A genome-wide association study of seed composition traits in wild soybean (Glycine soja)

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3397-4) contains supplementary material, which is available to authorized users.

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

“…3 decreased to half of its highest value at 7.5 kb when LD was calculated for the whole genome. Because LD in wild soybean was lower than in domesticated soybean, Leamy et al (2017) suggested that more QTLs would be found if more markers were used in wild soybean populations. This value is lower than that in wild soybean population in the studies of Zhou et al (2015) and Leamy et al (2017) (27 and >100 kb, respectively).…”

“…This process increases the cost of oil and produces trans fats, which are associated with increased risk of heart disease, stroke, and diabetes (Mozaffarian and Rimm, 2006). Even so, only one recent study examined the phenotypic variation of primarily Korean and Japanese wild soybean seed compositions for protein, oil, and five fatty acids from the USDA G. soja collection (Leamy et al, 2017). Therefore, two of the goals of soybean breeding to improve oil quality are (i) to reduce the content of linolenic acid and (ii) to increase the content of oleic acid (Lee et al, 2007;Yoon et al, 2009).…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Resequencing of 28 Brazilian soybean cultivars suggested that, despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity (Maldonado dos Santos et al, 2016). In recent years, genotyping by sequencing, skim sequencing, diversity array technology (DArT)-seq and restriction site associated DNA sequencing approaches were also employed for developing high density genetic maps, refining the QTL mapping and identifying trait linked markers in legumes Kale et al, 2015;Contreras-Soto et al, 2017;Leamy et al, 2017;Valdisser et al, 2017). Nevertheless, the percentage of missing data points and the SNP calling rates greatly reduce the number of final SNPs for different studies and this has been a concern.…”

Genome-wide association for mapping QTLs linked to protein and oil contents in soybean

“…The QTL of chromosome 2 was also detected by Zhang et al (2004). Leamy et al (2017), in turn, found QTLs on chromosome 3 and 20 in wild soybean. Although none of these QTLs were observed in the present study, the eight QTLs identified were located in regions that have QTLs mapped for oil and fatty acid contents in the consensus map (USDA, 2016).…”

“…In Brazil, Soares et al (2008) detected QTLs on chromosomes 3, 6, 15, 18, and 19, explaining from 38.84 to 55.53% of the variation in protein content in soybean, depending on the cultivation site. QTLs for protein content in soybean have also been found on chromosome 20 (Chung et al, 2003;Nichols et al, 2006), chromosome 18 (Panthee Leamy et al, 2017), and chromosome 14 (Zhang et al, 2004;Leamy et al, 2017 None of the assessed varieties had alleles associated with high or low protein contents on all of the seven markers. The ten varieties with the highest protein content had 4-6 loci with alleles associated with high protein content on the seven markers considered.…”