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Significance Statement: Interspecific introgression from Gossypium hirsutum has reorganized the genomic architecture of Gossypium barbadense. In this study, the genetic basis of population differentiation and the genetic diversity were deciphered and the introgression events and haplotype selection affecting associated fiber quality and environmental adaptation traits were illuminated in Gossypium barbadense. This study provides new insights into the breeding history of Gossypium barbadense and will guard the breeding programs of modern cultivated Gossypium barbadense. [ABSTRACT FROM AUTHOR]

SUMMARY: 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 BC2F5 population. GmMPK1, encoding a mitogen‐activated 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. Significance Statement: We reported novel loci that control isoflavone content in soybean seeds by genome‐wide association mapping and linkage analysis using a high‐density haplotype map and genetic linkage map. Of these loci, a major QTL qISO8‐1 and its causal gene GmMPK1, underlying the isoflavone content of soybean, was fine mapped. The novel gene GmMPK1 could influence the isoflavone content in soybean and could also be involved in the soybean response to Phytophthora root rot. [ABSTRACT FROM AUTHOR]

Soybean white mold (SWM), caused by Sclerotinia sclerotiorum ((Lib.) W. Phillips), is currently considered to be the second most important cause of soybean yield loss due to disease. Research is needed to identify SWM-resistant germplasm and gain a better understanding of the genetic and molecular basis of SWM resistance in soybean. Stem pigmentation after treatment with oxaloacetic acid is an effective indicator of resistance to SWM. A total of 128 recombinant inbred lines (RILs) derived from a cross of 'Maple Arrow' (partial resistant to SWM) and 'Hefeng 25' (susceptible) and 330 diverse soybean cultivars were screened for the soluble pigment concentration of their stems, which were treated with oxalic acid. Four quantitative trait loci (QTLs) underlying soluble pigment concentration were detected by linkage mapping of the RILs. Three hundred and thirty soybean cultivars were sequenced using the whole-genome encompassing approach and 25 179 single-nucleotide polymorphisms (SNPs) were detected for the fine mapping of SWM resistance genes by genome-wide association studies. Three out of five SNP markers representing a linkage disequilibrium (LD) block and a single locus on chromosome 13 (Gm13) were significantly associated with the soluble pigment content of stems. Three more SNPs that represented three minor QTLs for the soluble pigment content of stems were identified on another three chromosomes by association mapping. A major locus with the largest effect on Gm13 was found both by linkage and association mapping. Four potential candidate genes involved in disease response or the anthocyanin biosynthesis pathway were identified at the locus near the significant SNPs (<60 kbp). The beneficial allele and candidate genes should be useful in soybean breeding for improving resistance to SWM. [ABSTRACT FROM AUTHOR]