Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed

Abstract

Soybean [Glycine max (L.) Merr.] is a valuable and nutritious crop in part due to the high protein meal and vegetable oil produced from its seed. Soybean producers desire cultivars with both elevated seed protein and oil concentrations as well as specific amino acid and fatty acid profiles. Numerous studies have identified quantitative trait loci (QTLs) associated with seed composition traits, but validation of these QTLs has rarely been carried out. In this study, we have collected information, including genetic location and additive effects, on each QTL for seed contents of protein and oil, as well as amino acid and fatty acid compositions from over 80 studies. Using BioMercator V. 4.2, a meta-QTL analysis was performed with genetic information comprised of 175 QTLs for protein, 205 QTLs for oil, 156 QTLs for amino acids, and 113 QTLs for fatty acids. A total of 55 meta-QTL for seed composition were detected on 6 out of 20 chromosomes. Meta-QTL possessed narrower confidence intervals than the original QTL and candidate genes were identified within each meta-QTL. These candidate genes elucidate potential natural genetic variation in genes contributing to protein and oil biosynthesis and accumulation, providing meaningful information to further soybean breeding programs.

Keywords: amino acids; fatty acids; meta-analysis; oil; protein; quantitative trait loci; soybean.

Figure 1

Comparisons among protein, oil, protein+oil and protein+Cys+Met meta-quantitative trait loci (meta-QTLs) on Chromosome (Chr) 20 (Linkage group I; LG I). Projected QTL are displayed to the left of Chr 20 for each trait or trait combination. A 95% of confidence interval of each meta-QTL is represented as filled colors on the chromosome arm, with four, five, four and four meta-QTLs identified for protein, oil, protein+oil and protein+Cys+Met, respectively. A detailed view of the projected QTL contributing to each meta-QTL cluster #2 of Chr 20 (Table 1) are also shown on the right of the chromosome. In the detailed view, each bar represents a projected QTL and is color-coded for each trait (protein, khaki; oil, red; cysteine, green; and methionine, blue).

Figure 2

Overview of metabolic processes involved by positional and functional candidate genes. Candidate genes names from Glyma.Wm82.a2.v1 (Gmax2.0) (available online: http://soybase.org) are shown in bold and color-coded by chromosomes.