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We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.

It is often assumed that the northern peripheral populations of species' ranges are genetically depauperate due in part to founder effects from postglacial colonization. The majority of federally protected plant species are peripheral in Canada, yet we have little information about their patterns of genetic diversity and structure. In British Columbia, the majority of these protected plant species occur in two threatened habitats: the Garry oak and Okanagan shrub-steppe ecosystems. Using universal noncoding chloroplast DNA markers, we investigated genetic diversity and genetic structure in four rare and common plant species pairs inhabiting these two ecosystems. We found that rare species had lower genetic diversity than their common congeners, and detected contrasting patterns of regional diversity and structure based on ecosystem. Species from the Garry oak ecosystem showed lower genetic diversity in the northern deglaciated region and significant differentiation between regions, likely due to limited dispersal between Vancouver Island and the mainland. Species from the Okanagan shrub-steppe, however, tended to have uniform diversity across their range and lack regional structure. This study provides an important first look at the phylogeographic patterns of four rare plant species in British Columbia. Key words: conservation genetics, British Columbia, rare plants, chloroplast DNA, phylogeography, genetic diversity, Garry oak ecosystem, shrub-steppe ecosystem, Introduction Genetic diversity is critical to the long-term viability of wild plant and animal species (Frankham 1996; Hughes et al. 2008) and is considered a prerequisite for adaptation to changing [...]

Subalpine fir, Abies lasiocarpa, occurs throughout western North America, often in forest-tundra parkland. To resolve the presence of varieties in this species, we surveyed microsatellite genetic markers in 11 populations containing three putative varieties of Abies lasiocarpa: (1) var. lasiocarpa, (2) var. bifolia, and (3) var. arizonica. We tested primers from related taxa, and 13 of the best primer pairs were used for assays. Within populations, both heterozygosity and allelic richness were approximately 10% lower in var. lasiocarpa. The STRUCTURE procedure struggled to assign populations to groups correctly; at K = 3, individuals were assigned to their putative varieties with approximately 70% accuracy. Regardless, both lasiocarpa and bifolia were correctly assigned more than expected by chance, indicating that these taxa are distinct. A dendrogram of genetic distances showed var. arizonica to exhibit higher evolutionary distance from the other two varieties and serves as an outgroup. The dendrogram also showed a nesting of var. bifolia clades within var. lasiocarpa, indicating a complex relationship between var. lasiocarpa and var. bifolia. Comparisons among the STRUCTURE population assignments for K = 2, K = 3, and K = 4 identified populations with cryptic admixture and indicate a 'lasiocarpa-bifolia' subspecies complex that warrants further study. Key words: Abies lasiocarpa, population structure, microsatellites, varietal differentiation Le sapin subalpin, Abies lasiocarpa, est present dans tout l'ouest de l'Amerique du Nord, souvent dans les forets- parcs de toundra. Afin de confirmer la presence de sous-especes (varietes) chez cette espece, nous avons etudie les marqueurs genetiques microsatellites dans 11 populations contenant trois varietes putatives d'Abies lasiocarpa : (1) var. lasiocarpa, (2) var. bifolia et (3) var. arizonica. Nous avons teste des amorces provenant de taxons apparentes, et 13 des meilleures paires d'amorces ont ete utilisees pour les analyses. Au sein des populations, l'heterozygotie et la richesse allelique etaient toutes deux inferieures d'environ 10 % chez var. lasiocarpa. La procedure STRUCTURE a eu du mal a affecter correctement les populations aux groupes; a K = 3, les individus ont ete affectes a leurs sous-especes putatives avec une precision d'environ 70 % . Malgre tout, lasiocarpa et bifolia ont ete correctement assignes plus que ce qui serait attendu par le hasard, ce qui indique que ces taxons sont distincts. Un dendrogramme des distances genetiques a montre que var. arizonica presentait une distance evolutive plus elevee par rapport aux deux autres varietes, et qu'elle servait de groupe externe. Le dendrogramme a montre l'imbrication des clades de var. bifolia au sein de var. lasiocarpa, indiquant une relation complexe entre var. lasiocarpa et var. bifolia. Les comparaisons entre les assignations de population STRUCTURE pour K = 2, K = 3 et K = 4 ont identifie des populations avec un melange cryptique et indiquent un complexe de sous-especes << lasiocarpa-bifolia >> qui merite une etude plus approfondie. [Traduit par la Redaction] Mots-cles : Abies lasiocarpa, structure de population, microsatellites, differenciation varietale, Introduction Subalpine fir, Abies lasiocarpa (Hook.) Nuttal 1849, is a conspicuous icon of the meadows of the montane coniferous forests of western North America (Burns et al. 1990). It has [...]

Summary: Forests face many threats. While traditional breeding may be too slow to deliver well‐adapted trees, genomic selection (GS) can accelerate the process. We describe a comprehensive study of GS from proof of concept to operational application in western redcedar (WRC, Thuja plicata).Using genomic data, we developed models on a training population (TrP) of trees to predict breeding values (BVs) in a target seedling population (TaP) for growth, heartwood chemistry, and foliar chemistry traits. We used cross‐validation to assess prediction accuracy (PACC) in the TrP; we also validated models for early‐expressed foliar traits in the TaP.Prediction accuracy was high across generations, environments, and ages. PACC was not reduced to zero among unrelated individuals in TrP and was only slightly reduced in the TaP, confirming strong linkage disequilibrium and the ability of the model to generate accurate predictions across breeding generations. Genomic BV predictions were correlated with those from pedigree but displayed a wider range of within‐family variation due to the ability of GS to capture the Mendelian sampling term.Using predicted TaP BVs in multi‐trait selection, we functionally implemented and integrated GS into an operational tree‐breeding program. [ABSTRACT FROM AUTHOR]

Ref.: Botany. 101(1): 1-14 (2023). https://doi.org/10.1139/cjb-2022-0064 In the originally published article, the author contributions were listed incorrectly. The corrected statement is below, and the original article is corrected. EJW and [...]

Summary: Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect‐resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees.To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell‐type‐specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development.A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees.The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation. [ABSTRACT FROM AUTHOR]

Background Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Results Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Conclusions Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.