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.

Limber pine (Pinus flexilis James) genetic map constructed by exome‐seq provides insight into the evolution of disease resistance and a genomic resource for genomics‐based breeding

“…The final composite map positioned 9612 genes with high density spanning 12 LGs. A high proportion of DNA variations in the protein‐coding regions were nonsynonymous and are likely to cause functional changes in the encoded proteins (Liu et al ., ). As SNPs identified by exome‐seq are localized within expressed genes, exome‐seq‐derived maps should be beneficial for functional genomics.…”

“…In recent years, genomic resources have been developed in a few five‐needle pines, including genome‐wide marker discovery (Liu et al ., ; Syring et al ., ), high‐density genetic maps (Jermstad et al ., ; Friedline et al ., ), transcriptome profiles (Lorenz et al ., ; Liu et al ., , ; Gonzalez‐Ibeas et al ., ; Baker et al ., ) and whole‐genome sequences (Stevens et al ., ). These genomics resources and tools open up a completely new avenue for the capture and use of genome‐wide variability in breeding programs; however, the genomic information available so far is still too limited to generate a sufficient foundation of knowledge required for the genetic improvement of five‐needle pines (Liu et al ., ).…”

“…Although partial resistance studies with limber pine are just getting underway (Schoettle et al ., ), extensive investigations of quantitative resistance to C. ribicola have been conducted with some North American white pine species, which is most notable in western white pine, whitebark pine ( Pinus albicaulis ), and southwestern white pine ( Pinus strobiformis ) (Sniezko et al ., , ). Association studies revealed nucleotide variations in several genes (encoding PR10, chitinase, thaumatin, anti‐microbial protein and others) that made significant contributions to phenotypic traits of partial resistance against C. ribicola in sugar pine (Vázquez‐Lobo et al ., ), western white pine (Liu et al ., , ) and whitebark pine (Liu et al ., ); however, so far no WPBR‐resistant QTLs have been mapped on LGs in five‐needle pines. In this study, we detected 38 genetic bins with the co‐localization of at least four NBS‐LRR sequences and eight of them were heterogeneous clusters that co‐localized with genetic bins of other defense‐related genes.…”

Association analysis and in-vitro anti-fungal assay reveal a role for the Pinus monticola PR10 gene (PmPR10-3.1) in quantitative resistance to white pine blister rust

“…To gain a global view of PR10 genes expressed in western white pine, PmPR10 proteins identi ed in a previous study [27] were used as queries for a Blastx search with the lowest E-value < e-05 and minimum length of 100 amino acids in needle and stem transcriptomes in response to infection by C. ribicola [28,29]. To classify novel PmPR10s and analyze their phylogenetic relationship with other members, putative PR10 sequences were mined out from the genome sequence of sugar pine [29] and transcriptomes of limber pine and whitebark pine [25,31]. The proteins with full-length amino acid sequences were aligned by Clustal Omega with default parameters.…”

“…Thus far, quantitative trait loci (QTLs) for genetic resistance to WPBR have not been well characterized in western white pine and other ve-needle pines. Moreover, little is known about genetic mechanisms and functional genes underlying QR to WPBR [25,26].…”