title: Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.
abstract: Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Erin J
authors.initials: EJ
authors.lastname: Gilchrist
authors.forename: George W
authors.initials: GW
authors.lastname: Haughn
authors.forename: Cheng C
authors.initials: CC
authors.lastname: Ying
authors.forename: Sarah P
authors.initials: SP
authors.lastname: Otto
authors.forename: Jun
authors.initials: J
authors.lastname: Zhuang
authors.forename: Dorothy
authors.initials: D
authors.lastname: Cheung
authors.forename: Björn
authors.initials: B
authors.lastname: Hamberger
authors.forename: Fariba
authors.initials: F
authors.lastname: Aboutorabi
authors.forename: Tatyana
authors.initials: T
authors.lastname: Kalynyak
authors.forename: Lee
authors.initials: L
authors.lastname: Johnson
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Brian E
authors.initials: BE
authors.lastname: Ellis
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.forename: Quentin C B
authors.initials: QC
authors.lastname: Cronk
mesh_terms: D002170:Canada; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification; D017753:Ecosystem; D017343:Genes, Plant; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D015810:Linkage Disequilibrium; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000145:classification / Q000235:genetics*; D014481:United States
chemical_list: D018744:DNA, Plant