Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

Abstract

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.

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

“…18 (Gm18-1979161) associated with IP was found to be located at 290 kb upstream of three key genes (Glyma.18g022400, Glyma.18g022500, and Glyma.18g022700) in rhg1, which consistently contributes much more effective SCN resistance than any other known loci (Cregan et al 1999). The distance from marker to causal genes (rhg1) in our study was shorter than that (350 kb) reported by Vuong et al (2015), but longer than that (5 kb) reported by Han et al(2015). Note that the two functional SNP markers (GSM381 and GSM383) have been developed from Glyma.18 g022500 for the selection of the rhg1 resistance (Shi et al 2015).…”

“…8 (Gm08-8281564) associated with IP was found to be located within an exon of one putative rhg4 gene (Glyma.08g107700, Lightfoot and Meksem 2002), but 110 kb away from another gene (Glyma.08 g108900) identified by Liu et al (2012). Moreover, Gm18-1979161and Gm08-8281564 also overlapped with the same loci associated with resistance to SCN HG type 0 (Han et al 2015), confirming that they can be used as molecular markers to accelerate the development of soybean varieties with the resistance to both SCN HG type 0 and HG type 2.5.7. Previous studies have identified that Peking needs both rhg1 and Rhg4 resistance alleles for a resistant phenotype (Liu et al 2012;Meksem et al 2001).…”

“…18 (rhg1) and 8 (Rhg4) have been consistently mapped in a bi-parental population and a variety of soybean germplasm (Meksem et al 2001;Kim et al 2010;Liu et al 2012;Han et al 2015;Vuong et al 2015). Two loci, rhg1 and Rhg4, represent the major sources of resistance in soybean cultivars (Concibido et al 2004).…”

“…Since the variance explained by the validated SNPs is similar with the heritability, therefore, there is no failure of the validated SNP associations to explain the estimated heritability like the previous Chr chromosome a Position in base pairs for the peak SNP was provided according to Glycine max Wm82.a2.v1, and the corresponding position on Glycine max Wm82.a1.v1 was also provided in the parentheses b Allele with underline stands for resistance allele c The position of significant SNP is located in one of the QTL intervals as reported previously (http://www.soybase.org/search/index. php?qtl=SCN) d N stands for candidates not located in any known QTL intervals e A plausible biological candidate gene in the locus or the nearest annotated gene (Glycine max Wm82.a2.v1) to the peak SNP GWAS result (Han et al 2015). Note that the known loci rhg1 on Chr.…”

“…18 underlying resistance to SCN HG type 0 (Bao et al 2014). By using a data set of 55,159 SNPs across 440 diverse soybean landraces and elite cultivars, Han et al (2015) also identified 19 association loci significantly related to the resistance for two SCN HG types. Another GWAS was performed by using a diverse set of 553 soybean PIs belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG type 0 (Vuong et al 2015).…”