Data from: Genome-wide association genetics of an adaptive trait in lodgepole pine

Pine cones that remain closed and retain seeds until fire causes the cones
to open (cone serotiny) represent a key adaptive trait in a variety of
pine species. In lodgepole pine, there is substantial geographic variation
in serotiny across the Rocky Mountain region. This variation in serotiny
has evolved as a result of geographically divergent selection, with
consequences that extend to forest communities and ecosystems. An
understanding of the genetic architecture of this trait is of interest due
to the wide-reaching ecological consequences of serotiny, and also because
of the repeated evolution of the trait across the genus. Here we present
and utilize an inexpensive and time effective method for generating
population genomic data. The method uses restriction enzymes and PCR
amplification to generate a library of fragments that can be sequenced
with a high level of multiplexing. We obtained data for more than 95,000
single nucleotide polymorphisms across 98 serotinous and non serotinous
lodgepole pines from three populations. We used a Bayesian generalized
linear model to test for an association between genotypic variation at
these loci and serotiny. The probability of serotiny varied by genotype at
11 loci and the association between genotype and serotiny at these loci
was consistent in each of the three populations of pines. Genetic
variation across these 11 loci explained 50% of the phenotypic variation
in serotiny. Our results provide a first genome-wide association map of
serotiny in pines and demonstrate an inexpensive and efficient method for
generating population genomic data.