Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja)

Abstract

Soybean cyst nematode (SCN) is the most destructive soybean pest worldwide. Host plant resistance is the most environmentally friendly and cost-effective way of mitigating SCN damage to soybeans. However, overuse of the resistant soybean [Glycine max (L.) Merr.] cultivars from limited genetic resources has resulted in SCN race shifts in many soybean-growing areas. Thus, exploration of novel sources of SCN resistance and dissection of the genetic basis are urgently needed. In this study, we screened 235 wild soybean (Glycine soja Sieb. & Zucc.) accessions to identify genotypes resistant to SCN HG Type 2.5.7 (race 5), a less investigated type but is prevalent in the southeastern US. We also dissected the genetic basis of SCN resistance using a genome-wide association study with SNPs genotyped by SoySNP50k iSelect BeadChip. In total, 43 resistant accessions (female index < 30) were identified, with 10 SNPs being significantly associated with SCN HG 2.5.7 resistance in this wild species. Furthermore, four significant SNPs were localized to linked regions of the known quantitative trait locus (QTL) rhg1 on chromosome 18. The other four SNPs on chromosome 18 and two SNPs on chromosome 19 are novel. Genes encoding disease resistance-related proteins with a leucine-rich region, a mitogen-activated protein kinase (MAPK) on chromosome 18, and a MYB transcription factor on chromosome 19 were identified as promising candidate genes. The identified SNPs and candidate genes will benefit future marker-assisted breeding and dissection of the molecular mechanisms underlying the soybean-SCN interaction.

Genetic architecture of wild soybean (Glycine soja) response to soybean cyst nematode (Heterodera glycines)

“…In G. soja , the identification of superior characteristics in abiotic stress tolerance (Qi et al 2014) and biotic stress resistance (Tian and Smith 2015) suggests that G. soja harbor promising novel genetic resources in biotic and abiotic resistance/tolerance. As expected, over a dozen of G. soja accessions were identified resistant to HG type 2.5.7 (race 5) in recent studies (Kim et al 2011; Kim and Diers 2013; Zhang et al 2016b). However, no G. soja resistance showed high levels of resistance to race 1 (FI<10).…”

“…This lack of resistance might be due to the completely distinct molecular mechanisms of G. soja defending against race 5 (HG type 2.5.7) vs. race 1. Our recent study (Zhang et al (2016b) identified different SNPs and candidate genes involved in G. soja resistant to race 5 (type 2.5.7) compared to this current study on SCN race 1.…”

“…Another six SNPs were located in intergenic regions. In addition, genes within 50 kb at either side of significant SNPs were also retrieved, as previously described (Zhang et al 2016b). As a result, a total of 83 gene models were predicted within the search region (Table S2), thirteen of which might be involved in plant disease resistance based on reference annotations and results from published literature (Table 1).…”

“…Genes located within 50 kb on both sides of the significant SNPs were selected as the source for candidate gene identification as previously described (Zhang et al 2016b). Annotations for the gene list and protein sequences could be retrieved from the public database Phytozome (https://phytozome.jgi.doe.gov).…”

“…Long-term exposure to the combination of various harsh environmental stresses has led G. soja to possess superior characteristics in abiotic stress tolerance (Qi et al 2014) and biotic stress resistance (Kim et al 2011; Tian and Smith 2015). To date, few studies have used G. soja to identify QTLs for SCN resistance (Kim et al 2011; Kim and Diers 2013; Zhang et al 2016b), whereas no studies have applied high-density SNP markers to understand the genetic architecture of the G. soja response to race 1.…”