Genes and Genomics

The Genetics Society of Korea (한국유전학회)
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Assessment of genetic diversity and population structure in mungbean

  • Gwag, Jae-Gyun (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Dixit, Anupam (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Park, Yong-Jin (College of Industrial Science, Kongju National University) ;
  • Ma, Kyung-Ho (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Kwon, Soon-Jae (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Cho, Gyu-Taek (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Lee, Gi-An (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Lee, Sok-Young (National Agrobiodiversity Center, National Academy of Agricultural Science, RDA) ;
  • Kang, Hee-Kyoung (College of Industrial Science, Kongju National University) ;
  • Lee, Suk-Ha (Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Plant Genomics and Breeding Institute, Seoul National University)
  • Received : 2010.02.08
  • Accepted : 2010.04.20
  • Published : 2010.08.30
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Abstract

This study was carried out to assess the genetic diversity and to analyze the population genetic structure for a total of 692 mungbean accessions preserved at National Agrobiodiversity Center (NAC) of the Rural Development Administration (RDA), Korea. Mungbean accessions were collected from 27 countries in nine different geographic regions, and were geno-typed using 15 microsatellite markers, which were developed in our previous study. A total of 66 alleles were detected among 692 accessions at all the loci with an average of 4.4 alleles per locus. All the microsatellite loci were found to be polymorphic. The expected heterozygosity (HE) and polymorphism information content (PIC) ranged from 0.081 to 0.588 (mean = 0.345) and from 0.080 to 0.544 (mean = 0.295), respectively. Of the 66 alleles, 17 (25.8%) were common (frequency range between 0.05 and 0.5), 15 (22.7%) were abundant (frequency range > 0.5), and 34 (51.5%) were rare (frequency range < 0.05). Locus GB-VR-7 provided the highest number of rare alleles(eight), followed by GB-VR-91(six) and GB-VR-113(four). Country-wide comparative study on genetic diversity showed that accessions from the USA possessed the highest genetic diversity (PIC) followed by Nepal, Iran, and Afghanistan. And region-wide showed that accessions from Europe possessed the highest average genetic diversity, followed by accessions from the USA, South Asia, West Asia, and Oceania. Twenty-seven countries were grouped into seven clades by phylogenetic relationship analysis, but clustering pattern did not strictly follow their geographical origin because of extensive germplasm exchange between/among countries and regions. As a result of a model-based analysis (STRUCTURE) of microsatellite data, two distinct genetic groups were identified which shared more than 75% membership with one of the two genetic groups. However the genetic group pattern did not reflect their geographical origin. The Duncan's Multiple Range Test among these two genetic groups and an admixed group, with a mean of 16 phenotypic traits, showed significant difference in 12 quantitative and qualitative traits on the basis of ANOVA. These 15 newly developed SSR markers proved to be useful as DNA markers to detect genetic variation in mungbean germplasm for reasonable management and crossbreeding purposes.

Keywords

References

  1. Anderson JA, Churchill GA, Autrique JE, Tanksley SD and Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181-186. https://doi.org/10.1139/g93-024
  2. Bae KG, Nam SW, Kim KN and Hwang YH (2004) Growth of soybean sprouts and concentration of ${CO_2}$ produced in culture vessel affected by watering methods. Kor.ean J. Crop Sci. 49: 167-171.
  3. Barkley NA, Roose ML, Krueger RR and Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 112: 1519-1531. https://doi.org/10.1007/s00122-006-0255-9
  4. Betal S, Chowdhury PR, Kundu S and Raychaudhuri SS (2004) Estimation of genetic variability of Vigna radiata cultivars by RAPD analysis. Biol. Planta. 48: 205-209.
  5. Botstein D, White RL, Skolnick M and Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Human Genet. 32: 314.
  6. Capo-chichi LJA, Weaver DB and Morton CM (2003) The use of molecular markers to study genetic diversity in Mucuna. Tropic. Subtropic. Agroecosys. 1: 309-318.
  7. Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD and Varshney RK (2008) Isolation and characterization of novel microsatellites markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol. 8: 55 doi:10.1186/1471-2229-8-5.
  8. Evanno G, Regnaut S and Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molec. Ecol. 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  9. Gupta PK, Roy JK and Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr. Sci. 80: 524-535.
  10. Gwag JG (2008) Molecular diversity assessment and population structure analysis in mung bean, Vigna radiata (L.) Wilczek. PhD Thesis Seoul National University pp 1-112.
  11. Humphry M, Konduri V, Lambrides C, Magner T, McIntyre C, Aitken E and Liu C (2002) Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) reveals a high level of colinearity between the two genomes. Theor. Appl. Genet. 105: 160-166. https://doi.org/10.1007/s00122-002-0909-1
  12. Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT and Howarth CJ (2008) Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breed. 127: 33-37.
  13. Kumar SV, Tan SG, Quah SC and Yusoff K (2002a) Isolation of microsatellite markers in mungbean, Vigna radiata. Molec. Ecol. Notes 2: 96-98. https://doi.org/10.1046/j.1471-8286.2002.00158.x
  14. Kumar SV, Tan SG, Quah SC and Yusoff K (2002b) Isolation and characterization of seven tetranucleotide microsatellite loci in mungbean, Vigna radiata. Molec. Ecol. Notes 2: 293-295. https://doi.org/10.1046/j.1471-8286.2002.00239.x
  15. Lakhanpaul S, Chadha S and Bhat KV (2000) Random amplified polymorphic DNA (RAPD) analysis in Indian mung bean (Vigna radiata (L.) Wilczek) cultivars. Genetica 109: 227-234. https://doi.org/10.1023/A:1017511918528
  16. Lee JR, Hong GY, Dixit A, Chung JW, Ma KH, Lee JH, Kang HK, Cho YH, Gwag JG andPark YJ (2008). Characterization of microsatellite loci developed for Amaranthus hypochondriacus and their cross-amplifications in wild species. Conserv. Genet. 9: 243-246. https://doi.org/10.1007/s10592-007-9323-1
  17. Lee YS and Kim YH (2004) Changes in postharvest respiration, growth, and vitamin C content of soybean sprouts under different storage temperature conditions. Kor.ean J. Crop Sci. 49: 410-414.
  18. Litt M and Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Human Genet. 44: 397.
  19. Liu K and Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129. https://doi.org/10.1093/bioinformatics/bti282
  20. Malhotra VV, Singh S and Singh KB (1974) Yield components in greengram (Phaseolus aureus Roxb). Indian J. Agric. Sci. 44: 136-141.
  21. Maras M, Jelka SV, Branka J and Vladimir M (2008) The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L.) Acta Agric. Slovenica 91: 87-96.
  22. Mather DE, Hyes PM, Chalmers KJ, Eglinton J, Matus I, Richardson K, Von Zitzewitz J, Marquez-Cedillo L, Hearnden P and Pal N (2004) Use of SSR marker data to study linkage disequilibrium and population structure in Hordeum vulgare: Prospects for association mapping in barley. In: International barley genetics symposium, Brno, Czech Republic, 20-26 June 2004, pp. 302-307
  23. Mullis K, Faloona F, Scharf S, Saiki R, Horn G and Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51: 263-273. https://doi.org/10.1101/SQB.1986.051.01.032
  24. Newbury H and Ford-Lloyd BV (1997) Estimation of genetic diversity. In: Plant genetic conservation-the in situ approach, Maxted N, Ford-Lloyd BV, Hawkes JG. Eds., Chapman and Hall, London, UK, pp. 192-206.
  25. Pallottini L, Garcia E, Kami J, Barcaccia G and Gepts P (2004) The genetic anatomy of a patented yellow bean. Crop Sci. 44: 968-977. https://doi.org/10.2135/cropsci2004.0968
  26. Petit E, Balloux F and Goudet J (2001) Sex-biased dispersal in a migratory bat: A characterization using sex-specific demographic parameters. Evolution 55: 635-640. https://doi.org/10.1554/0014-3820(2001)055[0635:SBDIAM]2.0.CO;2
  27. Poehlman JM (1991) The mungbean. Published in India by Mohan Primlani for Oxford & IBH Publishing Co, pp. 195-222.
  28. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S and Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm anlysis. Mol. Breed. 2: 225-238. https://doi.org/10.1007/BF00564200
  29. Pritchard JK, Stephens M and Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
  30. Queller DC, Strassmann JE and Hughes CR (1993) Microsatellites and kinship. Trends in Ecol. Evol. 8: 285-288. https://doi.org/10.1016/0169-5347(93)90256-O
  31. Roussel V, Koenig J, Beckert M and Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor. Appl. Genet. 108: 920-930. https://doi.org/10.1007/s00122-003-1502-y
  32. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotech. 18: 233-234. https://doi.org/10.1038/72708
  33. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl.eic Acids Res. 17: 6463-6471. https://doi.org/10.1093/nar/17.16.6463
  34. Tomooka N, Lairungreang C, Nakeeraks P, Egawa Y and Thavarasook C (1992) Center of genetic diversity and dissemination pathways in mungbean deduced from seed protein electrophoresis. Theor. Appl. Genet. 83: 289-293.
  35. Vos P, Hogers R, Bleeker M, Reijans M, Van De, Lee T, Hornes M, Frijters A, Pot J, Peleman J and Kuiper M (1995) AFLP: A new technique for DNA fingerprinting. Nucl.eic Acids Res. 23: 4407-4414. https://doi.org/10.1093/nar/23.21.4407
  36. Weber JL and May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Human Genet. 44: 388.
  37. Welsh J and McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucl.eic Acids Res. 18: 7213-7218. https://doi.org/10.1093/nar/18.24.7213
  38. Westman AL and Kresovich S (1997) Use of molecular marker techniques for description of plant genetic variation. In: Callow JA, Ford-Lloyd BV, Newbury HJ (eds) Plant Genetic Resources: Conservation and Use CAB Int., Wallingford, UK, pp. 9-48.
  39. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA and Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl.eic Acids Res. 18: 6531-6535. https://doi.org/10.1093/nar/18.22.6531
  40. Yifru T, Hammer K, Huang XQ and Roder MS (2006) Regional patterns of microsatellite diversity in Ethiopian tetraploid wheat accessions. Plant Breed. 125: 125-130. https://doi.org/10.1111/j.1439-0523.2006.01147.x

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