Isoflavone, a secondary metabolite produced by Glycine max (L.) Merr. (soybean), is valuable for human and plant health. The genetic architecture of soybean isoflavone content remains unclear, however, despite several mapping studies. We generated genomic data for 200 soybean cultivars and 150 recombinant inbred lines (RILs) to localize putative loci associated with soybean seed isoflavone content. Using a genome-wide association study (GWAS), we identified 87 single-nucleotide polymorphisms (SNPs) that were significantly associated with isoflavone concentration. Using linkage mapping, we identified 37 quantitative trait loci (QTLs) underlying the content of four isoflavones found in the RILs. A major locus on chromosome 8 (qISO8-1) was co-located by both the GWAS and linkage mapping. qISO8-1 was fine mapped to a 99.5-kb region, flanked by SSR_08_1651 and SSR_08_1656, in a BC 2 F 5 population. GmMPK1, encoding a mitogenactivated protein kinase, was identified as the causal gene in qISO8-1, and two natural GmMPK1 polymorphisms were significantly associated with isoflavone content. Overexpression of GmMPK1 in soybean hairy roots resulted in increased isoflavone concentrations. Overexpressing GmMPK1 in transgenic soybeans had greater resistance to Phytophthora root rot, suggesting that GmMPK1 might increase soybean resistance to biotic stress by influencing isoflavone content. Our results not only increase our understanding of the genetic architecture of soybean seed isoflavone content, but also provide a framework for the future marker-assisted breeding of high isoflavone content in soybean cultivars.

Seed weight (SW) is the important soybean (Glycine max [L.] Merr.), yield component and also affected the quality of soybean‐derived foods. The aim of this study was to identify the quantitative trait loci (QTL) underlying SW through 112 recombinant inbred lines (RILs) derived from the cross between “Zhongdou27” (G. max, designated by its bigger seed size, 21.9 g/100 seeds) and “Jiunong 20” (G. max, smaller seed size, 17.5 g/100 seeds). Phenotypic data were collected from this RIL population after it was grown in the sixteen tested environments. A total of eight QTL (QSW1‐1, QSW2‐1, QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1) were identified, and they could explain 4.23%–14.65% of the phenotypic variation. Among these eight QTL, three QTL (QSW1‐1 located on the interval of Sat_159‐Satt603 of chromosome (Chr) 1 (LGD1a), QSW19‐1 located on the interval of Sat_340‐Satt523 of Chr 19 (LGL) and QSW20‐1 located on Sat_418‐Sat_105 of Chr 20 (LGI)) were newly identified and could explain 4.235%–10.08%, 8.45%–13.49% and 8.08%–10.18% of the phenotypic variation, respectively. Six of the eight identified QTL including QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1 exhibited a significant additive (a) effect, while two QTL (QSW2‐1 and QSW19‐1) only displayed significant additive‐by‐environment (ae) effects. A total of four epistatic pairwise QTL for SW were identified in the different environments. These eight QTL and their genetic information obtained here were valuable for molecular marker‐assisted selection and the realization of a reasonable SW breeding programme in soybean.

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.

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