期刊
MOLECULAR ECOLOGY RESOURCES
卷 13, 期 2, 页码 306-323出版社
WILEY
DOI: 10.1111/1755-0998.12056
关键词
genotype accuracy; high-throughput SNP genotyping; hybridization; Populus balsamifera; Populus trichocarpa
资金
- Genome British Columbia Applied Genomics Innovation Program [103BIO]
- BioEnergy Science Center, a U.S. Department of Energy Bioenergy Research Facility
- Office of Biological and Environmental Research in the DOE Office of Science
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 34131 SNPs, the majority of which are located in, or within 2kb 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.
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