Tree architecture, light interception and water‐use related traits are controlled by different genomic regions in an apple tree core collection

Tree architecture shows large genotypic variability, but how this affects water‐deficit responses is poorly understood. To assess the possibility of reaching ideotypes with adequate combinations of architectural and functional traits in the face of climate change, we combined high‐throughput field phenotyping and genome‐wide association studies (GWAS) on an apple tree (Malus domestica) core‐collection. We used terrestrial light detection and ranging (T‐LiDAR) scanning and airborne multispectral and thermal imagery to monitor tree architecture, canopy shape, light interception, vegetation indices and transpiration on 241 apple cultivars submitted to progressive field soil drying. GWAS was performed with single nucleotide polymorphism (SNP)‐by‐SNP and multi‐SNP methods. Large phenotypic and genetic variability was observed for all traits examined within the collection, especially canopy surface temperature in both well‐watered and water deficit conditions, suggesting control of water loss was largely genotype‐dependent. Robust genomic associations revealed independent genetic control for the architectural and functional traits. Screening associated genomic regions revealed candidate genes involved in relevant pathways for each trait. We show that multiple allelic combinations exist for all studied traits within this collection. This opens promising avenues to jointly optimize tree architecture, light interception and water use in breeding strategies. Genotypes carrying favourable alleles depending on environmental scenarios and production objectives could thus be targeted.