Genome-Wide Association Study of Resistance to Five Races of Phytophthora Sojae in Soybean.

 Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to $2 billion worldwide. Varieties with P. sojae resistance are environmental friendly to effectively reduce disease damages. In order to improve the resistance of P. sojae and broaden the genetic diversity in Southern soybean cultivars and germplasm, our study aimed to establish a P. sojae resistance gene pool that is high in genetic diversity to be employed in Southern soybean breeding programs, and to explore P. sojae resistance gene regions underlying the host resistance to P. sojae races 1, 3, 7, 17 and 25 for molecular breeding selection. A soybean germplasm panel from maturity groups (MGs) IV and V including 189 accessions original from 10 countries were used in this study. They were high in allelic diversity based on 32,358 SNPs genotypic data among 6,749 MGs IV and V accessions in USDA soybean germplasm collection. The disease evaluation data of P. sojae races 1, 3, 7, 17 and 25 were collected by USDA-ARS germplasm curation program and are publically available. Five accessions in this panel were resistant to all races, so they could be used as potential parental lines in Southern soybean breeding programs to develop P. sojae resistant varieties. The genome-wide association analysis identified a total of 32 significant SNPs. One SNP ss715585768 was strongly associated with resistance to races 1 and 7. The SNPs were also clustered into beneficial significant regions. Most resistant accessions had one to two beneficial significant regions. In the gene expression analysis, ss715619920 was only 3,000 base pairs away from Glyma.14g087500, a subtilisin protease, which was down-regulated more than 4 fold (log2 fold > 2.2) in response to P. sojae infection. The findings in this study will greatly help the Southern soybean breeders to develop elite varieties with broad genetic diversity and P. sojae resistance using identified SNPs and beneficial significant regions specifically for this gene pool.