Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association

Area of Science:

• Plant Pathology
• Genetics
• Agricultural Science

Background:

• Asian Soybean Rust (ASR), caused by *Phakopsora pachyrhizi*, poses a significant threat to soybean production in Brazil.
• The *Rpp1* locus is a key genetic region conferring resistance to ASR, but effective resistance alleles against Brazilian strains need identification.

Purpose of the Study:

• To identify single nucleotide polymorphism (SNP) markers associated with resistance within the *Rpp1* locus effective against Brazilian ASR populations.
• To pinpoint SNP markers differentiating soybean accessions with various *Rpp1* alleles and susceptible cultivars.

Main Methods:

• Genome-Wide Association Studies (GWAS) and re-sequencing analyses were employed.
• SNP markers were identified and validated using bi-parental populations and diverse Rpp sources.
• Haplotype analysis was performed on a global collection of soybean genomes.

Main Results:

• Seven SNP markers associated with ASR resistance were identified via GWAS.
• Three distinct haplotypes were defined, efficiently distinguishing ASR-resistant and susceptible soybean accessions.
• New potential sources of *Rpp1/Rpp1-b* alleles were discovered in worldwide soybean germplasm.
• Nucleotide differences, including in *ULP1-NBS-LRR* genes, were observed within the *Rpp1* locus.

Conclusions:

• The identified SNP markers and haplotypes effectively co-segregate with ASR resistance.
• These findings provide valuable genetic insights for breeding ASR-resistant soybean varieties.
• The study highlights potential new genetic resources for enhancing soybean disease resistance.