Genome‐wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge.
We measured 14 morphological and physiological traits and identified SNP‐phenotype associations in a Populus trichocarpa population distributed from California to British Columbia. We used whole genome re‐sequencing data of 882 trees with more than 6.78 million SNPs, coupled with multi‐trait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data.
Broad‐sense heritability (H2) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. A total of 4 and 20 gene models were detected using the single‐trait and multi‐trait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co‐expression networks, metabolite analyses, and direct confirmation of gene function through RNAi.
Multi‐trait association identified many more significant associations than single‐trait association, potentially revealing pleiotropic effects of individual genes. This can be particularly useful for challenging physiological traits like water‐use efficiency or complex traits like leaf morphology, for which we were able to identify credible candidate genes by combining multi‐trait association with gene co‐expression and co‐methylation data.
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