Mining QTLs and candidate genes for seed protein and oil contents across multiple environments and backgrounds in soybean.

Soybean is important due to its seed protein and oil, but its seed protein and oil contents need to be improved. In view of this, two genetically related F6:7 recombinant inbred line (RIL) populations, derived from Zheng92116×Qihuang30 (ZQ) and Zheng92116× Liaodou14 (ZL), were genotyped with a SoySNP 6K chip and evaluated for seed protein and oil contents in four different environments. In total, ten stable collocating or overlapping additive QTL clusters, which explained 2.6~23.3% of the phenotypic variation, were identified in the ZQ population in different environments, four of which were further verified in the ZL population. One major and stable QTL controlling seed oil content, qOIL-A1, was detected in all four environments in ZQ and was validated in three environments in the ZL population, with the PVE (phenotypic variation explained) ranging from 4.8 to 22.1% and four of the PVE values exceeding 10% (22.1%, 19.3%, 10.9%, and 12.9%). Another major and stable QTL controlling seed protein content, qPRO-J, was detected in different environments in ZQ and was further verified in the ZL population, with a PVE of 14.1% and 23.2% in ZQ and a PVE of 9.5% in ZL. Moreover, the individuals in the RIL population and another cultivar-based population (320 varieties and landraces) with different genotypes at the common flanking markers for the QTL clusters showed extremely significantly different protein and oil contents, which further validated the QTL mapping results. Based on these findings, eight novel candidate genes with very different expression levels at different soybean seed growth and developmental stages between ZQ and ZL RIL parents were identified in the qOIL-A1 region through transcriptome sequencing and were finally verified by real-time qPCR. Thus, these stable QTL clusters can be applied in marker-assisted selection breeding or map-based candidate gene cloning in soybean for seed protein and oil genetic improvements in the future. [ABSTRACT FROM AUTHOR]