Genetic loci and candidate genes with pleiotropic effects for tofu and soymilk weights across multiple environments in soybean (Glycine max)

Soybean provides large amounts of protein for human, and the most popular consumption pattern is tofu and soymilk. Recently, the demand of tofu and soymilk is increased, and the breeding of special variety becomes very urgent. To illustrate the genetic basis of these traits, 269 accessions were evaluated under six environments, and 32 associated SNPs were identified on nine chromosomes across multiple environments or conferring diverse traits. Of these SNPs, 16 were demonstrated by BLUP values. Seven adjacent-SNPs were first identified to associate with tofu and soymilk weights in an 1.02-Mb region on chromosome 8, which were verified by BLUP-values. Meanwhile, four neighbouring SNPs in a 0.32-Mb region on chromosome 12 were first identified to associate with these traits across multiple environments, of which three were detected in BLUP values. Furthermore, some candidate genes, that is, alpha-glucan water dikinase Glyma.08G283700 and E3 SUMO-protein ligase Glyma.12G071300, were screened out with differential expressions between the high- and low-tofu/soymilk-output accessions. Thus, these associated SNPs and candidate genes provide new insight into the genetic basis of tofu and soymilk processing quality in soybean.

Automated summary

Through evaluating the performance of 269 different accessions under six environments, 32 associated SNPs were identified on nine chromosomes that are correlated with the weight of tofu and soymilk. Among them, 7 adjacent-SNPs were identified for the first time in a 1.02-Mb region on chromosome 8, and 4 neighboring SNPs were first found in a 0.32-Mb region on chromosome 12, all showing associations with these traits across multiple environments. In addition, some candidate genes, including alpha-glucan water dikinase Glyma.08G283700 and E3 SUMO-protein ligase Glyma.12G071300, were screened out based on differential expressions between high- and low-tofu/soymilk-output accessions. Thus, these associated SNPs and candidate genes provide new insights into the genetic basis of tofu and soymilk processing quality in soybean.