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Abstract
BackgroundCultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits.ResultsWe discovered 29 SNPs located on ten different chromosomes that are significantly associated with the seven seed composition traits in our wild soybean sample. Eight SNPs co-localized with QTLs previously uncovered in linkage or association mapping studies conducted with cultivated soybean samples, while the remaining SNPs appeared to be in novel locations. Twenty-four of the SNPs significantly associated with fatty acid variation, with the majority located on chromosomes 14 (6 SNPs) and seven (8 SNPs). Two SNPs were common for two or more fatty acids, suggesting loci with pleiotropic effects. We also identified some candidate genes that are involved in fatty acid metabolism and regulation. For each of the seven traits, most of the SNPs produced differences between the average phenotypic values of the two homozygotes of about one-half standard deviation and contributed over 3% of their total variability.ConclusionsThis is the first GWA study conducted on seed composition traits solely in wild soybean populations, and a number of QTLs were found that have not been previously discovered. Some of these may be useful to breeders who select for increased protein/oil content or altered fatty acid ratios in the seeds. The results also provide additional insight into the genetic architecture of these traits in a large sample of wild soybean, and suggest some new candidate genes whose molecular effects on these traits need to be further studied.
Highlights
Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil
One-way ANOVAs showed that mean protein levels did not significantly differ between seeds originating in Japan versus those from South Korea (P = 0.19), but mean levels of oil and all five fatty acids did exhibit significant differences (P < 0.05)
As computer and statistical techniques for the detection of epistasis in these studies evolve, we predict that these effects will explain some of the hidden genetic variability in many traits, including those we have analyzed in wild soybeans. This genome-wide association (GWA) study is the first conducted on seed composition traits measured solely in a wild soybean population, and revealed a number of QTLs that have not been previously discovered
Summary
Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Much of our genetic knowledge has come from discovery of quantitative trait loci (QTLs) located at various sites on all of the 20 chromosomes throughout the soybean genome that affect one or more of these traits [5, 6, 8,9,10] Many of these QTLs were discovered through linkage mapping that requires F2, backcross, or recombinant inbred populations derived from original biparental crosses. These large genomic regions may contain many underlying genes, making the search for putative candidates difficult
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