SNP markers associated with soybean partial resistance to Phytophthora sojae

Abstract

Phytophthora root and stem rot is one of the most aggressive diseases in soybean crop. The use of resistant cultivars is the main strategy to reduce losses caused by the pathogen. This study aims to identify SNP markers associated with genes or QTLs that provide soybean with partial resistance to Phytophthora sojae. A total of 169 soybean cultivars were inoculated with Phytophthora sojae and genotyped with 3,807 SNP markers. Genome-wide association analysis was carried out via multiple linear models, followed by multiple linear regression and linkage disequilibrium analysis. Four QTLs associated with the characteristic were identified: two on chromosome 3 and two on chromosome 15. The regions containing these QTLs contain genes already annotated as providers of resistance to pathogens, in plants. The use of those markers in the selection of resistant plants can increase the efficiency of breeding programs in the development of soybean varieties resistant to P. sojae.

Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions

“…In total, twelve QDRL, or 27%, colocalized with previously identified loci from GWA analyses, non-meta-QDRL for P. sojae resistance or meta-QDRL. This is similar to previous GWA studies where approximately 33% of QDRL co-localized with results from other studies [55,57,59]. Five of the 22 meta-QDRL colocalized with QDRL we identified in this study, strongly supporting the involvement of these regions in QDR to P. sojae.…”

“…We identified regions most often associated with resistance by comparing current results with the four previous GWA analyses for QDR to P. sojae [55][56][57][58][59], as well as the meta-QDRL (Table 5). QDRL C2-02-1, C2-03-3, C2-13-7, and C2-17-2 were < 500kb from regions identified in previous GWA analyses, adding evidence to these regions being important in QDR.…”

“…This includes a study of 797 plant introductions (PIs) from SK [55] which had previously been shown to be a source of Rps-genes and high levels of QDR against P. sojae [56], 175 Chinese soybean breeding lines [57], and 279 breeding lines from the Yangtze-Huai Chinese breeding program [58]. Recently, a collection of 169 Brazilian cultivars was used to identify QDRL in regional germplasm [59]. Similar to loci identified by biparental mapping, these GWA studies identified small-effect QDRL.…”

Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL

“…This has led to the identification of a single major QTL confirmed by several powerful GWAS statistical models. In the last decade, many efforts have been made to study the genetic architecture of soybean resistance against P. sojae through GWAS, which has led to the identification of many QTL (Sun et al., 2014; Li et al., 2016; Ludke et al., 2019; Rolling et al., 2020; Schneider et al., 2016). In contrast to most of these prior studies, a major QTL, coidentified by different statistical models, which can, on average, increase the degree of resistance by as much as 60%, was found here, one which would be attractive for breeders to use in marker–assisted selection.…”

“…In the specific context of the soybean– P. sojae interaction, different genotyping approaches have been used. These include simple sequence repeats (Sun et al., 2014), sequence‐based restriction‐site‐associated DNA (Li et al., 2016), and chip‐based genotyping with the SoySNP50K iSelect BeadChip (Ludke et al., 2019; Qin et al., 2017; Rolling et al., 2020; Schneider et al., 2016; Van et al., 2021). Advances in high‐throughput sequencing technologies have enabled rapid, affordable, and accurate whole‐genome sequencing (WGS) of a large number of individuals (Huang et al., 2013; Mace et al., 2013; Zhou et al., 2015).…”