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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]

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]

Sclerotinia stem rot (SSR) is a devastating fungal disease that causes severe yield losses of soybean worldwide. In the present study, a representative population of 185 soybean accessions was selected and utilized to identify the quantitative trait nucleotide (QTN) of partial resistance to soybean SSR via a genome-wide association study (GWAS). A total of 22,048 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) > 5% and missing data < 3% were used to assess linkage disequilibrium (LD) levels. Association signals associated with SSR partial resistance were identified by two models, including compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM). Finally, seven QTNs with major effects (a known locus and six novel loci) via CMLM and nine novel QTNs with minor effects via mrMLM were detected in relation to partial resistance to SSR, respectively. One of all the novel loci (Gm05:14834789 on Chr.05), which was co-located by these two methods, might be a stable one that showed high significance in SSR partial resistance. Additionally, a total of 71 major and 85 minor candidate genes located in the 200-kb genomic region of each peak SNP detected by CMLM and mrMLM were found, respectively. By using a gene-based association, a total of six SNPs from three major effects genes and eight SNPs from four minor effects genes were identified. Of them, Glyma.18G012200 has been characterized as a significant element in controlling fungal disease in plants. [ABSTRACT FROM AUTHOR]

As an important and complex trait, inflorescence length (IL) of soybean [Glycine max (L.) Merr.] significantly affected seed yields. Therefore, elucidating molecular basis of inflorescence architecture, especially for IL, was important for improving soybean yield potentials. Longer IL meaned to have more pod and seed in soybean. Hence, increasing IL and improving yield are targets for soybean breeding. In this study, a association panel, comprising 283 diverse samples, was used to dissect the genetic basis of IL based on genome-wide association analysis (GWAS) and haplotype analysis. GWAS and haplotype analysis were conducted through high-throughout single-nucleotide polymorphisms (SNP) developed by SLAF-seq methodology. A total of 39, 057 SNPs (minor allele frequency ≥ 0.2 and missing data ≤ 10%) were utilized to evaluate linkage disequilibrium (LD) level in the tested association panel. A total of 30 association signals were identified to be associated with IL via GWAS. Among them, 13 SNPs were novel, and another 17 SNPs were overlapped or located near the linked regions of known quantitative trait nucleotide (QTN) with soybean seed yield or yield component. The functional genes, located in the 200-kb genomic region of each peak SNP, were considered as candidate genes, such as the cell division/ elongation, specific enzymes, and signaling or transport of specific proteins. These genes have been reported to participant in the regulation of IL. Ten typical long-IL lines and ten typical short-IL lines were re-sequencing, and then, six SNPs from five genes were obtained based on candidate gene-based association. In addition, 42 haplotypes were defined based on haplotype analysis. Of them, 11 haplotypes were found to regulate long IL (> 14 mm) in soybean. The identified 30 QTN with beneficial alleles and their candidate genes might be valuable for dissecting the molecular mechanisms of IL and further improving the yield potential of soybean. [ABSTRACT FROM AUTHOR]

Key message: Association analysis techniques were used to identify and verify twelve single nucleotide polymorphisms (SNPs) associated with Fusarium graminearum resistance. Two novel candidate genes were obtained.Abstract: Fusarium graminearum causes seed and root rot and seedling damping-off of soybean, leading to severe yield loss. Presently, the genetic basis of resistance to F. graminearum is elucidated in only four soybean accessions, which is not sufficient for resistance improvement. The objective of the present study was to identify the genome-wide genetic architecture of resistance to F. graminearum in landraces and cultivated soybeans based on a growth room evaluation. The resistance levels of 314 diverse accessions were tested, and 22,888 single nucleotide polymorphisms (SNPs) with a minor allele frequency of > 0.05 were developed using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Twelve SNPs were identified as associated with F. graminearum resistance, and these SNPs were located at 12 genomic regions on eight chromosomes (Chr.) and could explain 5.53-14.71% of the observed phenotypic variation. One SNP, rs9479021, located on Chr.6, overlapped with qRfg_Gm06, the known QTL for resistance to F. graminearum. The other SNPs were novel and associated with resistance to F. graminearum. Nine novel candidate genes were predicted to contribute to resistance to F. graminearum according to the haplotype and transcript abundance analysis of the candidate genes. The identified markers and resistant cultivars are valuable for the improvement of resistance to F. graminearum. [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]

Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the present study, we assessed the distinctness and uniformity of five soybean cultivars using both single nucleotide polymorphism (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, and simple sequence repeat (SSR) markers. The phylogenetic tree and principal component analysis (PCA) from both the SLAF-seq and SSR methods showed a clear distinction among cultivars Zhonghuang 18, Zhonghuang 68 and Zhonghuang 35, while no clear distinction was observed between cultivars Zhonghuang 13 and Hedou 13. Using the SLAF-seq method, we determined the proportion of homozygous loci for the five soybean cultivars. The heterozygosity of each individual plant was estimated for the assessment of cultivar purity and the purity levels of the five soybean cultivars ranged from 91.89% to 93.96%. To further validate the applicability of the SLAF-seq approach for distinctness testing, we used the SNP information of 150 soybean cultivars with different origins. The cultivars were also distinguished clearly. Taken together, SLAF-seq can be used as an accurate and reliable method in the assessment of the distinctness and uniformity of soybean cultivars. [ABSTRACT FROM AUTHOR]

Background: The advances of hyperspectral technology provide a new analytic means to decrease the gap of phenomics and genomics caused by the fast development of plant genomics with the next generation sequencing technology. Through hyperspectral technology, it is possible to phenotype the biochemical attributes of rice seeds and use the data for GWAS. Results: The results of correlation analysis indicated that Normalized Difference Spectral Index (NDSI) had high correlation with protein content (PC) with RNDSI2 = 0.68. Based on GWAS analysis using all the traits, NDSI was able to identify the same SNP loci as rice protein content that was measured by traditional methods. In total, hyperspectral trait NDSI identified all the 43 genes that were identified by biochemical trait PC. NDSI identified 1 extra SNP marker on chromosome 1, which annotated extra 22 genes that were not identified by PC. Kegg annotation results showed that traits NDSI annotated 3 pathways that are exactly the same as PC. The cysteine and methionine metabolic pathway identified by both NDSI and PC was reported important for biosynthesis and metabolism of some of amino acids/protein in rice seeds. Conclusion: This study combined hyperspectral technology and GWAS analysis to dissect PC of rice seeds, which was high throughput and proven to be able to apply to GWAS as a new phenotyping tool. It provided a new means to phenotype one of the important biochemical traits for the determination of rice quality that could be used for genetic studies. [ABSTRACT FROM AUTHOR]