A Genome-Wide Perspective on Variation and Selection in Populations of Arabidopsis halleri From The Alps

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing climatic conditions. We examined genetic variation on a genome-wide scale in Arabidopsis halleri, a strictly outcrossing plant species, using a next-generation genome re-sequencing approach of population pools (Pool-Seq). The investigated populations were sampled in the Alps, a highly heterogeneous environment. More than two million SNPs were found and genomic regions showing evidence for recent selective sweeps were identified using different population genomic approaches. We tested the identified outlier SNPs for associations with climatic factors, identified potential gene functions by Gene Ontology analysis, and assessed frequencies of synonymous and non-synonymous nucleotide substitutions using a new ‘major allele consensus haplotypes’ approach (MACH). Moreover, we validated allele frequency estimates obtained from Pool-Seq by genotyping the same samples with an individual-based pyrosequencing method and found that the Pool-Seq approach does provide highly accurate estimates of population allele frequencies. Our results provide a genome-wide perspective on the distribution of genetic variation in natural populations that are distributed in a heterogeneous environment and identify candidate genes that carry the signature of selection and may underlie adaptation of A. halleri to environmental heterogeneity in the Alps.