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Title: LINKAGE DISEQUILIBRIUM IN FOUR SOYBEAN POPULATIONS

Author
item Hyten, David
item SONG, QIJIAN - UNIVERSITY OF MARYLAND
item COSTA, JOSE - UNIVERSITY OF MARYLAND
item Cregan, Perry

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: 3/20/2003
Publication Date: 3/20/2003
Citation: Hyten, D.L., Song, Q., Costa, J., Cregan, P.B. 2003. Linkage disequilibrium in four soybean populations [abstract]. BARC Poster Day. Abstract 14.

Interpretive Summary:

Technical Abstract: Linkage disequilibrium (LD) is the "non-random association of alleles" in a population. Estimation of LD is important because it can be utilized through association analysis to discover quantitative trait loci (QTL). The effectiveness of association analysis depends on the structure and the extent of LD in the population. If a population has extensive LD, few markers will be needed to scan the whole genome for QTL but the positions of these QTL will not be well defined. Conversely, in a population with limited LD, genetic factors can be fine mapped. Studies on the extent and structure of LD in plants have been limited and it is unclear how the extent of LD is affected by domestication and selection and whether a block-like structure exists in plants. Soybean [Glycine max (L.) Merr.] is an autogamous plant species that has undergone domestication and selection which may have affected the extent of LD. Our goal was to provide an initial assessment of LD in four distinct soybean populations, which represent pre-domestication, post-domestication, and selected populations. The four populations include Glycine soja, the wild soybean, Asian Glycine max, N. Am. cultivar ancestors, and N. Am. public cultivars released in the 1980s. Multiple fragments throughout a 500-kb region were sequenced and genotyped. The domesticated Asian Glycine max population LD did not decline along the 500-kb fragment while the wild Glycine soja population had extensive LD decline with LD blocks averaging 12-kb in length. The N. Am ancestor population was selected from Asian Glycine max accessions and demonstrates similar levels of LD as the Asian Glycine max population. The N. Am ancestors have contributed to 86% of the germplasm pool from which the N. Am. elite public cultivars were developed through artificial hybridization and intensive selection for agronomically favorable traits such as yield. In this study the elite cultivars had more rapid LD decline than the N. Am ancestor population but more extensive LD than the Glycine soja population. The structure of LD in the elite cultivars forms two distinct LD blocks with a low multilocus D´ between the two blocks suggesting historical recombination between the two blocks. The four populations all differed in their degree of LD decline. These differences in LD could make genetic association analysis feasible including whole genome scans in populations similar to the Asian Glycine max and the N. Am. Ancestor populations while fine mapping of genetic factors may be possible in G. soja given the lower level of LD.