BackgroundSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistance are urgently needed for effective management of SCN via the development of resistant cultivars. The aim of the present study was to investigate the genetic architecture of resistance to SCN HG Type 0 (race 3) and HG Type 1.2.3.5.7 (race 4) in landraces and released elite soybean cultivars mostly from China.ResultsA total of 440 diverse soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7. Exactly 131 new sources of SCN resistance were identified. Lines were genotyped by SNP markers detected by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 36,976 SNPs were identified with minor allele frequencies (MAF) > 4 % that were present in 97 % of all the genotypes. Genome-wide association mapping showed that a total of 19 association signals were significantly related to the resistance for the two HG Types. Of the 19 association signals, eight signals overlapped with reported QTL including Rhg1 and Rhg4 genes. Another eight were located in the linked regions encompassing known QTL. Three QTL were found that were not previously reported. The average value of female index (FI) of soybean accessions with resistant alleles was significantly lower than those with susceptible alleles for each peak SNP. Disease resistance proteins with leucine rich regions, cytochrome P450s, protein kinases, zinc finger domain proteins, RING domain proteins, MYB and WRKY transcription activation families were identified. Such proteins may participate in the resistant reaction to SCN and were frequently found in the tightly linked genomic regions of the peak SNPs.ConclusionsGWAS extended understanding of the genetic architecture of SCN resistance in multiple genetic backgrounds. Nineteen association signals were obtained for the resistance to the two Hg Types of SCN. The multiple beneficial alleles from resistant germplasm sources will be useful for the breeding of cultivars with improved resistance to SCN. Analysis of genes near association signals may facilitate the recognition of the causal gene(s) underlying SCN resistances.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1800-1) contains supplementary material, which is available to authorized users.

BackgroundSoybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans.ResultsA total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance.ConclusionsA total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3843-y) contains supplementary material, which is available to authorized users.

Soybean (Glycine max [L.] Merrill) seeds are a major source of tocopherols (Toc), which could significantly improve immune system health of human and prevent or treat many serious diseases. Selection for higher Toc contents of seeds could increase nutritional value of soybean‐derived food, laying on an important breeding goal for many soybean breeders. The present objectives of the work were to evaluate various genetic effects of QTL associated with individual and total Toc content based on a RIL population (“Beifeng 9” × “Freeborn”) in six environments to improve the efficiency of molecular marker‐assisted selection (MAS) for high‐Toc breeding. The results described that eighteen, thirteen, eleven and thirteen QTL were associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc content, respectively, and have additive main effects (a) and/or additive × environment interaction effects (ae) in certain environments. Among them, four QTL for α‐Toc, two QTL for γ‐Toc, one QTL for δ‐Toc and four QTL for total Toc could increase α‐Toc, γ‐Toc, δ‐Toc and total Toc content via significant a effect, respectively, which have stronger stability in different years and locations. It implied a value for MAS. Additionally, twenty‐five, fifteen, eleven and twenty epistatic pairwise QTL associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc contents, respectively, were detected. The genetic information of the QTL effects obtained here would be beneficial for breeding soybean variety with high‐Toc content by MAS.

Vitamin E (VE) is an important antioxidant supplement for human health. Soybean seed extracts are the main source of VE supplements. Therefore, increasing the VE content of soybean seeds is important issue in breeding programmes. To detect quantitative trait loci (QTL) associated with VE in soybean seeds, 238 F6:7 recombinant inbred lines (RILs) were created by crossing a high VE cultivar, ‘Beifeng 9’, with a low VE cultivar, ‘Freeborn’. A genetic map was constructed using 218 polymorphic simple sequence repeat (SSR) markers. Composite interval mapping analysis detected 66 QTLs for contents of individual and total VE, 21 for α‐tocopherol, seventeen for γ‐tocopherol, thirteen for δ‐tocopherol and fifteen for total VE. The QTLs were located on chromosomes 9, 10, 15, 18 and 19. Phenotypic variance underlain by each QTL ranged from 2.4% to 32.6%. Two major QTLs (BARCSOYSSR_10_1140–BARCSOYSSR_10_1188 and BARCSOYSSR_15_0855 to BARCSOYSSR_15_0887) associated with α‐Toc, γ‐Toc, δ‐Toc and total VE contents were mapped on chromosomes 10 and 15. They explained 12.0% and 32.6% of phenotypic variance for α‐Toc; 5.5% and 13.0% for γ‐Toc; 6.6% and 23.6% for δ‐Toc; and 19.6% and 21.8% for total VE. QTL intervals BARCSOYSSR_15_0790–BARCSOYSSR_15_0855 (Qα15_1, Qγ15_1), BARCSOYSSR_15_1113–BARCSOYSSR_15_1159 (Qα15_3, Qδ15_2, QTVE15_4) and BARCSOYSSR_15_1159–BARCSOYSSR_15_1190 (Qα15_4, Qγ15_5, QTVE15_5) were associated with α‐Toc and explained 22.2%, 23.8% and 24.4% of the phenotypic variation in multiple environments. BARCSOYSSR_09_1098–BARCSOYSSR_09_1128 (QTVE9_1) and BARCSOYSSR_15_0887–BARCSOYSSR_15_0935 (QTVE15_2, Qγ15_3) associated with total VE content explained 21.8% and 16.4% of the phenotypic variation in two environments. These QTLs allow for marker‐assisted selection for cultivars with high VE contents.