Genome-Wide Association Analysis and QTL Mapping for Resistance to Pythium sylvaticum in Soybean (Glycine max L.)

Pythium root rot (PRR) is an increasing threat for soybean growers in the United States. The disease is caused by several oomycete pathogens classified to the genus Pythium, such as P. sylvaticum, P. oopapillum, and P. irregulare. Previous studies have identified several putative quantitative trait loci (QTL) that confer resistance to P. irregulare in soybean, however, little study has been done for resistance to P. sylvaticum, which is the most prevalent Pythium species in Michigan. An elite cultivar E09014 developed at Michigan State University (MSU) was found to carry good resistance to P. sylvaticum, and a mapping population of 120 F4:7 recombinant inbred lines (RILs) was developed by crossing E09014 with E05226-T, which is moderate resistant. 87 of the RILs were genotyped with BARCSoySNP6K BeadChips, and a high density linkage map with 1438 single nucleotide polymorphism (SNP) markers were established into 29 linkage groups. QTL analysis suggested four putative QTLs on chromosome 9 (q09, LOD=3.13), 10 (q10, LOD=2.78), 19 (q19, LOD=4.72) and 20 (q20, LOD=3.49), each explaining 9.4% ~ 14.3% of phenotypic variations. Of them, q09 was contributed by E09014, and q10, q19 and q20 were contributed by E05226-T. Moreover, an association panel consisting of 99 accessions of MSU developed elite lines and 125 accessions from Plant Introductions were genotyped by BARCSoySNP50K BeadChips and used for genome wide association study (GWAS). Analyses with general linear model (GLM) identified significant markers (q<0.05) that were located in similar regions with q09, q10, q19, and q20, respectively. These results can also be supported by analysis with mixed linear model. In summary, these results indicated that four QTLs on chr.09, 10, 19 and 20 make major contributions to resistance against Py. sylvaticum in soybean.