- Library Home /
- Search Collections /
- Open Collections /
- Browse Collections /
- UBC Research Data /
- Data from: A 34K SNP genotyping array for Populus trichocarpa:...
Open Collections
UBC Research Data
Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species Geraldes, Armando; DiFazio, Steve P.; Slavov, Gancho T.; Ranjan, Priya; Muchero, Wellington; Hannemann, Jan; Gunter, Lee E.; Wymore, Ann M.; Grassa, Christopher J.; Farzaneh, Nima; Porth, Ilga; Mckown, Athena D.; Skyba, Oleksandr; Li, Eryang; Fujita, Miki; Klápště, Jaroslav; Martin, Joel; Schackwitz, Wendy; Pennacchio, Christa; Rokhsar, Daniel; Friedmann, Michael C.; Wasteneys, Geoffrey O.; Guy, Robert D.; El-Kassaby, Yousry A.; Mansfield, Shawn D.; Cronk, Quentin C. B.; Ehlting, Juergen; Douglas, Carl J.; Tuskan, Gerald A.
Description
Abstract
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.
Usage notes
genotype_file_MER_Geraldesetal2012.csv
Item Metadata
| Title |
Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species
|
| Creator |
Geraldes, Armando; DiFazio, Steve P.; Slavov, Gancho T.; Ranjan, Priya; Muchero, Wellington; Hannemann, Jan; Gunter, Lee E.; Wymore, Ann M.; Grassa, Christopher J.; Farzaneh, Nima; Porth, Ilga; Mckown, Athena D.; Skyba, Oleksandr; Li, Eryang; Fujita, Miki; Klápště, Jaroslav; Martin, Joel; Schackwitz, Wendy; Pennacchio, Christa; Rokhsar, Daniel; Friedmann, Michael C.; Wasteneys, Geoffrey O.; Guy, Robert D.; El-Kassaby, Yousry A.; Mansfield, Shawn D.; Cronk, Quentin C. B.; Ehlting, Juergen; Douglas, Carl J.; Tuskan, Gerald A.
|
| Date Issued |
2021-05-19
|
| Description |
Abstract
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.; Usage notes genotype_file_MER_Geraldesetal2012.csv |
| Subject | |
| Type | |
| Notes |
Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/l-HNLVio3OTbAeXtlN13UaL5xeSQ3PFagLPvaZxm5Fo</p> Storage size: 24073619 Visibility: public |
| Date Available |
2020-06-24
|
| Provider |
University of British Columbia Library
|
| License |
CC0 1.0
|
| DOI |
10.14288/1.0397654
|
| URI | |
| Publisher DOI | |
| Rights URI | |
| Aggregated Source Repository |
Dataverse
|
Item Media
Item Citations and Data
License
CC0 1.0