In Chile, stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) has been the main disease threatening wheat production since 2018. During the last two decades new races of Pst with increased aggressiveness, broader virulence profiles, and tolerance to high temperatures have spread worldwide, producing devastating epidemics in both common and durum wheat.

Pst pathotypes isolated in Chile are among the most aggressive identified worldwide and can produce total yield loss if not controlled on time. The rapid erosion of Pst resistance genes caused by the appearance of new races of the pathogen, the lack of knowledge about the genetic basis of resistance to local races, and the rapid loss of resistance in Chilean commercial varieties during recent years, evidence the urgent need of finding new sources of resistance effective against local races.

To detect effective resistance loci that can be efficiently deployed in breeding programs, an association mapping panel of 180 common wheat cultivars and breeding lines from Chile, Uruguay and Mexico was evaluated for both adult-plant and seedling stage resistance to Pst. Field evaluations were conducted in five environments in Chile (2 locations in 2022-23 and 3 locations in 2023-24 seasons), while seedling stage screening was conducted for three Pst genetic groups (PstS7, PstS10, PstS13) at INIA-Uruguay.

Genotyping with the Illumina® iSelect® 25K Infinium® Single Nucleotide Polymorphism (SNP) genotyping array yielded 11,555 polymorphic markers after QC analyses (missing data < 10% and MAF > 0.05). Undergoing genome-wide association analyses have identified several significant QTL with some of them being consistent across multiple environments and explaining up to ~50% of the trait phenotypic variance for infection type and severity.

Our preliminary results revealed a high phenotypic variation for resistance to Chilean stripe rust races in the panel studied, and represent a step towards the diversification of current resistance genes deployed in local varieties. In addition, molecular markers (i.e., KASP assays) will be developed for SNPs associated with stripe rust resistance, providing a valuable tool for wheat breeding programs to facilitate their rapid adoption.