Single- and multiple-trait quantitative trait locus analyses for seed oil and protein contents of soybean populations with advanced breeding line background.

Unlabelled: Soybean seed oil and protein contents are negatively correlated, posing challenges to enhance both traits simultaneously. Previous studies have identified numerous oil and protein QTLs via single-trait QTL analysis. Multiple-trait QTL methods were shown to be superior but have not been applied to seed oil and protein contents. Our study aimed to evaluate the effectiveness of single- and multiple-trait multiple interval mapping (ST-MIM and MT-MIM, respectively) for these traits using three recombinant inbred line populations from advanced breeding line crosses tested in four environments. Using original and simulated data, we found that MT-MIM did not outperform ST-MIM for our traits with high heritability (H > 0.84). Empirically, MT-MIM confirmed only five out of the seven QTLs detected by ST-MIM, indicating single-trait analysis was sufficient for these traits. All QTLs exerted opposite effects on oil and protein contents with varying protein-to-oil additive effect ratios (-0.4 to -4.8). We calculated the economic impact of the allelic variations via estimated processed values (EPV) using the National Oilseed Processors Association (NOPA) and High Yield + Quality (HY + Q) methods. Oil-increasing alleles had positive effects on both EPV and EPV when the protein-to-oil ratio was low (-0.4 to -0.7). However, when the ratio was high (-4.1 to -4.8), oil-increasing alleles increased EPV and decreased EPV, which penalizes low protein meal. In conclusion, single-trait QTL analysis is adequately effective for high heritability traits like seed oil and protein contents. Additionally, the populations' elite pedigrees and varying protein-to-oil ratios provide potential lines for further yield assessment and direct integration into breeding programs.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01489-2.