Nuclear and Organelle Population Structure in Eastern Cottonwood (Populus deltoides)

Knowledge about a species’ genetic diversity and population structure is fundamental for the development of effective conservation, management and breeding strategies. Nuclear and organelle markers provide complementary information about population differentiation. While nuclear genomes inform about the effects of gene flow through pollen and seed dispersal on genetic structure, organelle genomes (haploid and mostly maternally inherited in flowering plants) reflect only gene flow through seed dispersal. To analyze population structure and genetic diversity in eastern cottonwood (Populus deltoides), 495 unrelated individuals collected across the southeastern native range of the species were genotyped by resequencing 18,153 genes and 23,835 intergenic regions. A set of 535,532 single nucleotide polymorphisms (SNPs) was identified in the nuclear genome. Additionally, off-target reads were aligned to Populus trichocarpa organelle reference sequences to identify SNPs in chloroplasts and mitochondria. A set of 9,038 nuclear intergenic SNPs was used to analyze population structure using the software STRUCTURE. Principal component analysis was used to assess organelle population structure utilizing 304 and 584 SNPs detected in chloroplasts and mitochondria, respectively. Nuclear markers divided the population into two groups that follow largely a eastern and western distribution, with a pairwise F_ST value of 0.072. Organelle markers revealed genetic structure patterns that differed from the nuclear genome. Chloroplast SNPs didn’t identify a clear pattern of genetic differentiation, while mitochondrial SNPs further subdivided the eastern and western subpopulations into smaller groups. These results highlight the advantages of including nuclear and organelle markers in population genetics studies to attain a higher resolution of a species’ genetic structure.