Abstract
BackgroundSoybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean.ResultsIn this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20–1 and qSPC_20–2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20–1 and qSPC_20–2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait.ConclusionsThese results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.
Highlights
Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil
16,546 homologous single nucleotide polymorphism (SNP) markers showing the expected segregation 1:1 ratio in the recombinant inbred lines (RILs) population were used for genetic linkage analysis and linkage map construction using the MPR method (Fig. 2a)
Our experiments identified nine most promising differentially expressed genes (DEGs) with the significant differences in major quantitative trait loci (QTL) regions by RNA sequencing (RNA-seq) analysis, and nine DEGs were further screened by qRT-PCR and cloning and sequencing analysis
Summary
Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean. There is a wide variation of seed protein content (SPC) in soybean. While increasing SPC of soybean cultivars has been a major objective of many soybean breeding programs for decades, the strong negative correlations of SPC with seed oil content and seed yield improve three traits simultaneously a challenging task using conventional breeding [2,3,4]. In cultivar development, breeders generally select for the best seed yield potential with little attention to seed protein or oil content [5].
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