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Genetic diversity and population structure of Indian soybean [Glycine max (L.) Merr.] revealed by simple sequence repeat markers

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Abstract

Genetic diversity in 90 Indian soybean cultivars was assessed using 45 SSR markers distributed on 20 soybean chromosomes. Forty-five SSR markers generated 232 alleles with an average of five alleles/locus. The observed frequencies of the 232 alleles ranged from 0.01 to 0.94 with an average of 0.19. The polymorphic information content (PIC) value of the SSR markers varied from 0.10 to 0.83 with an average of 0.61 and about 71% markers have a PIC value of >0.5. In this study, 54 rare alleles including 19 genotype specific alleles were also identified. The observed hetrozygosity for SSR markers ranged from 0 to 0.11 with a mean of 0.10. Cluster analysis grouped the 90 soybean cultivars into three major clusters and principal coordinates analysis (PCoA) results were similar to those of the cluster analysis. A combination of eight SSR markers successfully differentiated all 90 soybean cultivars. The population structure analysis distributed the 90 soybean genotypes into two populations with mean alpha (α) value of 0.1873. In AMOVA analysis, proportion of variation within population was high (88%), whereas only 12% occurred among populations. In cluster and structure analyses, most of the genotypes with similar pedigree were grouped together. Soybean cultivars DS228, MACS-13, LSb-1, Hardee, Improved Pelican, and Pusa-24 were the six most genetically distinct cultivars identified. The study reported a moderate genetic diversity in Indian soybean cultivars and findings would be useful to the soybean breeders in selecting genetically distinct parents for a soybean improvement program.

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References

  • Anonymous. 2014. Annual report 2013–14, AICRP on Soybean, Directorate of Soybean Research, Indore, India

    Google Scholar 

  • Asare AT, Gowda BS, Galyuon IKA, Aboagye LL, Takrama JF, Timko MP. 2010. Assessment of the genetic diversity in cowpea (Vigna unguiculata L. Walp.) germplasm from Ghana using simple sequence repeat markers. Plant Genet. Resour. 8: 142–150

    Article  CAS  Google Scholar 

  • Bar-Hen A, Charcosset A, Bourgoin M, Cuiard J. 1995. Relationships between genetic markers and morphological traits in a maize inbred lines collection. Euphytica 84: 145–154

    Article  Google Scholar 

  • Barrett BA, Kidwell KK. 1998. AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Sci. 38: 1261–1271

    Article  CAS  Google Scholar 

  • Bharadwaj CH, Satyavathi CT, Tiwari SP, Karmakar PG. 2002. Genetic base of soybean (Glycine max) varieties released in India as revealed by coefficient of parentage. Indian J. Agri. Sci. 72(8): 467–469

    Google Scholar 

  • Bisen A, Khare D, Nair P, Tripathi N. 2015. SSR analysis of 38 genotypes of soybean (Glycine Max (L.)Merr.) genetic diversity in India. Physiol. Mol. Biol. Plants 21: 109–115

    Article  CAS  PubMed  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brown-Guedira GL, Thompson JA, Nelson RL, Warburton ML. 2000. Evaluation of genetic diversity of soybean introductions and North American ancestors using RAPD and SSR markers. Crop Sci. 40: 815–823

    Article  CAS  Google Scholar 

  • Burle ML, Fonseca JR, Kami JA, Gepts P. 2010. Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor. Appl. Genet. 121: 801–813

    Article  PubMed  PubMed Central  Google Scholar 

  • Chauhan DK, Bhat JA, Thakur AK, Kumari S, Hussain Z, Satyawathi CT. 2015. Molecular characterization and genetic diversity assessment in soybean [Glycine max (L.) Merr.] varieties using SSR markers. Ind. J. Biotechnol. 14: 504–510.

    Google Scholar 

  • Diwan N, Cregan PB. 1997. Automated sizing of Xuorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean. Theor. Appl. Genet. 95: 723–733

    Article  CAS  Google Scholar 

  • Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, Datta S, et al. 2011. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol. 11: 17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Earl DA, von Holdt BM. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4(2): 359–361

    Article  Google Scholar 

  • Fu YB, Peterson GW, Morrison MJ. 2007. Genetic diversity of Canadian soybean cultivars and exotic germplasm revealed by simple sequence repeat markers. Crop Sci. 47: 1947–1954

    Article  CAS  Google Scholar 

  • Gupta SK, Bansal R, Vaidya UJ, Gopalakrishna T. 2013. Assessment of genetic diversity at molecular level in mungbean (Vigna radiata (L.) Wilczek). J. Food Legumes 26(3 & 4): 19–24

    Google Scholar 

  • Gupta SK, Gopalakrishna T. 2009. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi). Genome 52: 120–128

    Article  CAS  PubMed  Google Scholar 

  • Gupta SK, Gopalakrishna T. 2010. Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53: 508–523

    Article  CAS  PubMed  Google Scholar 

  • Halliburton R. 2004. Introduction to population genetics. Pearson/Prentice Hall, Upper Saddle River, NJ

    Google Scholar 

  • Hymowitz T. 1969. The soybeans of the Kumaon Hills of India. Econ. Bot. 23(1): 50–54

    Article  Google Scholar 

  • Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. 103: 16666–16671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jain S, Jain R, Mccouch S. 2004. Genetic analysis of Indian aromatic and qualityrice (Oryza sativa L.) germplasm using panels of Xuorescently-labled microsatellite markers. Theor. Appl. Genet. 109: 965–977

    Article  CAS  PubMed  Google Scholar 

  • Karp A, Edwards KJ, Bruford M, Funk S, Vosman B. 1997. Molecular technologies for biodiversity evaluation: opportunities and challenges. Nat. Biotechnol. 15: 625–628

    Article  CAS  PubMed  Google Scholar 

  • Kumawat G, Singh G, Gireesh C, Shivakumar M, Arya M, Agarwal DK, Husain SM. 2015. Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India. Physiol. Mol. Biol. Plants 21(1): 101–107

    Article  CAS  PubMed  Google Scholar 

  • Li C-D, Fatokun CA, Ubi B, Singh BB, Scoles GJ. 2001. Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite markers. Crop Sci. 41: 189–197

    Article  CAS  Google Scholar 

  • Li Y, Guan R, Liu Z, Ma Y, Wang L, Li L, Lin F, Luan W, Chen P, Qiu L. 2008. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor. Appl. Genet. 117: 857–871

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse S. 2005. Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Manjaya JG, Bapat VA. 2008. Studies on genetic divergence in soybean [Glycine max (L.) Merrill]. J. Oilseeds Res. 25: 178- 180

    Google Scholar 

  • Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and researchan update. Bioinformatics 28: 2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Flori A, Bonnot F. 2003. Data analysis methods. In: P Hamon PM Seguin M, PX errier X, JC Glaszmann, Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43–76

    Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2: 225–238

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Russell J, Fuller J, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W. 1997. Discriminating between barley genotypes using microsatellite markers. Genome 40: 442–450

    Article  CAS  PubMed  Google Scholar 

  • Singh BB. 2006. Success of soybean in India: The Early Challenges and Pioneer Promoters. Asian Agrihist. 10: 43–53

    Google Scholar 

  • Singh RK, Sharma RK, Singh AK, Singh VP, Singh NK, Tiwari SP, Mohapatra T. 2004. Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135: 135–143

    Article  CAS  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB. 2004. A new integrated genetic linkage map of the soybean. Theor. Appl. Genet. 109: 122–128

    Article  CAS  PubMed  Google Scholar 

  • Tantasawat P, Trongchuen J, Prajongjai T, Jenweerawat S, Chaowiset W. 2011. SSR analysis of soybean (Glycine max (L.) Merr.) genetic relationship and variety identification in Thailand. Aust. J. Crop Sci. 5(3): 283–290

    CAS  Google Scholar 

  • Tautz D, Renz P. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genome. Nucl. Acids Res. 12: 4127–4138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson JA, Nelson RL, Vodkin LO. 1998. Identification of diverse soybean germplasm using RAPD markers. Crop Sci. 38: 1348–1355

    Article  Google Scholar 

  • Tiwari SP. 2014. Raising the yield ceilings in soybean - An Indian Overview. Soybean Res. 12(2): 1–43

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucl. Acids Res. 23: 4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang LX, Guan RX, Liu ZX, Chang RZ, Qiu LJ. 2006. Genetic diversity of Chinese cultivated soybean revealed by SSR markers. Crop Sci. 46: 1032–1038

    Article  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18: 6531–6535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183

    Article  CAS  PubMed  Google Scholar 

Download references

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  1. Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India

    SK Gupta & JG Manjaya

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  1. SK Gupta
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  2. JG Manjaya
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Gupta, S., Manjaya, J. Genetic diversity and population structure of Indian soybean [Glycine max (L.) Merr.] revealed by simple sequence repeat markers. J. Crop Sci. Biotechnol. 20, 221–231 (2017). https://doi.org/10.1007/s12892-017-0023-0

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