RenSeq-derived SNPs used in mapping resistance to Phytophthora sojae and three Pythium spp. in multiple soybean RIL...

Phytophthora sojae and Pythium spp. cause important root diseases of soybeans resulting in millions of dollars of loss for producers every year. Our previous studies on mapping Rps (Resistance to Ph. sojae) genes and quantitative disease resistance loci (QDRL) towards Ph. sojae and Pythium species, respectively, identified key regions for resistance to these diseases on chromosomes 3, 6, 7, 8, 13, 14 and 18. The development of R gene enrichment and sequencing (RenSeq) have allowed for the expedited discovery of new nucleotide-binding, leucine-rich repeat (NLR)-encoding genes. This study focused on exploring the co-localization of Rps loci or QDRL regions with single nucleotide polymorphism (SNP) markers derived from sequences identified from a RenSeq study of germplasm varying for resistance to Ph. sojae or Pythium species. Another aspect of this study was to saturate the QDRL regions on chromosomes 6, 8 and 14 for resistance to multiple Pythium species utilizing conventional molecular and SNP markers developed from RenSeq analysis. Nineteen RenSeq SNP markers were selected for evaluation in six RIL populations related to resistance to Ph. sojae and/or Pythium as allele-specific KASP markers. Most RenSeq SNP markers co-localized within the Rps loci or QDRL regions in these RIL populations. The development of RenSeq SNPs and their co-localization with Rps loci or QDRL regions indicate their potential use in designing resistance gene-specific markers and their application for marker-assisted selection in soybean resistance breeding programs.

The online version contains supplementary material available at 10.1007/s11032-026-01686-1.