genotype_file_MER_Geraldesetal2012.csv

The file genotype_file_MER_Geraldesetal2012.csv contains the genotyping data used in Geraldes et al. 2012 "A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species". The file contains genotypes for 32,683 loci in 72 accessions. These loci were genotyped with the 34K Populus SNP array described in this manuscript. Details regarding each locus and the genotyping methods can be found in the manuscript. The file contains 32,684 lines and 73 fields per line separated with commas (.csv). The first line is a header line. The first field reads "SNP" and indicates that for each line, the first field contains the name of the Single Nucleotide Polymorphism (SNP). This name has three parts separated with underscores, where the first part is always "scaffold", the second part is the linkage group to which the locus is mapped and the last part is the location (in base pairs) in that linkage group. All names refer to version 2 of the Populus trichocarpa genome available at http://www.phytozome.net/. Each following field in line one, is the name of the accession genotyped. Accession details are provided in Geraldes et al 2012. Each subsequent line has the genotypes for each individual/locus. Each genotype is followed by a "|" and a number ranging from 0 to 1. This number is the GenCall Score, a measure of the confidence in the genotytpe call. Details are in Geraldes et al. 2012. If the Gencall Score is <0.15, the genotype is considered missing and is represented by "--". Other missing genotypes are indicated with #NA

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