GENETIC DIVERSITY AND LINKAGE DISEQUILIBRIUM IN WILD SOYBEAN, LANDRACES, ANCESTRAL, AND ELITE SOYBEAN POPULATIONS
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Domestication, founder effects, and artificial selection can impact populations by reducing genome diversity and increasing the extent of linkage disequilibrium (LD). To understand the impact of these genetic bottlenecks and selection on sequence diversity and LD within soybean [Glycine max (L.) Merr.], 111 genes and three chromosomal regions located on linkage groups A2, G, and J were characterized in soybean. Four soybean populations were evaluated: 1) the wild ancestor of soybean (G. soja), 2) the population resulting from domestication (landraces), 3) Asian introductions from which North American cultivars were developed (ancestors), and 4) elite cultivars from the 1980's (elite). A total of 438 single nucleotide polymorphisms (SNPs) and 58 insertions-deletions were discovered within the 102 genes. Sequence diversity was lower than expected in G. soja with an overall theta equal to 0.00235, and was less than half that value (theta = 0.00115) in the landraces. Domestication eliminated most unique haplotypes with G. soja containing 240 unique haplotypes while the landraces only contained 42 unique haplotypes. The founder effect of the introduction of soybean to North America followed by intensive artificial selection, resulted in only a 30% decrease in nucleotide diversity. A total of 738 SNPs were discovered and genotyped in the four populations throughout three chromosomal regions. In G. soja LD did not extend past 100 kb while in the three cultivated soybean populations LD extended from 90 kb up to 600+ kb, most likely as a result of increased inbreeding and domestication. The three chromosomal regions varied in the extent of LD within the populations. G. soja is the greatest resource for unique alleles and may be best suited for fine mapping utilizing association analysis. The landraces do not contain much more variability than the elite cultivars but may have enough diversity to facilitate genetic improvement of elite cultivars. Finally, due to the extended levels of LD in the landraces and the elite cultivars, whole genome association analysis may be possible for the discovery of QTL.