Dataset Information

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.

SUBMITTER: Liu JJ

PROVIDER: S-EPMC5161329 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America.

Liu Jun-Jun JJ Sniezko Richard R Murray Michael M Wang Ning N Chen Hao H Zamany Arezoo A Sturrock Rona N RN Savin Douglas D Kegley Angelia A

PloS one 20161216 12

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 ...[more]

PMID: 27992468

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Project description:Dispersal of whitebark pine (Pinus albicaulis Engelm.), a keystone species of many high-elevation ecosystems in western North America, depends on Clark's nutcracker (Nucifraga columbiana Wilson), a seed-caching bird with an affinity for whitebark seeds. To the extent that this dependence is mutual, declines in whitebark seed production could cause declines in nutcracker abundance. Whitebark pine is in decline across much of its range due to interacting stressors, including the non-native pathogen white pine blister rust (Cronartium ribicola J. C. Fisch.). We used avian point-count data and tree surveys from four national park units to investigate whether trends in whitebark pine can explain trends in Clark's nutcracker. Spatial trends were modeled using recent data from two parks, while temporal trends were modeled using longer time-series of nutcracker and whitebark data from two additional parks. To assess the potential dependence of nutcrackers on whitebark, we linked a model of nutcracker density (accounting for detection probability) with a model of whitebark trends, using a Bayesian framework to translate uncertainty in whitebark metrics to uncertainty in nutcracker density. In Mount Rainier National Park, temporal models showed dramatic declines in nutcracker density concurrent with significant increases in whitebark crown mortality and trees infected with white pine blister rust. However, nutcrackers did not trend with whitebark metrics in North Cascades National Park Service Complex. In spatial models of data from Yosemite National Park and Sequoia-Kings Canyon National Park, nutcracker density varied not only with local cover of whitebark but also with elevation and, in Sequoia-Kings Canyon, with cover of another species of white pine. Our results add support for the hypothesis that the mutualism between whitebark pine and Clark's nutcracker is vulnerable to disruption by blister rust, and our approach integrates data across monitoring programs to explore trends in species interactions.

Project description:There is widespread concern that fire exclusion has led to an unprecedented threat of uncharacteristically severe fires in ponderosa pine (Pinus ponderosa Dougl. ex. Laws) and mixed-conifer forests of western North America. These extensive montane forests are considered to be adapted to a low/moderate-severity fire regime that maintained stands of relatively old trees. However, there is increasing recognition from landscape-scale assessments that, prior to any significant effects of fire exclusion, fires and forest structure were more variable in these forests. Biota in these forests are also dependent on the resources made available by higher-severity fire. A better understanding of historical fire regimes in the ponderosa pine and mixed-conifer forests of western North America is therefore needed to define reference conditions and help maintain characteristic ecological diversity of these systems. We compiled landscape-scale evidence of historical fire severity patterns in the ponderosa pine and mixed-conifer forests from published literature sources and stand ages available from the Forest Inventory and Analysis program in the USA. The consensus from this evidence is that the traditional reference conditions of low-severity fire regimes are inaccurate for most forests of western North America. Instead, most forests appear to have been characterized by mixed-severity fire that included ecologically significant amounts of weather-driven, high-severity fire. Diverse forests in different stages of succession, with a high proportion in relatively young stages, occurred prior to fire exclusion. Over the past century, successional diversity created by fire decreased. Our findings suggest that ecological management goals that incorporate successional diversity created by fire may support characteristic biodiversity, whereas current attempts to "restore" forests to open, low-severity fire conditions may not align with historical reference conditions in most ponderosa pine and mixed-conifer forests of western North America.

Dataset Information

Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America.

Publications

Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America.

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