A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. (11th January 2013)

• Record Type: Journal Article
• Authors: Geraldes, A.; DiFazio, S. P.; Slavov, G. T.; Ranjan, P.; Muchero, W.; Hannemann, J.; Gunter, L. E.; Wymore, A. M.; Grassa, C. J.; Farzaneh, N.; Porth, I.; McKown, A. D.; Skyba, O.; Li, E.; Fujita, M.; Klápště, J.; Martin, J.; Schackwitz, W.; Pennacchio, C.; Rokhsar, D.; Friedmann, M. C.; Wasteneys, G. O.; Guy, R. D.; El‐Kassaby, Y. A.; Mansfield, S. D.; Cronk, Q. C. B.; Ehlting, J.; Douglas, C. J.; Tuskan, G. A.
• Is Part Of: Molecular ecology resources. Volume 13:Number 2(2013:Mar.)
• Page Start: 306
• Page End: 323
• Publication Date: 2013-01-11
• Subjects: genotype accuracy -- high‐throughput SNP genotyping -- hybridization -- Populus balsamifera -- Populus trichocarpa; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12056
• Languages: English
• ISSNs: 1755-098X

Abstract

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.