Genomic Markers and the Evolution of Sex Determination in Populus

Members of the genus Populus (poplars, cottonwoods, aspens) are dioecious, and dioecy is thought to be under strong genetic control. Previous work has identified various regions on chromosome XIX associated with gender, with the heterogametic gender being identified as female (ZW) or male (XY) depending on the species. With the ultimate aim of identifying the sex-determining region of Populus, we performed whole genome resequencing (Illumina 100bp PE sequencing, 15x coverage) of 52 Populus trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known gender. After verifying that there was no spurious correlation between gender and genome-wide patterns of population structure, we performed a genome-wide association study (GWAS) that identified hundreds of gender specific single nucleotide polymorphisms (SNPs) in genomic clusters with complete linkage. Association results were validated in independent samples of known gender. We used conserved regions within these clusters to design several PCR-based markers for the molecular identification of gender. Using allele-specific primers we also generated male and female haplotype sequences for a subset of the resequenced individuals, as well as for other species of poplar. We are able to report estimates of sequence divergence and phylogenetic pattern for the sex-linked region. Here we present the results of our GWAS and molecular work, shedding light on the evolution of the sex locus in Populus.