QTL mapping and GWAS for identification of loci conferring partial resistance to Pythium sylvaticum in soybean ( Glycine max (L.) Merr)

Pythium sylvaticum is one of the most prevalent and aggressive Pythium species causing seedling and root rot of soybean. In this study, two recombinant inbred line populations (POP1 and POP2) and a genome-wide association study (GWAS) panel were used for mapping loci conferring partial resistance to P. sylvaticum in soybean using a greenhouse assay. POP1 (“E09014” × “E05226-T”) and POP2 (“E05226-T” × ‘E09088”) each contains 113 and 79 lines, respectively, and all lines were genotyped using the SoySNP6K BeadChip. QTL mapping using composite interval mapping (CIM) identified 5 QTL on soybean chromosomes of 10 ( q10.1 and q10.2 ), 18 ( q18.1 and q18.2 ), and 20 ( q20.1 ), and each QTL explained 9.7–16.6% of phenotypic variation. The GWAS panel consisted of 214 soybean lines and was genotyped using the SoySNP50K BeadChip. A total of 7 significant SNP markers were identified on chromosomes 10, 18, and 20. Markers Gm10_42965189_G_T, Gm10_42975806_T_C, and Gm10_43004105_A_C were closely linked with q10.1 (<50 kb). Marker Gm18_7898429_A_C was co-localized with q18.2 and was located within the coding region of Glyma.18 g081700 . Further investigation revealed that Gm20_2245263_G_A co-localized with qRRW20 , a QTL previously identified for partial resistance to P. irregulare. All of the QTL identified in this study can be incorporated into soybean lines to improve enduring partial resistance to Pythium diseases using marker assisted breeding.