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United States Department of Agriculture

Agricultural Research Service

Title: Linkage Disequilbrium and Association Analysis for Qtl Discovery

Authors
item Cregan, P - ARS BELTSVILLE MD
item Zhu, Y - ARS BELTSVILLE MD
item Song, Q - ARS BELTSVILLE MD
item Hofmann, N - ARS BELTSVILLE MD
item Yaklich, R - ARS BELTSVILLE MD
item Specht, J - U NEBRASKA-LINCOLN
item Nelson, Randall

Submitted to: Cellular and Molecular Biology of Soybean Biennial Conference
Publication Type: Proceedings
Publication Acceptance Date: August 31, 2002
Publication Date: August 20, 2002
Citation: CREGAN, P.B., ZHU, Y.L., SONG, Q.J., HOFMANN, N.E., YAKLICH, R.W., SPECHT, J.E., NELSON, R.L. LINKAGE DISEQUILBRIUM AND ASSOCIATION ANALYSIS FOR QTL DISCOVERY. CELLULAR AND MOLECULAR BIOLOGY OF SOYBEAN BIENNIAL CONFERENCE. 2002. p. 106.

Technical Abstract: Sequence and haplotype diversities as well as the level of linkage disequilibrium (LD) are important considerations for assessing the likelihood of successfully applying association analysis for QTL or gene discovery. In its simplest form association analysis (originally proposed by Risch and Merikangas, Science 273:1516) compares DNA marker allele frequency across the genomes of two groups of individuals with contrasting phenotypes. Those regions in the genome at which significant marker allele frequency differences are detected between the two groups would putatively contain genes controlling phenotypes. The virtue of such an approach to QTL or gene discovery is that a formal population structure is not required. In addition, extensive sets of phenotypic data are already available on large numbers of genotypes in germplasm collections. In an attempt to define sequence and haplotype variation in soybean 46607 bp of DNA (17010 bp coding, 6247 bp UTR, 1686 bp intron, 6764 bp genomic sequence) was sequenced in each of 18 North American ancestral cultivars; 52 diverse G. Max accessions from Asia; 24 cultivars representative of currently grown North American soybeans; as well as 24 diverse G. Soja genotypes from Asia. Eighty-four fragments averaging 555 bp in length and derived from 73 genes and 11 genomic fragments were included in the analysis that discovered 471 SNPs. The mean nucleotide diversity (theta symbol) was very similar in the North American ancestral cultivars and Asian G. max genotypes (theta symbol equals 0.00135 and 0.00130, respectively). Somewhat less variability was present in modern cultivars (theta symbol equals 0.00092). In contrast, the corresponding value in G. Soja indicated a level of diversity (theta symbol equals 0.00246) which was approximately twice as high as that of cultivated soybeans. An analysis of LD in a 10 centiMorgan region on linkage group G showed a very significant decline suggesting that like in Arabidopsis, another autogamous species, LD decays over distances that are sufficiently short to permit successful association analysis. In order to test this possibility, we have undertaken a study to compare association analysis with classical QTL analysis. Seed size which is an easily measured quantitative variable will be determined in a set of large (less than 25 g/100seeds) vs. small (greater than 8 g/100 seeds) seeded germplasm accessions and will also be determined in progeny of a large x small-seeded genotypes. The genomes of all individuals will be scanned using SNPs. SNP loci with significant allele frequency differences between the large vs. small germplasm lines will suggest the presence of seed size QTL. These will be compared with QTL discovered by standard QTL analysis of progeny from the large x small seeded-cross.

Last Modified: 10/25/2014