Association Genetics Of An Adaptive Trait In Lodgepole Pine

Cone serotiny (the retention of seeds in tightly closed cones until fire opens them) represents a key adaptive trait in a variety of pine species. Lodgepole pine exhibits substantial geographical variation in serotiny, which has evolved as a result of geographically divergent selection and has consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is of interest owing to the wide-reaching ecological consequences of serotiny and also because of the repeated evolution of the trait across the genus. We developed a restriction enzyme guided method for genomic complexity reduction that is fast, inexpensive, and allows high levels of multiplexing on the Illumina platform. We obtained data for more than 95,000 single nucleotide polymorphisms across 98 serotinous and nonserotinous lodgepole pines from three populations, and used a Bayesian generalized linear model (GLM) to test for associations 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 was consistent in each of the three populations. Genetic variation across these 11 loci explained 50% of the phenotypic variation in serotiny. Analyses using a Bayesian multi-SNP association procedure (piMASS) led to similar estimates of the genetic architecture. These results provide a first genome-wide association map of serotiny in pines and form the basis for future mapping, landscape and comparative studies. The inexpensive and time-effective method for generating population genomic data that we developed can, with appropriate computational methods, be applied to any taxon and many ecological and evolutionary questions.