---
identifier: mixed.gwas.Zhang_Song_2017

taxid: 3848

scientific_name: Glycine soja

scientific_name_abbrev: glyso

genotype: 
  - 1032 accessions of Glycine soja, representing 88.3% of the USDA wild soybean germplasm collection. 

synopsis: GWAS of Soybean Cyst Nematode (SCN) resistance in 1032 accessions of Glycine soja, using the SoySNP50K marker set relative to the Wm82.gnm1 assembly

genotyping_platform: SoySNP50K

genotyping_method: SoySNP50K Infinium BeadChip 

description: "The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G. soja resistance to SCN race 1. Ten SNPs were significantly associated with the response to race 1. Three SNPs on chromosome 18 were localized within the previously identified quantitative trait loci (QTLs), and two of which were localized within a strong linkage disequilibrium block encompassing a nucleotide-binding (NB)-ARC disease resistance gene (Glyma.18G102600). Genes encoding methyltransferases, the calcium-dependent signaling protein, the leucine-rich repeat kinase family protein, and the NB-ARC disease resistance protein, were identified as promising candidate genes. The identified SNPs and candidate genes can not only shed light on the molecular mechanisms underlying SCN resistance, but also can facilitate soybean improvement employing wild genetic resources."

data_curators: Samuel Clouse, Steven Cannon

publication_doi: 10.1007/s00438-017-1345-x

citation: "Zhang H, Song Q, Griffin JD, Song BH. Genetic architecture of wild soybean (Glycine soja) response to soybean cyst nematode (Heterodera glycines). Mol Genet Genomics. 2017 Dec;292(6):1257-1265. doi: 10.1007/s00438-017-1345-x. Epub 2017 Jul 14. PMID: 28710561; PMCID: PMC5680095."

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

contributors: Zhang H, Song Q, Griffin JD, Song BH.