Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

Genetic mapping of quantitative traits requires genotypic data for large
numbers of markers in many individuals. For such studies, the use of large
single nucleotide polymorphism (SNP) genotyping arrays still offers the
most cost-effective solution. Herein we report on the design and
performance of a SNP genotyping array for Populus trichocarpa (black
cottonwood). This genotyping array was designed with SNPs pre-ascertained
in 34 wild accessions covering most of the species latitudinal range. We
adopted a candidate gene approach to the array design that resulted in the
selection of 34 131 SNPs, the majority of which are located in, or within
2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was
selected based on patterns of variation among the SNP discovery
accessions. We show that more than 95% of the loci produce high quality
genotypes and that the genotyping error rate for these is likely below 2%.
We demonstrate that even among small numbers of samples (n = 10) from
local populations over 84% of loci are polymorphic. We also tested the
applicability of the array to other species in the genus and found that
the number of polymorphic loci decreases rapidly with genetic distance,
with the largest numbers detected in other species in section Tacamahaca.
Finally, we provide evidence for the utility of the array to address
evolutionary questions such as intraspecific studies of genetic
differentiation, species assignment and the detection of natural hybrids.