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Tocopherol (Toc) occurs in soybean seeds and is extracted together with the soybean oil. Toc is utilized as an antioxidant in food and an additive in animal feed. A total of 180 representative accessions and 144 recombinant inbred lines (RILs) from the cross of 'Hefeng 25' and 'OAC Bayfield' were selected to evaluate individuals and total Toc concentrations in soybean seeds. The 180 soybean samples were sequenced by the approach of Specific Locus Amplified Fragment Sequencing (SLAF-seq). A total of 22,611 single nucleotide polymorphisms (SNPs) were developed. Nineteen quantitative trait nucleotides (QTNs) were identified associated with individual or total-Toc based on genome-wide association analysis (GWAS). Among them, three QTNs located near known QTLs, and 16 were novel. Eighteen QTLs and nine eQTLs were also detected by linkage mapping. The QTN rs9337368 on Chr.02 was colocalized according to the linkage mapping of the RILs and genome-wide association analysis and regarded as a stable locus for mining the candidate genes in association with Toc. A total of 42 candidate genes near the 200 kbp flanking region of this identified locus were found. Upon a gene-based association, 11 SNPs from five genes out of the 42 candidates were detected. Expression level analysis of five candidate genes revealed that two genes were significantly related to Toc content. The identified loci, along with the candidate genes, might be valuable for increasing the Toc concentration in soybean seeds and improving the nutritional value of soybean oil. [ABSTRACT FROM AUTHOR]

Saturated fatty acids (FA), an important component of soybean oil, plays a crucial role in the nutritional value of soybean oil through different concentration and relative proportions. In this study, an association population of 185 diverse soybean accessions was used to identify quantitative trait nucleotide (QTN) and scan candidate genes via genome‐wide association analysis (GWAS), which was based on high throughout single‐nucleotide polymorphisms (SNPs) developed via the Specific Locus Amplified Fragment Sequencing (SLAF‐seq) approach. A total of 33,149 SNPs were identified with minor allele frequencies (MAF) >4%, which covered 97% of the soybean whole genome. For the two saturated FA concentration, including palmitic acid (PA) and stearic acid (SA), up to 65 SNPs were verified via GWAS. Among them, 35 and 16 SNPs loci were the novel loci for PA and SA, respectively. There were other six loci for PA and eight loci for SA overlapped or located in the linked genomic regions reported by the previous study. Furthermore, many loci were repeated in more than two environments, and four pair of pleiotropic loci (PA‐3‐2 and SA‐3‐2, PA‐11‐2 and SA‐11‐1, PA‐12‐2 and SA‐12‐1, and PA‐17‐1 and SA‐17‐2) had similar genomic regions, which might control both PA and SA simultaneously. A total of 49 genes, which could participate in lipid biosynthesis pathway or hormone metabolism, were identified as the potential candidate genes associated with saturated FA. The identified loci with beneficial alleles and the candidate genes would be valuable for studying the molecular mechanisms of saturated FA and further for improving nutritional value of soybean oil. [ABSTRACT FROM AUTHOR]

Sclerotinia stem rot (SSR) is a disease of soybean [ Glycine max (L.) Merr] that causes severe yield losses. We studied 185 representative soybean accessions to evaluate partial SSR resistance and sequenced these by the specific-locus amplified fragment sequencing method. In total, 22,048 single-nucleotide polymorphisms (SNPs), with minor allele frequencies (MAF) ≥5% and missing data <3%, were developed and applied to genome-wide association study of SSR responsiveness and assess linkage disequilibrium (LD) level for candidate gene selection. We identified 18 association signals related to SSR partial resistance. Among them, six overlapped the regions of previous quantitative trait loci, and twelve were novel. We identified 243 candidate genes located in the 200 kb genomic region of these peak SNPs. Based on quantitative real-time polymerase chain reaction and haplotype analysis, Glyma.03G196000 and Glyma.20G095100 , encoding pentatricopeptide repeat proteins, might be important factors in the resistance response of soybean to SSR. • Sclerotinia stem rot is a destructive disease, causing severe soybean yield losses • 18 loci associated with partial resistance to SSR were identified based on GWAS • Beneficial alleles and genes might be helpful to analyze SSR genetic resistance [ABSTRACT FROM AUTHOR]

• Screening for excellent soybean germplasms with high tocopherol concentration. • The genetic structure of the Toc concentration of the test sample was identified. • Haplotypes significantly associated with tocopherol concentration were detected. • Glyma.17G061900 may regulate tocopherol concentration in soybean seeds. Tocopherol (Toc) in soybean seeds has value for foods, medicines, cosmetics, and animal husbandry. Soybean breeders and soybean-derived food industries have thus focused on breeding new soybean cultivars with higher seed Toc content. In this study, an association panel consisting of 180 diverse soybean accessions were used to detect quantitative trait nucleotides (QTNs) and scan possible candidate genes based on genome-wide association analysis (GWAS) and high-throughput single-nucleotide polymorphisms (SNP). Approximately 22,611 SNPs were identified using the specific locus amplified fragment sequencing (SLAF-seq) approach and based on minor allele frequencies (MAFs) > 5 %, which spanned 84.10 % of the soybean whole genome. For the three individuals including α-tocopherol (α-Toc), γ- tocopherol (γ-Toc), δ- tocopherol (δ -Toc), and total tocopherol (total Toc) levels, a total of 18 quantitative trait nucleotides (QTNs) distributed on the 18 genomic regions of 10 chromosomes were verified via GWAS. Seven QTNs (rs55811336, rs7975863, rs37094897, rs7097743, rs17125409, rs330000, and rs4730199) could be identified in more than three environments, and the other eleven could be identified in least two environments. A total of 6, 8, 4, and 10 QTNs were novel loci for α-Toc, γ-Toc, δ-Toc, and total Toc, respectively. Nine QTNs (rs37505279, rs37686178, rs36359429, rs6898494, rs7097743, rs17125409, rs10200201, rs21080726, and rs5680781) were associated with more than one Toc component. A total of 216 candidate genes near the 200-kb flanking region of these identified QTNs were identified as potential candidate genes associated with soybean seed Toc levels. Of these genes, Glyma.17G061900 (located near QTN rs4730199 on Chr.17), a homogentisate phytyltransferase 1 that catalytic homogentisate to 2-methyl-6-phyl-1,4-benzoquinol in Toc biosynthesis, was detected through association analysis, haplotype analysis, and expression pattern analysis. The identified QTNs with beneficial alleles and the candidate genes would be valuable for improving Toc levels in soybean seeds and improving the nutritional value of soybean oil. [ABSTRACT FROM AUTHOR]