Identifying water stress response haplotypes in barley using latent environmental covariates
PurposeGenotype-by-environment (G x E) interactions represent a major obstacle to increasing genetic gain in crop breeding, with the underlying physiological drivers often remaining obscured within conventional statistical models. This case study presents a novel framework that transforms the latent factors from Factor Analytic (FA) multi-environment trial (MET) models into heritable quantitative traits, enabling the genetic dissection of adaptive response patterns. MethodsA Factor Analytical Linear Mixed Model (FA-LMM) was fit to plot-level yield data for 1,036 barley genotypes across eight Australian trials. ResultsCorrelation of the factor loadings with APSIM-simulated environmental covariates demonstrated that the second latent factor FA2 was strongly correlated with the Water Stress Index (r = -0.83) during the critical flowering period, establishing water availability as the main biological axis of crossover Gx E. Genotypic scores for the derived traits, Overall Performance (OP) and Water Stress Response (WSR), were subjected to high-resolution haplotype-based mapping using local Genomic Estimated Breeding Values (GEBV). ConclusionThis analysis successfully identified major genomic regions that accounted for a substantial proportion of the additive genetic variance. Gene Ontology enrichment of candidate genes within the top haploblocks implicated fundamental pathways related to energy homeostasis, root development, and stress response, with notable candidates including FTsH11, BPS1, and TDP1. The distribution of favourable Haplotypes of Interest (HOI) in elite cultivars suggested a historical signature of inadvertent selection for these adaptive mechanisms. This framework provides an explicit bridge between statistical modelling and functional genomics, offering breeders actionable genetic targets for accelerated development of climate-resilient cereals.