Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.

key messageSoybean rust-associated haplotypes around significant SNPs show variable effects across diverse accessions, while distinct soybean mosaic virus-resistant haplotypes were identified at the Rsv1 locus on chromosome 13. Soybean rust (SBR), caused by the fungal pathogen Phakopsora pachyrhizi, significantly affects soybean yield and quality globally. Here, we present an association and haplotype analysis of 2,815 phenotypically diverse soybean accessions to identify durable sources of genetic variation associated with SBR. We characterised allelic diversity and local haplotype effects at two important SBR loci on chromosomes 13 and 18 (Rpp1). At these genomic regions, marker groups containing tightly linked single-nucleotide polymorphisms (SNPs) associated with reduced disease severity were identified. In accessions showing reddish-brown lesion, marker groups associated with increased disease severity include gene variants in Glyma.18G280400 and Glyma.18G280300, indicating potential for resistance improvement. Within the delimited genomic region on chromosome 13, which is reported to be associated with multiple soybean diseases, we also mapped resistance-specific haplotypes associated with soybean mosaic virus, including in the Rsv1 carrier PI 96983, identifying candidate genes that may contribute to resistance. Cross-population haplotype transfer analysis between reddish-brown and tan lesion accessions for SBR around all significant loci showed context dependence of variation patterns, with stable loci on chromosome 07, having gene variants for Glyma.07G261000. These findings provide insights into the genetic architecture associated with soybean disease resistance and contribute to haplotype-based resistance breeding efforts; however, future functional validation of identified candidate causal alleles and genes is required. Our results also demonstrate the potential of local haplotyping with newer phenotypic data for SBR to identify linked causal alleles and individuals containing beneficial alleles, for breeding applications.