Abstract
Wheat stripe rust (Puccinia striiformis) is a fungal disease responsible for substantial yield losses globally. To maintain crop productivity in future climates, the identification of genetics offering durable resistance across diverse growing conditions is crucial. To stay one-step ahead of the pathogen, Australian wheat breeders are actively selecting for adult plant resistance (APR), which is considered more durable than seedling resistance. However, deploying resistance that is stable or effective across environments and years is challenging as expression of underling APR loci often interact with environmental conditions. To explore the underlying genetics and interactions with the environment for stripe rust resistance, we employ haplotype-based mapping using the local GEBV approach in elite wheat breeding populations. Our multi-environment trial (MET) analyses comprising 35,986 inbred lines evaluated across 10 environments revealed significant genotype by environment (GxE) interactions for stripe rust. A total of 32 haploblocks associated with stripe rust resistance were identified, where 24 were unique to a specific environment and 7 were associated with stable resistance across environments. Population structure analysis revealed commercial or advanced breeding lines carried desirable resistance haplotypes, highlighting the opportunity to continue to harness and optimise resistance haplotypes already present within elite backgrounds. Further, we demonstrate that in-silico stacking of multiple resistance haplotypes through a whole-genome approach has the potential to substantially improve resistance levels. This represents the largest study to date exploring commercial wheat breeding populations for stripe rust resistance and highlights the breeding opportunities to improve stability of resistance across and within target environments.