title: Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America.
abstract: Whitebark pine (WBP, Pinus albicaulis Engelm.) is an endangered conifer species due to heavy mortality from white pine blister rust (WPBR, caused by Cronartium ribicola) and mountain pine beetle (Dendroctonus ponderosae). Information about genetic diversity and population structure is of fundamental importance for its conservation and restoration. However, current knowledge on the genetic constitution and genomic variation is still limited for WBP. In this study, an integrated genomics approach was applied to characterize seed collections from WBP breeding programs in western North America. RNA-seq analysis was used for de novo assembly of the WBP needle transcriptome, which contains 97,447 protein-coding transcripts. Within the transcriptome, single nucleotide polymorphisms (SNPs) were discovered, and more than 22,000 of them were non-synonymous SNPs (ns-SNPs). Following the annotation of genes with ns-SNPs, 216 ns-SNPs within candidate genes with putative functions in disease resistance and plant defense were selected to design SNP arrays for high-throughput genotyping. Among these SNP loci, 71 were highly polymorphic, with sufficient variation to identify a unique genotype for each of the 371 individuals originating from British Columbia (Canada), Oregon and Washington (USA). A clear genetic differentiation was evident among seed families. Analyses of genetic spatial patterns revealed varying degrees of diversity and the existence of several genetic subgroups in the WBP breeding populations. Genetic components were associated with geographic variables and phenotypic rating of WPBR disease severity across landscapes, which may facilitate further identification of WBP genotypes and gene alleles contributing to local adaptation and quantitative resistance to WPBR. The WBP genomic resources developed here provide an invaluable tool for further studies and for exploitation and utilization of the genetic diversity preserved within this endangered conifer and other five-needle pines.
authors.affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada.
authors.forename: Jun-Jun
authors.initials: JJ
authors.lastname: Liu
authors.affiliation: USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Sniezko
authors.affiliation: Ministry of Forests, Lands and Natural Resource Operations, Nelson, BC, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Murray
authors.affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada.|Qinghai University, Academy of Agriculture and Forestry Science, 253 Ningda Road, Xining, Qinghai, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Wang
authors.affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada.
authors.forename: Arezoo
authors.initials: A
authors.lastname: Zamany
authors.affiliation: Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada.
authors.forename: Rona N
authors.initials: RN
authors.lastname: Sturrock
authors.affiliation: USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America.
authors.forename: Douglas
authors.initials: D
authors.lastname: Savin
authors.affiliation: USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America.
authors.forename: Angelia
authors.initials: A
authors.lastname: Kegley
mesh_terms: D003247:Conservation of Natural Resources; D060467:Disease Resistance; D056727:Endangered Species; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009656:North America; D010802:Phylogeny; D028223:Pinus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*