The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high (50 accessions) and low (50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm (G´) method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G´ values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched (P<0.05) Gene Ontology (GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments, five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked-segregant analysis-based sequencing (BSA-seq) approach provide new insights for exploring future molecular breeding efforts to produce soybean cultivars with high carotenoid content.

Soluble sugar is a key quality trait of soybean seeds. We developed rapid and economic extraction and quantification methods for seed soluble sugars using an ultra-high performance liquid chromatography system with a refractive index detector. We evaluated the soluble sugar compositions of 1164 soybean accessions collected from diverse ecoregions and grown in multiple locations and years. Total soluble sugar (TSS) content was influenced by accession type, year of cultivation, and ecoregion. The mean contents of fructose, glucose, sucrose, raffinose, stachyose and TSS were 3.31, 5.21, 55.60, 6.60, 35.47, and 106.19 mg g⁻¹, respectively. The highest mean TSS content (108.71 mg g⁻¹) was observed in accessions from Northern Region of China. Cultivars contained higher contents of sucrose, raffinose, and TSS, whereas landraces had a higher content of stachyose. Fourteen accessions with mean TSS contents > 130 mg g⁻¹ were identified as elite soybean resources. TSS was correlated with sucrose, raffinose, stachyose, protein, oil and total tocopherol. The main soluble sugar components were correlated with latitude and longitude, indicating that the geographical origin of the accessions affected their seed soluble sugar compositions. The developed methods and elite identified accessions can be used in the food and feed industry and in soybean breeding programs aimed at improving soybean seed nutrition.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically damaging disease of soybean worldwide, and breeding host plant resistance is the most feasible option for SCN management. In this review, we summarise the progress made so far in identifying nematode-resistance genes, the currently available sources of resistance, possible mechanisms of SCN resistance and strategies for soybean breeding. To date, only two sources of SCN resistance have been widely used, from the accessions PI 88788 and Peking, which has resulted in a shift in SCN resistance and created a narrow genetic base for SCN resistance. These resistant germplasms for SCN are classified into two types according to their copy number variation in a 31-kb genomic region: PI 88788-type resistance requires high copy numbers of a rhg1 resistance allele (rhg1-b) and Peking-type resistance requires both low copy numbers of a different rhg1 resistance allele (rhg1-a) and a resistant allele at another locus, Rhg4. Resistance related to rhg1 primarily involves impairment of vesicle trafficking through disruption of soluble NSF-attachment protein receptor (SNARE) complexes. By contrast, resistance via Rhg4 involves disturbance of folate homeostasis at SCN feeding sites due to alteration of the enzymatic activity of serine hydroxymethyltransferase (SHMT). Other potential mechanisms, including plant defences mediated by salicylic acid (SA) and jasmonic acid (JA) signalling modulation, have also been suggested for SCN resistance. Indeed, genome-wide association studies (GWAS) have identified other candidate SCN resistance genes, such as GmSNAP11. Although gene functional analysis in a transient expression system could increase the efficiency of candidate gene identification, information on novel genes and mechanisms for SCN resistance remains limited. Any beneficial candidate genes identified might, when fully exploited, be valuable for improving the efficiency of marker-assisted breeding and dissecting the molecular mechanisms underlying SCN resistance.

The stability of soybean (Glycine max L. Merrill) oil is determined mainly by its fatty acid (FA) composition. We evaluated the FA composition of 1025 Chinese soybean accessions collected from diverse ecoregions and grown in multiple locations and years. We observed highly significant differences (P < 0.001) between accessions in palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LNA) contents. Growth year affected (P < 0.001) the abundance of all FAs except PA. The mean PA, SA, OA, LA, and LNA contents were 12.2%, 3.8%, 21.5%, 54.2%, and 8.3%, respectively. The geographical origin of the accession influenced seed FA composition, indicating that accessions originating in each ecoregion tend to have distinct FA composition. We observed significant positive correlations among the three locations and between the two years, suggesting the high heritability and stability of individual accessions across contrasting environments. We also observed a relatively high negative correlation between the contents of OA and both LA and LNA (r = −0.90 and −0.59, respectively, each significant at P < 0.001), providing a potential entry point for developing strains producing oil with higher OA and lower LA and LNA levels. These would be appropriate for specialized use in the food industry. Our results will be useful in breeding soybean with improved quality to meet human nutritional and industrial needs.

Soybean isoflavones are essential secondary metabolites synthesized in the phenylpropanoid pathway and benefit human health. In the present study, high-resolution QTL mapping for isoflavone components was performed using specific-locus amplified fragment sequencing (SLAF-seq) with a recombinant inbred line (RIL) population (F_5:7) derived from a cross between two cultivated soybean varieties, Luheidou 2 (LHD2) and Nanhuizao (NHZ). Using a high-density genetic map comprising 3541 SLAF markers and the isoflavone contents of soybean seeds in the 200 lines in four environments, 24 stable QTL were identified for isoflavone components, explaining 4.2%–21.2% of phenotypic variation. Of these QTL, four novel stable QTL (qG8, qMD19, qMG18, and qTIF19) were identified for genistin, malonyldaidzin, malonylgenistin, and total isoflavones, respectively. Gene annotation revealed three genes involved in isoflavone biosynthesis (Gm4CL, GmIFR, and GmCHR) and 13 MYB-like genes within genomic regions corresponding to stable QTL intervals, suggesting candidate genes underlying these loci. Nine epistatic QTL were identified for isoflavone components, explaining 4.7%–15.6% of phenotypic variation. These results will facilitate understanding the genetic basis of isoflavone accumulation in soybean seeds. The stable QTL and tightly linked SLAF markers may be used for marker-assisted selection in soybean breeding programs.