Euphytica

, Volume 162, Issue 2, pp 179–191

Association analysis using SSR markers to find QTL for seed protein content in soybean

  • Tae-Hwan Jun
  • Kyujung Van
  • Moon Young Kim
  • Suk-Ha Lee
  • David R. Walker
Article

DOI: 10.1007/s10681-007-9491-6

Cite this article as:
Jun, T., Van, K., Kim, M.Y. et al. Euphytica (2008) 162: 179. doi:10.1007/s10681-007-9491-6

Abstract

Association analysis studies can be used to test for associations between molecular markers and quantitative trait loci (QTL). In this study, a genome-wide scan was performed using 150 simple sequence repeat (SSR) markers to identify QTL associated with seed protein content in soybean. The initial mapping population consisted of two subpopulations of 48 germplasm accessions each, with high or low protein levels based on data from the USDA’s Germplasm Resources Information Network website. Intrachromosomal LD extended up to 50 cM with r2 > 0.1 and 10 cM with r2 > 0.2 across the accessions. An association map consisting of 150 markers was constructed on the basis of differences in allele frequency distributions between the two subpopulations. Eleven putative QTL were identified on the basis of highly significant markers. Nine of these are in regions where protein QTL have been mapped, but the genomic regions containing Satt431 on LG J and Satt551 on LG M have not been reported in previous linkage mapping studies. Furthermore, these new putative protein QTL do not map near any QTL known to affect maturity. Since biased population structure was known to exist in the original association analysis population, association analyses were also conducted on two similar but independent confirmation populations. Satt431 and Satt551 were also significant in those analyses. These results suggest that our association analysis approach could be a useful alternative to linkage mapping for the identification of unreported regions of the soybean genome containing putative QTL.

Keywords

Association mappingGlycine maxLinkage disequilibrium (LD)Population structureQuantitative trait loci (QTL)Seed protein contentSimple sequence repeat (SSR)

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Tae-Hwan Jun
    • 1
  • Kyujung Van
    • 1
  • Moon Young Kim
    • 1
    • 2
  • Suk-Ha Lee
    • 1
  • David R. Walker
    • 3
  1. 1.Department of Plant ScienceSeoul National UniversitySeoulThe Republic of Korea
  2. 2.Research Institute for Agriculture and Life SciencesSeoul National UniversitySeoulThe Republic of Korea
  3. 3.Soybean/Maize Germplasm, Pathology, and Genetics Research UnitUSDA-ARS, 232 National Soybean Research CenterUrbanaUSA