Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea

Abstract

BackgroundPhytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae.ResultsResistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes.ConclusionsQTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial resistance to P. sojae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2918-5) contains supplementary material, which is available to authorized users.

Quantitative Disease Resistance Loci towards Phytophthora sojae and Three Species of Pythium in Six Soybean Nested Association Mapping Populations

“…This is a critical finding, as breeding for resistance to traits controlled by minor QDRL is different from those of major gene or few major QDRL (Bernardo, 2008;St. The major QDRL for P. sojae identified on chromosome 13 with the resistance allele from HS6-3976 was identified previously from Conrad , PI 408105A (Nguyen et al, 2012), and in a genome-wide association study for quantitative resistance to P. sojae (Schneider et al, 2016). The major QDRL for P. sojae identified on chromosome 13 with the resistance allele from HS6-3976 was identified previously from Conrad , PI 408105A (Nguyen et al, 2012), and in a genome-wide association study for quantitative resistance to P. sojae (Schneider et al, 2016).…”

“…Resistance towards P. sojae has been identified in numerous soybean genotypes; >25 single Rps genes as well as numerous quantitative trait loci (QTL) have been mapped (Dorrance and Schmitthenner, 2000;Wang et al, 2010Wang et al, , 2012bLee et al, 2014;Matthiesen et al, 2016;Schneider et al, 2016;Dorrance, 2018). Although resistance towards Pythium has been identified in several soybean genotypes (Griffin, 1990;Bates et al, 2008;Ellis et al, 2013;Balk, 2014), it has only been mapped towards three species of Pythium to date (Rosso et al, 2008;Ellis et al, 2013;Stasko et al, 2016;Urrea et al, 2017;Lin et al, 2018;Klepadlo et al, 2018).…”

Phenotypic Characterization of a Major Quantitative Disease Resistance Locus for Partial Resistance to Phytophthora sojae

“…Many QDRLs associated with partial resistance to P. sojae have been shown to have an effect in the greenhouse or laboratory (Lee et al, 2014;Schneider et al, 2016;Stasko et al, 2016), but few have been tested in the field (Li et al, 2010;Wang et al, 2012) where more environmental variation exists. In NIL set 4060, the resistant introgression R105B significantly increased yield under disease conditions compared to the susceptible introgression derived from OX20-8 (SOX).…”

“…More than 35 quantitative disease resistance loci (QDRLs) distributed across 17 chromosomes have been identified for partial resistance to P. sojae (Burnham et al, 2003;Weng et al, 2007;Han et al, 2008;Li et al, 2010;Tucker et al, 2010;Wang et al, 2010;Wu et al, 2011b;Lee et al, 2013aLee et al, , 2013bAbeysekara et al, 2016;Schneider et al, 2016;Stasko et al, 2016). However, the majority of these QDRLs explained <15% of the phenotypic variation.…”

GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

“…GWAS is based on use of whole genome genotyping and a detailed phytopathological and morphological description of collections with a high level of genetic diversity (Klein, 2007). A survey of recent reports has shown successful use of GWAS for studying soybean resistance to fungal diseases (Bao et al, 2015;Iquira et al, 2015;Schneider et al, 2016;Qin et al, 2017).…”