Running title: Association mapping in Populus tremula Nucleotide polymorphism and phenotypic associa- tions within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae)

We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80 kb region surrounding the phytochromeB2 locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 SNPs that were subsequently scored in a mapping population consisting of 120 trees. We identified two non-synonymous single nucleotide polymorphisms (SNPs) in the phytochromeB2 gene that were independently associated with variation in the timing of bud set, and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have previously shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates of being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) one is located in the ”hinge region”, close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggest that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.