Seed coat cracking (SCC) is a major factor that affects seed appearance quality, pathogen infection, humility absorption and seed storage in soybean. In view of this, a recombinant inbred line (RIL) population and a natural population were genotyped by SoySNP6K and were evaluated for type-I SCC percentage. Eight QTLs were identified on six chromosomes with phenotypic variation explanations ranging from 3.46% to 34.71% in RIL population. Twenty-three SNPs associated with cracking percentage were identified on eight chromosomes in natural population. More importantly, the association SNP ss715593768 in natural population was the left marker of qSCC-C2-1 in RIL population, which were detected across all of the environments and BLUP values. Two genes, Glyma.06G197300 and Glyma.06G202100, were proposed in this QTL region. These two genes showed differential expressions at seed developmental stages between RIL parents in the seed transcriptome sequencing and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, and also showed differential expressions between two germplasms with different cracking percentage in natural population. Thus, the results provide novel insight into the genetic basis and molecular improvement of SCC in soybean.
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, α‐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.
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