Soybean ( Glycine max L.) is an important food and oil crop widely planted by intercropping in southwest China. The shade caused by intercropping changes plant growth traits, such as soybean leaf and dry mass, thereby reducing yields. To improve the yield and elucidate the genetic mechanism of the leaf-related traits in intercropped soybeans, we measured the F 6:7–8 recombinant inbred lines (RILs) derived from the cross of ‘Nandou 12’ and ‘Jiuyuehuang’ for six leaf-related traits under monoculture and relay intercropping in 2015 and 2016. We found 6366 single-nucleotide polymorphisms (SNPs) markers that covered the whole genome of soybean distributed in 20 linkage groups, which spanned 2818.67 cM with an average interval of 0.44 cM between adjacent markers. Nineteen quantitative trait loci (QTLs) were detected in two environments in 2 years. Three candidate genes associated to leaf-related traits were found according to gene expression and GO enrichment analyses. These results revealed the susceptibility of leaf phenotype to shading and helped elucidate the mechanisms that control leaf-related traits.

The relative contents of glycinin and β-conglycinin from storage protein are closely related to the quality and function of soybean seeds. However, it is not clear whether or how glycinin and β-conglycinin contents change in maize-soybean strip intercropping system. The glycinin and β-conglycinin relative contents of the recombinant inbred lines (RILs) derived from the cross of 'Nandou 12' and 'Jiuyuehuang' were measured under different environments (E1: 2017, Renshou; E2: 2017, Ya'an; E3: 2016, Renshou) and planting patterns (M: monoculture; RI: relay intercropping), among which the differences were significant or extremely significant in parents and RILs. Based on a genetic linkage map with 6366 SNP markers, we detected ten QTLs for glycinin and β-conglycinin relative contents which were distributed in nine linkage groups with the phenotypic variation of 5.63%-9.68%. According to the soybean genomic information, 65 candidate genes were screened in the region of above-mentioned QTLs. These results lay a theoretical foundation for soybean quality breeding.