Population Genomics of Vegetative Phenology in Populus

Shoot phenology interacts with crown morphology to determine leaf production and duration over the growing season and throughout a tree’s life span, thereby determining whole-tree photosynthesis and biomass yield. We are using QTL mapping in interspecific pedigrees, genome-scale association studies, and transgenic approaches to discover and characterize molecular determinants of these processes in the model tree Populus. We used QTL mapping in a hybrid pedigree with 712 progeny and 3,559 SNP markers to identify 28 QTL for vegetative bud flush and bud set, and various crown architecture traits.  We also performed association mapping for these same traits using 1099 P. trichocarpa growing in three common gardens spanning 8 degrees of latitude. We are focusing in particular on a set of dormancy candidate genes in the phytochrome (PHY) and the MORE AXILLARY BRANCHING (MAX) pathways. The latter are involved in the synthesis and perception of upwardly mobile strigolactones that inhibit axillary bud outgrowth. We identified SNP in 32 genes and 2 kb of flanking sequence using Sanger and Illumina sequencing. There was a significant excess of latitudinal gradients in allele frequencies for several genes. Furthermore, 18 candidate genes had SNPs associated with dormancy and/or crown architecture traits, individually accounting for up to 1.8 percent of the phenotypic variation. The functional roles of the MAX genes in controlling bud outgrowth in Populus are being explored using RNAi transgenics and nitrogen and auxin treatments. This is the first study to combine functional characterization with studies of natural variation in these centrally-important genes.