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Title: DETECTING THE EXTENT OF POPULATION STRATIFICATION IN A SOYBEAN POPULATION FOR USE IN A CASE-CONTROL ASSOCIATION ANALYSIS

Author
item Hofmann, Nicolle
item SONG, QIJIANG - UNIVERSITY OF MARYLAND
item SPECHT, JAMES - UNIVERSITY OF NEBRASKA
item Yaklich, Robert
item Cregan, Perry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/5/2005
Publication Date: 3/5/2005
Citation: Hofmann, N.E., Song, Q., Specht, J., Yaklich, R.W., Cregan, P.B. 2005. Detecting the extent of population stratification in a soybean population for use in a case-control association analysis. Meeting Abstract. Plant & Animal Genome XIII Abstract. P448.

Interpretive Summary:

Technical Abstract: Identifying genetic factors controlling complex traits has been and continues to be a challenge in human as well as in plant and animal genetics. Association analysis is an approach that has been proposed to increase the efficiency of discovery of quantitative trait loci underlying complex traits. One study design being tested is case-control genetic association analysis. A case-control study compares marker allele frequencies among a case group and a control group from an existing population. A difference in allele frequency is an indication that the marker is linked with the gene affecting the trait of interest. If the genetic background of the case and control group are not well matched spurious associations between a phenotype and an unlinked marker may be identified as a result of population stratification. There have been several statistical methods proposed, such as genomic control and structure association which use a set of unlinked markers to estimate the degree of stratification and to adjust for population structure. To determine population stratification among soybean germplasm, a total of 380 genotypes from populations of Chinese, Japanese, and elite US cultivars; US ancestral cultivars as well as a large set of unimproved germplasm lines was assayed with a set of 48 simple sequence repeat (SSR) markers distributed throughout the genome. These data will be used to determine the presence of population stratification and if necessary to reduce or eliminate spurious associations with quantitative traits including seed size and maturity.