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United States Department of Agriculture

Agricultural Research Service

Title: Sequence Variation, Haplotype Diversity and Linkage Disequilibrium in Cultivated and Wild Soybean

Authors
item Cregan, Perry
item Nelson, Randall
item Zhu, Youlin - CHINA
item Song, Qijian - CHINA

Submitted to: International Conference on Legume Genomics and Genetics
Publication Type: Abstract Only
Publication Acceptance Date: May 23, 2002
Publication Date: N/A

Technical Abstract: Sequence and haplotype diversity and linkage disequilibrium (LD) are important in assessing approaches to genome manipulation. A total of 46607 bp of DNA was sequenced in each of 18 ancestral cultivars of N. Am. soybean; 52 diverse G. max accessions from Asia; 24 cultivars representative of currently grown N. Am. soybean; as well as 24 diverse G. soja genotypes from Asia. Ninety fragments averaging 518 bp in length and derived from 80 genes were included in the analysis that discovered 471 SNPs. The mean nucleotide diversity (ND) was very similar in the N. American and Asian G. max genotypes (ND = 0.0012 and 0.0011, respectively). In contrast, the corresponding value in G. soja indicated twice the level of diversity of (ND = 0.0022). Haplotype analysis indicated a severe deficiency of haplotypes versus what would be anticipated at linkage equilibrium. The mean number of haplotypes/fragment was similar in the N. Am. ancestors and Asian G. max genotypes, 2.0 and 2.5 , respectively. Twice the number of haplotypes/fragment were found in wild soybean further indicating the greater genetic variability in G. soja. LD was assayed in one 12 cM region and 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.

Last Modified: 10/24/2014
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