Exploring standing genetic variation for barley leaf rust resistance in Australian breeding panel

KEY MESSAGE: A genotype-by-environment interaction analysis and haplotype mapping approach identifies novel haplo-blocks that can be combined with Rph20 for enhanced resistance against barley leaf rust. Barley (Hordeum vulgare L.) production worldwide is threatened by different rust diseases, particularly barley leaf rust (BLR) caused by fungus Puccinia hordei. Yet, very limited works have explored BLR resistance mechanism across multiple environments. This study explored genotype-by-environment interactions (GEI) in a BLR disease screening dataset collected over multiple years using a multi-environment trial (MET) analysis followed by iClass method. A haplotype-based approach, using local genomic estimated breeding values (LGEBVs), identified five environmentally stable genomic regions (haplo-blocks: 2HS-b000305, 5HS-b001038, 5HS-b001039, 5HS-b001040 and 5HL-b001125) associated with BLR resistance at adult plant stage. While haplo-block co-locating popular adult plant resistance (APR) gene Rph20 was validated as a key genomic region to drive stability in resistance across multiple environments, other haplo-blocks with high-effect haplotypes were also reported as prospective novel sources of stability. Notably, environmentally specific haplo-blocks offered insights into GEI-driven resistance mechanisms. The study also highlighted the potential of haplo-block stacking to improve adult plant resistance as genotypes with multiple favorable haplotypes demonstrated a linear relationship with enhanced BLR resistance. These findings hold practical implications for barley breeders, paving the way for more resilient cultivars and advancing breeding methodologies for complex traits like disease resistance.