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A 34K SNP genotyping array for Populus trichocarpa : Design, application to the study of natural populations and transferability to other Populus species
Author(s) -
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.,
ElKassaby Y. A.,
Mansfield S. D.,
Cronk Q. C. B.,
Ehlting J.,
Douglas C. J.,
Tuskan G. A.
Publication year - 2013
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12056
Subject(s) - biology , genotyping , populus trichocarpa , snp genotyping , molecular inversion probe , snp , genetics , single nucleotide polymorphism , snp array , intraspecific competition , genotype , gene , genome , ecology
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 SNP s 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 SNP s, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNP s 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.