Genotypic variations in fruit tree architectural and functional traits have been reported but their genetic bases and the existence of common geneticdeterminants have rarely been investigated in wide genetic diversity. We made use of innovative in-eld high-throughput phenotyping on anassociation panel of 241 genotypes to quantify architectural and functional traits on 4-years old apple trees. T-Lidar technology was used for estimatingarchitectural traits (number of branches, tree height, STAR…), airborne thermal and multispectral imagery for assessing canopy temperature (a proxyof transpiration rate) and vegetation indices (NDVI, MCARI2, GNDVI). This dataset was complemented with yield-related traits (number of fruits, averagefruit weight). We explored genome wide associations on 16 traits with high density (275K) genotypic data. GWAS was run with a multi-locus mixedmodel using genetic kinship matrix and assuming different thresholds for SNP signicance: (i) the Bonferroni correction (Bonfth, -logpval > 6.7), (ii) acorrection based on an estimated number of independent SNPs (Bonfcor, -logpval > 5.7) and (iii) value based on common practices (-logpval = 5).Signicant SNPs with -logpval > 5 were detected for most traits with a number of them displaying -logpval above Bonfcor and above Bonfth. One to foursignicant SNPs were identied by variable with a proportion of variance explained by each SNP ranging from 6% to 14% and the total proportion ofvariance explained by all signicant SNPs exceeding up to 30% for the number of branches, STAR, MCARI2, number of fruit and crop load. SNPscontrolling different traits were detected on LG9 (height, STAR, volume) and LG13 (volume, MCARI2, NDVI, GNDVI). Analyses of the LD between SNPsallowed determining possible colocations within regions. Notably, some signicant SNPs were localized in genomic regions previously reported as QTLsfor similar traits in bi-parental population. This suggests their robustness and encourages further investigations.