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Theoretical and Applied Genetics

, Volume 119, Issue 7, pp 1247–1254 | Cite as

Development of SSR markers for studies of diversity in the genus Fagopyrum

  • Kyung-Ho Ma
  • Nam-Soo Kim
  • Gi-An Lee
  • Sok-Young Lee
  • Ju Kyong Lee
  • Jung Yoon Yi
  • Yong-Jin Park
  • Tae-San Kim
  • Jae-Gyun Gwag
  • Soon-Jae KwonEmail author
Original Paper

Abstract

The numbers of SSR markers and their utilization have not been determined and investigated as extensively in Fagopyrum species as compared to other crop species. The current report presents 136 new SSR markers in Fagopyrum esculentum ssp. esculentum and their application to related species in the genus Fagopyrum. Of the 136 SSRs, 10 polymorphic SSR markers were utilized in a genetic diversity analysis of a common buckwheat population consisting of 41 accessions of diverse origin. The study showed observed (H O) and expected (H E) heterozygosities ranging from 0.071 to 0.924 (mean = 0.53) and from 0.073 to 0.902 (mean = 0.412), respectively. Forty-one of the 136 SSRs amplified sequences in other Fagopyrum species, including the cymosum and urophyllum groups. The phylogenetic relationships revealed using the SSRs was consistent with results obtained using other marker systems, with one exception. The sequence and diversity information obtained using these new SSRs and their cross-transferability to related Fagopyrum species will increase our understanding of genetic structures and species relationships within the Fagopyrum genus.

Keywords

Similarity Coefficient Polymorphism Information Content Common Buckwheat Polymorphic SSRs High Polymorphism Information Content 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This study was supported by the Biogreen 21 project (#20080401034058) of the Rural Development Administration (RDA), a grant (Code #200803101010290), and the 2009 Postdoctoral Course Program from the National Institute of Agricultural Biotechnology, RDA, Republic of Korea. We appreciate Dr. G. Fedak for critical reading and editing the manuscript.

Supplementary material

122_2009_1129_MOESM1_ESM.xls (2.1 mb)
Supplementary material 1 (XLS 2146 kb)

References

  1. Amos W, Sawcer SJ, Feakes RW, Rubinsztein DC (1996) Microsatellites show mutational bias and heterozygote instability. Nat Genet 13:390–391CrossRefPubMedGoogle Scholar
  2. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186CrossRefPubMedGoogle Scholar
  3. Butcher PA, Decroocq S, Gray Y, Moran GF (2000) Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium. TAG Theoret Appl Genet 101:1282–1290CrossRefGoogle Scholar
  4. Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite’evolution’: directionality or bias? Nat Genet 11:360–362CrossRefPubMedGoogle Scholar
  5. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374CrossRefGoogle Scholar
  6. Guo W, Wang W, Zhou B, Zhang T (2006) Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium. TAG Theoret Appl Genet 112:1573–1581CrossRefGoogle Scholar
  7. Hagenblad J, Nordborg M (2002) Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161:289–298PubMedGoogle Scholar
  8. Holasova M, Fiedlerova V, Smrcinova H, Orsak M, Lachman J, Vavreinova S (2002) Buckwheat—the source of antioxidant activity in functional foods. Food Res Int 35:207–211CrossRefGoogle Scholar
  9. Iwata H, Imon K, Tsumura Y, Ohsawa R (2005) Genetic diversity among Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars as determined from amplified fragment length polymorphism and simple sequence repeat markers and quantitative agronomic traits. Genome 48:367–377CrossRefPubMedGoogle Scholar
  10. Kim KY (2004) Developing one step program (SSR Manager) for rapid identification of clones with SSRs and primer designing. MS thesis, Seoul National University, Seoul, The Republic of KoreaGoogle Scholar
  11. Konishi T, Yasui Y, Ohnishi O (2005) Original birthplace of cultivated common buckwheat inferred from genetic relationships among cultivated populations and natural populations of wild common buckwheat revealed by AFLP analysis. Genes Genet Syst 80:113–119CrossRefPubMedGoogle Scholar
  12. Konishi T, Iwata H, Yashiro K, Tsumura Y, Ohsawa R, Yasui Y, Ohnishi O (2006) Development and characterization of microsatellite markers for common buckwheat. Breed Sci 56:277–285CrossRefGoogle Scholar
  13. Kreft I (2001) Buckwheat research, past, present and future perspectives 20 years of internationally coordinated research. Current Advances in Buckwheat Research. In: Proceedings of the 8th international symposium on buckwheat, August, pp 361–366Google Scholar
  14. Kuleung C, Baenziger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye, and triticale. TAG Theoret Appl Genet 108:1147–1150CrossRefGoogle Scholar
  15. Kwon SJ, Lee JK, Kim NS, Yu JW, Dixit A, Cho EG, Park YJ (2005) Isolation and characterization of microsatellite markers in Perilla frutescens Brit. Mol Ecol Notes 5:455–457CrossRefGoogle Scholar
  16. Litt M, 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 44:397–401Google Scholar
  17. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Oxford University Press, Oxford, pp 2128–2129Google Scholar
  18. Murai M, Ohnishi O (1996) Population genetics of cultivated common buckwheat, Fagopyrum esculentum Moench. X. Diffusion routes revealed by RAPD markers. Genes Genet Syst 71:211–218CrossRefPubMedGoogle Scholar
  19. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, USAGoogle Scholar
  20. Ohnishi O (1998) Search for the wild ancestor of buckwheat III. The wild ancestor of cultivated common buckwheat, and of tatary buckwheat. Econ Bot 52:123–133Google Scholar
  21. Ohnishi O, Matsuoka Y (1996) Search for the wild ancestor of buckwheat II. Taxonomy of Fagopyrum (Polygonaceae) species based on morphology, isozymes and cpDNA variability. Genes Genet Syst 71:383–390CrossRefGoogle Scholar
  22. Ohsako T, Ohnishi O (1998) New Fagopyrum species revealed by morphological and molecular analyses. Genes Genet Syst 73:85–94CrossRefGoogle Scholar
  23. Ohsako T, Yamane K, Ohnishi O (2002) Two new Fagopyrum (Polygonaceae) species, F. gracilipedoides and F. jinshaense from Yunnan, China. Genes Genet Syst 77:399–408CrossRefPubMedGoogle Scholar
  24. Peakall R, Smouse P (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  25. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287PubMedGoogle Scholar
  26. Pomeranz Y (1983) Buckwheat: structure, composition, and utilization. Crit Rev Food Sci Nutr 19:213–258CrossRefPubMedGoogle Scholar
  27. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, New YorkGoogle Scholar
  28. Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. TAG Theoret Appl Genet 109:783–791CrossRefGoogle Scholar
  29. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234CrossRefPubMedGoogle Scholar
  30. Sharma T, Jana S (2002) Species relationships in Fagopyrum revealed by PCR-based DNA fingerprinting. TAG Theoret Appl Genet 105:306–312CrossRefGoogle Scholar
  31. Stajner N, Jakse J, Kozjak P, Javornik B (2005) The isolation and characterisation of microsatellites in hop (Humulus lupulus L.). Plant Sci 168:213–221CrossRefGoogle Scholar
  32. Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. TAG Theoret Appl Genet 111:723–730CrossRefGoogle Scholar
  33. Suvorova GN, Fesenko NN, Kostrubin MM (1994) Obtaining of interspecific buckwheat hybrid (Fagopyrum esculentum Moench × Fagopyrum cymosum Meissn.). Fagopyrum 14:13–16Google Scholar
  34. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci 98:9161–9166CrossRefPubMedGoogle Scholar
  35. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55CrossRefPubMedGoogle Scholar
  36. Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WD, Smith JSC, Doebley J (2002) Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19:1251–1260PubMedGoogle Scholar
  37. Wang Y, Scarth R, Campbell GC (2005) Inheritance of seed shattering in interspecific hybrids between Fagopyrum esculentum and F. homotropicum. Crop Sci 45:693–697CrossRefGoogle Scholar
  38. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388PubMedGoogle Scholar
  39. Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer, SunderlandGoogle Scholar
  40. Yap IV, Nelson RJ (1996) Winboot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI Discussion Paper series 14, International Rice Research Institute, Manila, Philippines. http://www.irri.org/science/software/winboot.asp
  41. Yasui Y, Ohnishi O (1996) Comparative study of rbcL gene sequences in Fagopyrum and related taxa. Genes Genet Syst 71:219–224CrossRefPubMedGoogle Scholar
  42. Yasui Y, Ohnishi O (1998a) Interspecific relationships in Fagopyrum (Polygonaceae) revealed by the nucleotide sequences of the rbcL and accD genes and their intergenic region. Am J Bot 85:1134 1134CrossRefGoogle Scholar
  43. Yasui Y, Ohnishi O (1998b) Phylogenetic relationships among Fagopyrum species revealed by the nucleotide sequences of the ITS region of the nuclear rRNA gene. Genes Genet Syst 73:201–210CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Kyung-Ho Ma
    • 1
  • Nam-Soo Kim
    • 2
  • Gi-An Lee
    • 1
  • Sok-Young Lee
    • 1
  • Ju Kyong Lee
    • 3
  • Jung Yoon Yi
    • 1
  • Yong-Jin Park
    • 4
  • Tae-San Kim
    • 1
  • Jae-Gyun Gwag
    • 1
  • Soon-Jae Kwon
    • 1
    Email author
  1. 1.National Agrobiodiversity CenterNational Academy of Agricultural ScienceSuwonKorea
  2. 2.College of Biosciences and BiotechnologyKangwon National UniversityChuncheonKorea
  3. 3.College of Agriculture and Life SciencesKangwon National UniversityChuncheonKorea
  4. 4.Department of Plant ResourcesKongju National UniversityYesanKorea

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