gene for double podding in chickpea. J Hered 91:234–236

    Article  PubMed  CAS  Google Scholar 

  • Labdi M, Robertson L, Singh K, Charrier A (1996) Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphisms. Euphytica 88:181–188

    Article  CAS  Google Scholar 

  • Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang H (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 110:492–510

    Article  PubMed  CAS  Google Scholar 

  • Paran I, Goldman I, Tanksley S, Zamir D (1995) Recombinant inbred lines for genetic mapping in tomato. Theor Appl Genet 90:542–548

    Article  CAS  Google Scholar 

  • Rajesh P, Tullu A, Gil J, Gupta V, Ranjekar P, Muehlbauer F (2002a) Identification of an STMS marker for the double-podding gene in chickpea. Theor Appl Genet 105:604–607

    Article  PubMed  CAS  Google Scholar 

  • Rajesh P, Tekeoglu M, Gupta V, Ranjekar P, Muehlbauer F (2002b) Molecular mapping and characterization of an RGA locus RGAPtokin 1–2171 in chickpea. Euphytica 128:427–433

    Article  CAS  Google Scholar 

  • Ratnaparkhe M, Santra D, Tullu A, Muehlbauer F (1998) Inheritance of inter simple-sequence-repeat polymorphism and linkage with fusarium wilt resistance gene in chickpea. Theor Appl Genet 96:348–353

    Article  CAS  Google Scholar 

  • Reiter R, Williams J, Kenneth A, Feldmann T, Rafalskit J, Tingryt S, Scolnik P (1992) Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc Natl Acad Sci USA 89:1477–1481

    Article  PubMed  CAS  Google Scholar 

  • Roman B, Satovic Z, Avila C, Rubiales D, Moreno M, Torres A (2003) Locating genes associated with Ascochyta fabae resistance in Vicia faba L. Aust J Agric Res 54:85–90

    Article  CAS  Google Scholar 

  • Roman B, Satovic Z, Pozarkova D, Macas J, Cubero J, Torres A (2004) Development of a composite map in Vicia faba, breeding applications and future prospects. Theor Appl Genet 108:1079–1088

    Article  PubMed  CAS  Google Scholar 

  • Rubio J, Flores F, Moreno M, Cubero J, Gil J (2004) Effects of the erect/bushy habit, single/double pod and late/early flowering genes on yield and seed size and their stability in chickpea. Field Crops Res 90:255–262

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Sethy N, Choudhary S, Shokeen B, Bhatia S (2006a) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112:347–357

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Sheldrake A, Saxena N, Krishnamurthy L (1979) The expression and influence on yield of the double podded character in chickpea (Cicer arietinum). Field Crops Res 1:243–253

    Article  Google Scholar 

  • Simon C, Muehlbauer F (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. J Heredity 88:115–119

    CAS  Google Scholar 

  • Tanksley S, Ganal M, Prince J, de Vicente M, Bonierbale M, Broun P, Fulton T, Giovannoni J, Grandillo S, Martin G, Messeguer R, Miller J, Miller L, Paterson A, Pineda O, Roder M, Wing R, Wu W, Young N (1992) High-density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    PubMed  CAS  Google Scholar 

  • Tanksley S, Young N, Paterson A, Bonierbale M (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–264

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Udupa S, Sharma A, Sharma A, Pai R (1993) Narrow genetic variability in Cicer arietinum as revealed by RFLP analysis. J Plant Biochem Biotechnol 2:83–86

    CAS  Google Scholar 

  • Upadhyaya H, Kumar S, Gowda C, Singh S (2006) Two major genes for seed size in chickpea (Cicer arietinum L.). Euphytica 147:311–315

    Article  CAS  Google Scholar 

  • van Ooijen J, Voorrips R (2001) JoinMap version 3.0: software for the calculation of genetic linkage maps. Plant Res Int, Wageningen

    Google Scholar 

  • Vaz Patto M, Torres A, Koblizkova A, Macas J, Cubero J (1999) Development of a genetic composite map of Vicia faba using F2 populations derived from trisomic plants. Theor Appl Genet 98:736–743

    Article  CAS  Google Scholar 

  • Vlacilova K, Ohri D, Wra´na J, Cihalikova J, Kubala´kova M, Kahl G, Dolezel J (2002) Development of cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.). Chromosome Res 10:695–706

    Article  PubMed  CAS  Google Scholar 

  • Voorrips R (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  PubMed  CAS  Google Scholar 

  • Wang S, Basten C, Zeng Z (2006) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://www.statgen.ncsu.edu/qtlcart/WQTLCart.htm)

  • Winter P, Benko-Iseppon A, Huttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant V, Rajesh P, Kahl G, Muehlbauer F (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 races 4 and 5. Theor Appl Genet 101:1155–1163

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch S (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled–haploid and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Financial assistance for this work was provided by The McKnight Foundation, USA. The authors acknowledge the support and initiative provided by Ms. Monali along with Drs. Vrinda Sant and PN Rajesh. SJM acknowledges the Council for Scientific and Industrial Research (CSIR), India, for Senior Research Fellowship.

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Authors and Affiliations

  1. Biochemical Sciences Division, National Chemical Laboratory, Pune, India

    P. Radhika, S. J. M. Gowda, N. Y. Kadoo, M. N. Sainani & V. S. Gupta

  2. Pulses Research Station, Mahatma Phule Krishi Vidyapeeth, Rahuri, India

    L. B. Mhase & B. M. Jamadagni

  3. Biotechnology Department, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India

    S. Chandra

Authors
  1. P. Radhika
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  2. S. J. M. Gowda
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  3. N. Y. Kadoo
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  4. L. B. Mhase
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  5. B. M. Jamadagni
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  6. M. N. Sainani
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  7. S. Chandra
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  8. V. S. Gupta
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Corresponding author

Correspondence to V. S. Gupta.

Additional information

Communicated by F. J. Muehlbauer.

P. Radhika and S.J.M. Gowda contributed equally to this study.

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Radhika, P., Gowda, S.J.M., Kadoo, N.Y. et al. Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115, 209–216 (2007). https://doi.org/10.1007/s00122-007-0556-7

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  • DOI: https://doi.org/10.1007/s00122-007-0556-7

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