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Construction of interspecific genetic linkage map of pigeonpea using SCoT, RAPD, ISSR markers and simple inherited trait loci

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Abstract

An interspecific genetic linkage map of pigeonpea (2n = 2x = 22) has been constructed with 31 SCoT (start codon targeted polymorphism), 148 RAPD (random amplified polymorphic DNA), six ISSR (inter simple sequence repeat) and six trait loci controlling plant habit (PTY), seed hilum (SHM), density of non glandular short trichome (NGST), resistance to pod borer (PPB1), resistance to plume moth (PPM1), resistance to blue butterfly (PBB1) using 116 interspecific F2 progenies derived from a cross of Cajanus cajan (cv. ICP-26) and C. scarabaeoides (acc. ICPW-94). These 191 markers were mapped into 11 linkage groups (LGs), varying between 320.63 and 43.38 cM and covering 1624.71 cM of the genome with an average marker interval of 8.51 cM. Four loci (PBB1, PPB1, NGST, PPM1) contributing resistance to pod borer complex were mapped to LG-2 as cluster and were flanked by OPB07860 (12.9 cM) and OPA09910 (12.5 cM). Likewise, the loci PTY and SHM were mapped to LG-1, and LG-7, respectively. The locus PTY flanked by OPB011580 (3.1 cM) and OPF021095 (3.5 cM), and the locus SHM was linked to OPE091110 with recombination fraction 0.258 (28.5 cM).

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References

  1. Aruna R, Rao M, Reddy LJ, Upadhyaya HD, Sharma HC. Inheritance of trichomes and resistance to pod borer (Helicoverpa armigera) and their association in interspecific crosses between cultivated pigeonpea (Cajanus cajan) and its wild relative C. scarabaeoides. Euphytica. 2005;145:247–57.

    Article  CAS  Google Scholar 

  2. Bohra A, Dubey A, Saxena RK, Penmetsa RV, Poornima KN, Kumar N, et al. Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea, (Cajanus spp.). BMC Plant Biol. 2011;11:56.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Bohra A, Saxena RK, Gnanesh BN, Saxena KB, Byregowda M, Rathore A, et al. An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. Theor Appl Genet. 2012;125:1325–38.

    Article  PubMed Central  PubMed  Google Scholar 

  4. Collard BCY, Mackill DJ. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Report. 2009;27:86–93.

    Article  CAS  Google Scholar 

  5. D’Cruz R, Pachpol LS, Deokar AB. Genetic studies in pigeonpea - IX. NP51 x prostrate. PKV Res J. 1974;2:77–81.

    Google Scholar 

  6. D’Cruz R, Deokar AB. Genetic studies in pigeonpea -I. N. green x red grained. Mahatma Phule Agric Univ Res J. 1970;1:44–53.

    Google Scholar 

  7. Datta S, Singh P, Mahfooz S, Patil GP, Chaudhary AK, Agbagwa IO, et al. Novel genic microsatellite markers from Cajanus scarabaeoides and their comparative efficiency in revealing genetic diversity in pigeonpea. J Genet. 2013;92:e24–30.

    PubMed  Google Scholar 

  8. Deokar AB, Bhole GR, D’Cruz R. Genetic studies in pigeonpea - VII - creeping 3-2-8 x prostrate. Mahatma Phule Agric Univ Res J. 1971;2:38–47.

    Google Scholar 

  9. Deokar AB, Manke BS, D’Cruz R. Genetic studies in pigeonpea – VI. Leaflet shape, pod and seed coat colour. Indian Agric. 1972;16:193–7.

    Google Scholar 

  10. Deokar AB, D’Cruz R. Genetic studies in pigeonpea III. Round leaf x creeping 3-2-3. J Univo Poona. 1971;40:23–30.

    Google Scholar 

  11. Dhanasekar P, Dhumail KN, Reddy KS. Identification of RAPD markers linked to plant type gene in pigeonpea. Indian J Biotechnol. 2010;9:58–63.

    CAS  Google Scholar 

  12. Dubey A, Farmer A, Schlueter J, Cannon SB, Abernathy B, Tuteja R, et al. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L. Millsp.). DNA Res. 2011;18:153–64.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Ganapathy KN, Byre GM, Venkatesha SC, Ramachandra R, Gnanesh BN, Girish G. Identification of AFLP markers linked sterility mosaic disease in pigeonpea Cajanus cajan (L.) Millsp. Int J Integr Biol. 2009;7:145–9.

    CAS  Google Scholar 

  14. Gnanesh BN, Bohra A, Sharma M, Byregowda M, Pandey S, Wesley V, et al. Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea [Cajanus cajan (L.) Millsp.]. Field Crop Res. 2011;123:53–61.

    Article  Google Scholar 

  15. Greilhuber J, Obermayer R. Genome size variation in Cajanus cajan Fabaceae: a reconsideration. Plant Syst Evol. 1998;212:135–41.

    Article  Google Scholar 

  16. Gupta M, Verma B, Kumar N, Chahota RK, Rathour R, Sharma SK, et al. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. J Genet. 2012;91:279–87.

    Article  CAS  PubMed  Google Scholar 

  17. Gupta SK, Charpe A, Koul S, Haque QMR, Prabhu KV. Development and validation of SCAR markers co-segregating with an Agropyron elongatum derived leaf rust resistance gene Lr24 in wheat. Euphytica. 2006;150:233–40.

    Article  CAS  Google Scholar 

  18. Kole C, Gupta PK. Genome mapping and map based cloning. In: Jain HK, Khrakwal MC, editors. Plant breeding- Mendelian to molecular approaches. New Delhi: Narosa Publising House; 2004. p. 257–99.

    Google Scholar 

  19. Kole C, Quijada P, Michaels AD, Amasino RM, Osborn TC. Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana. Theor Appl Genet. 2001;102:425–30.

    Article  CAS  Google Scholar 

  20. Kosambi D. The estimation of map distance from recombination values. Ann Eugen. 1943;12:172–5.

    Article  Google Scholar 

  21. Kotresh H, Fakrudin B, Punnuri SM, Rajkumar BK, Thudi M, Paramesh H, et al. Identification of two RAPD markers genetically linked to a recessive allele of a Fusarium wilt resistance gene in pigeonpea (Cajanus cajan L. Millsp.). Euphytica. 2006;149:113–20.

    Article  CAS  Google Scholar 

  22. Kreike CM, Stiekema WJ. Reduced recombination and distorted segregation in Solanum tuberosum (2x) x S. spegazzinii (2x) hybrid. Genome. 1997;40:180–7.

    Article  CAS  PubMed  Google Scholar 

  23. Kumawat G, Raje RS, Bhutani S, Pal JK, Mithra ASVCR, Gaikward K, et al. Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.). BMC Genet. 2012;13:84.

    Article  PubMed Central  PubMed  Google Scholar 

  24. Laucou V, Haurogne K, Ellis N, Rameau C. Genetic mapping in pea. 1. RAPD-based genetic linkage map of Pisum sativum. Theor Appl Genet. 1998;97:905–15.

    Article  CAS  Google Scholar 

  25. Lincoln S, Daly M, Lander E. Constructing the genetic map with MAPMAKER/EXP 3.0. Whitehead institute technical report. 3rd ed. Cambridge: Cambridge Press; 1992.

    Google Scholar 

  26. Liu RH, Meng JL. MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data. Yi Chuan. 2003;25:317–21.

    PubMed  Google Scholar 

  27. Mishra RR, Sahu AR, Rath SC, Behera B, Panigrahi J. Molecular mapping of locus controlling resistance to Helicoverpa armigera (Hubner) in Cajanus cajan L. (Millspaugh) using interspecific F2 mapping population. Nucleus. 2013;56:91–7.

    Article  Google Scholar 

  28. Mishra RR, Sahu AR, Rath SC, Mishra SP, Panigrahi J. Cyto-morphological and molecular characterization of Cajanus cajan x C. scarabaeoides F1 hybrid. Nucleus. 2012;55:27–35.

    Article  Google Scholar 

  29. Mishra RR. Molecular Mapping of genes conferring resistance to pod borer and pod fly in Cajanus cajan (L.) Millsp.). Ph.D. Dissertation, Utkal University, Bhubaneswar, India; 2014.

  30. Mukherjee AK, Mohapatra T, Varshney A, Sharma R, Sharma RP. Molecular mapping of a locus controlling resistance to Albugo candida in Indian mustard. Plant Breed. 2001;120:481–7.

    Article  Google Scholar 

  31. Nadimpalli RG, Jarret RL, Phatak SC, Kochen G. Phylogenetic relationships of the pigeonpea (Cajanus cajan) based on nuclear restriction fragment length polymorphism. Genome. 1993;36:216–23.

    Article  CAS  PubMed  Google Scholar 

  32. Odeny DA, Jayashree B, Ferguson M, Hoisington D, Crouch J, Gebhardt C. Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed. 2007;126:130–6.

    Article  CAS  Google Scholar 

  33. Panigrahi J, Mishra RR, Sahu AR, Rath SC, Kole C. Marker assisted breeding (MAB) for stress resistance in crop plants. In: Rout GR, Das AB, editors. Molecular stress physiology of plants. India: Springer; 2013. p. 387–426.

    Chapter  Google Scholar 

  34. Panigrahi J, Patnaik A, Kole P, Kole C. Addition of restriction fragment length polymorphism markers to the genetic linkage map of Brassica Rapa L. (syn. Campestris). Z Naturforsch. 2009;64C:882–90.

    Google Scholar 

  35. Paterson AH, DeVerna JW, Lanini B, Tanksley SD. Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics. 1990;124:735–42.

    PubMed Central  CAS  PubMed  Google Scholar 

  36. Pillen K, Steinruecken G, Wricke G, Herrman RG, Jung C. A linkage map of sugar beet (Beta vulgaris L.). Theor Appl Genet. 1992;84:129–35.

    Article  CAS  PubMed  Google Scholar 

  37. Pundir RSP, Singh RB. Inheritance in inter-generic crosses between Cajanus and Atylosia species. Indian J Genet. 1985;45:194–8.

    Google Scholar 

  38. Raju NL, Gananesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, et al. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol. 2010;10:45.

    Article  PubMed Central  PubMed  Google Scholar 

  39. Ratnaparkhe MB, Gupta VS, Ven Murthy MR, Ranjekar PK. Genetic fingerprinting of pigeonpea (Cajanus cajan (L.) Millsp.) and its wild relatives using RAPD markers. Theor Appl Genet. 1995;91:893–8.

    Article  CAS  PubMed  Google Scholar 

  40. Saxena KB, Saxena RK, Kumar RV, Varshney RK. Evidence of a unique inter-allelic epistatic interaction for seed coat color in pigeonpea [Cajanus cajan (L.) Millspaugh]. Euphytica. 2012;186:813–6.

    Article  CAS  Google Scholar 

  41. Saxena RK, Penmetsa RV, Upadhyaya HD, Kumar A, Carrasquilla-Gracia N, Schlueter JA, et al. Large-scale development of cost-effective single nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res. 2012;19:449–61.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Singh NK, Gupta DK, Pawan KJ, Ajay KM, Dutta S, Singh S, et al. The first draft of the pigeonpea genome sequence. J Plant Biochem Biotechnol. 2011;21:98–112.

    Article  PubMed Central  PubMed  Google Scholar 

  43. Sivaramakrishnan S, Seetha K, NageswarRao A, Singh L. RFLP analysis of cytoplasmic male-sterile lines of pigeonpea (Cajanus cajan (L.) Millsp.) developed by interspecific crosses. Euphytica. 1997;93:307–12.

    Article  CAS  Google Scholar 

  44. Slocum MK, Figdore SS, Kennard WC, Suzuki JY, Osborn TC. Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. Theor Appl Genet. 1990;80:57–64.

    Article  CAS  PubMed  Google Scholar 

  45. Souframanien J, Manjaya JG, Krishna TG, Pawar SE. Random amplified polymorphic DNA analyses of cytoplasmic male sterile and male fertile pigeonpea (Cajanus cajan (L.) Millsp.). Euphytica. 2003;129:293–9.

    Article  CAS  Google Scholar 

  46. Tadmor Y, Zamir D, Ladizinsky G. Genetic mapping of an ancient translocation in the genus Lens. Theor Appl Genet. 1987;73:883–92.

    Article  CAS  PubMed  Google Scholar 

  47. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broum P, et al. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992;132:1141–60.

    PubMed Central  CAS  PubMed  Google Scholar 

  48. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol. 2012;30:83–9.

    Article  CAS  Google Scholar 

  49. Varshney RK, Graner A, Sorrells ME. Genomics assisted breeding for crop improvement. Trends Plant Sci. 2005;10:621–30.

    Article  CAS  PubMed  Google Scholar 

  50. Varshney RK, Mohan SM, Gaur PM, Gangarao NV, Pandey MK, Bohra A, et al. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv. 2013;31:1120–34.

    Article  PubMed  Google Scholar 

  51. Varshney RK, Penmetsa RV, Dutta S, Kulwal PL, Saxena RK, Datta S, et al. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breeding. 2010;26:393–408.

    Article  Google Scholar 

  52. Verulkar SB, Singh DP, Bhattacharya AK. Inheritance of resistance to pod fly and pod borer in the interspecific cross of pigeonpea. Theor Appl Genet. 1997;95:506–8.

    Article  Google Scholar 

  53. Winter P, Benko-Iseppon AM, Hüttel B, Ratnaparke M, Tullu A, Sonnante G, et al. A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum x C. reticulatum cross: 1272 localization of resistance genes for Fusarium wilt races 4 and 5. Theor Appl Genet. 2000;101:1155–63.

    Article  CAS  Google Scholar 

  54. Wu Y, Ko P, Lee W, Wei F, Kuo S, Ho S, et al. Comparative analyses of linkage maps and segregation distortion of two F2 populations derived from japonica crossed with indica rice. Hereditas. 2010;147:225–36.

    Article  PubMed  Google Scholar 

  55. Yang SY, Saxena RK, Kulwal PL, Ash GJ, Dubey A, Harper JDI, et al. The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers. J Genet. 2011;90:103–9.

    Article  PubMed  Google Scholar 

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Acknowledgments

The authors are highly grateful to the Department of Biotechnology (F. No. BT/PR13468/AGR/02/702/2010), and University Grant Commission (F No. 37-331/2009) for financial support though R&D projects to the corresponding author (JP). The authors also acknowledge the indebtedness to Dr. H. D. Upadhyaya, Principal Scientist, ICRISAT for the germplasm.

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  1. Plant Biotechnology Laboratory, School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla-768019, Sambalpur, Odisha, India

    Alok Ranjan Sahu, Ramya Ranjan Mishra, Sobha Chandra Rath & Jogeswar Panigrahi

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  1. Alok Ranjan Sahu
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Sahu, A.R., Mishra, R.R., Rath, S.C. et al. Construction of interspecific genetic linkage map of pigeonpea using SCoT, RAPD, ISSR markers and simple inherited trait loci. Nucleus 58, 23–31 (2015). https://doi.org/10.1007/s13237-015-0129-0

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