Multi-Environment Multi-QTL Association Mapping in Barley

Diseases represent the main constraints for barley (Hordeum vulgare L.) production in Latin America. Spot blotch (caused by Cochliobolus sativus), stripe rust (caused by Puccinia striiformis f.sp. hordei) and leaf rust (caused by Puccinia hordei) are three of the most important diseases that affect the crop in the region. Chemical control of those diseases is not the best economically or environmentally sound solution, making the development of durable resistant varieties a priority for breeding programs. However, the availability of new resistance sources is a limiting factor. The objective of this work was to detect genomic regions associated with field level plant resistance to spot blotch, stripe rust and leaf rust in Latin American germplasm. Disease severities measured in several environments across the Americas and 1536 SNPs (belonging to the Barley OPA1) in a population of 360 genotypes were used to identify genomic regions associated with disease resistance. Best experimental design and spatial modeling were used in each trial to estimate genotypic means. GWAS in each environment with QTL as fixed effects and the best control for population structure and genetic relatedness as random effects was used to detect significant QTL. All significant environment-specific QTL were subsequently included in a Multi-Environment-Multi-QTL model and evaluated for main and QTL by environment (QEI) effects. Both global QTL (i.e. consistent across environments) and environment-specific QTL were detected. Significant marker-trait associations for spot blotch, leaf and stripe rust were detected that will be useful for future breeding efforts.