Jessica W. Wright

Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides)

Aspen (Populus tremuloides) is a temperate North American tree species with a geographical distribution more extensive than any other tree species on the continent. Because it is economically important for pulp and paper industries and ecologically important for its role as a foundation species in forest ecosystems, the decline of aspen in large portions of its range is of serious concern. The availability and annotation of the black cottonwood (Populus trichocarpa) genome enables a range of high throughput sequencing approaches that can be used to understand rangewide patterns of genetic variation, adaptation, and responses to environmental challenges in other Populus species, including aspen. Gene expression studies are particularly useful for understanding the molecular basis of ecological responses, but are limited by the availability of transcriptome data. We explored the aspen transcriptome through the use of high-throughput sequencing with two main goals: (1) characterization of the expressed portion of the P. tremuloides genome in leaves and (2) assessment of variation in gene expression among genets collected from distinct latitudes but reared in a common garden. We also report a large single nucleotide polymorphism dataset that provides the groundwork for future studies of aspen evolution and ecology, and we identify a set of differentially expressed genes across individuals and population boundaries for the leaf transcriptome of P. tremuloides.

Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata

Reduced water availability during drought can create major stress for many plant species. Within a species, populations with a history of seasonal drought may have evolved the ability to tolerate drought more than those in areas of high precipitation and low seasonality. In this study, we assessed response to water stress in a California oak species, Quercus lobata Née, by measuring changes in gene expression profiles before and after a simulated drought stress treatment through water deprivation of seedlings in a greenhouse setting. Using whole-transcriptome sequencing from nine samples from three collection localities, we identified which genes are involved in response to drought stress and tested the hypothesis that seedlings sampled from climatically different regions of the species range respond to water stress differently. We observed a surprisingly massive transcriptional response to drought: 35,347 of 68,434 contigs (52%) were differentially expressed before versus after drought treatment, of which 18,111 were down-regulated and 17,236 were up-regulated. Genes functionally associated with abiotic stresses and death were enriched among the up-regulated genes, whereas metabolic and cell part-related genes were enriched among the down-regulated. We found 56 contigs that exhibited significantly different expression responses to the drought treatment among the three populations (treatment × population interaction), suggesting that those genes may be involved in local adaptation to drought stress. These genes have stress response (e.g., WRKY DNA-binding protein 51 and HSP20-like chaperones superfamily protein), metabolic (e.g., phosphoglycerate kinase and protein kinase superfamily protein), transport/transfer (e.g., cationic amino acid transporter 7 and K+ transporter) and regulatory functions (e.g., WRKY51 and Homeodomain-like transcriptional regulator). Baseline expression levels of 1310 unique contigs also differed among pairs of populations, and they were enriched for metabolic and cell part-related genes. Out of the large fraction of the transcriptome that was differentially expressed in response to our drought treatment, we identified several novel genes that are candidates for involvement in local adaptation to drought.

Scaling up from greenhouse resistance to fitness in the field for a host of an emerging forest disease.

Forest systems are increasingly threatened by emergent, exotic diseases, yet management strategies for forest trees may be hindered by long generation times and scant background knowledge. We tested whether nursery disease resistance and growth traits have predictive value for the conservation of Notholithocarpus densiflorus, the host most susceptible to sudden oak death. We established three experimental populations to assess nursery growth and resistance to Phytophthora ramorum, and correlations between nursery‐derived breeding values with seedling survival in a field disease trial. Estimates of nursery traits’ heritability were low to moderate, with lowest estimates for resistance traits. Within the field trial, survival likelihood was increased in larger seedlings and decreased with the development of disease symptoms. The seed‐parent family wide likelihood of survival was likewise correlated with family predictors for size and resistance to disease in 2nd year laboratory assays, though not resistance in 1st year leaf assays. We identified traits and seedling families with increased survivorship in planted tanoaks, and a framework to further identify seed parents favored for restoration. The additive genetic variation and seedling disease dynamics we describe hold promise to refine current disease models and expand the understanding of evolutionary dynamics of emergent infectious diseases in highly susceptible hosts.

Alkanes and Terpenes in Wood and Leaves of Pinus jeffreyi and P. sabiniana

The wood oils of Pinus jeffreyi and P. sabiniana contain considerable amounts of heptane (76.6%, 92%), on a monoterpene basis. However, when entire wood extractables is considered, the amounts drop considerably (3.4%, 36.8%) with the major portion of the wood oils being diterpene acids. The leaf oil of P. jeffreyi is dominated by α-pinene (20.9%) and, a diterpene, thunbergol (9.2%) with moderate amounts of β-pinene, δ-3-carene, limonene, β-phellandrene, (Z)-β-ocimene, (E)-caryophyllene, δ-cadinene and cembrene. The leaf oil of P. sabiniana is dominated by α-pinene (39.1%) with moderate amounts of β-pinene, myrcene, limonene, β-phellandrene, (Z)-β-ocimene, methyl chavicol, decanal and thunbergol.

Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment

Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa. Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state.

Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species

Abstract Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population‐specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long‐term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.

Genetic Structure of Notholithocarpus densiflorus (Fagaceae) from the Species to the Local Scale: A Review of Our Knowledge for Conservation and Replanting

Abstract Tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh (Fagaceae), is an important component of mixed-evergreen forests and woodlands in coastal California and Oregon, with incursions into the Sierra Nevada and the Klamath Ranges. Sudden Oak Death (SOD) is causing severe dieback and mortality in tanoak and could transform these ecosystems in areas where the pathogen Phytophthora ramorum S. Werres, A.W.A.M. de Cock can become established. Knowledge of genetic diversity within the species is important for both disease resistance screening, conservation and replanting in sites with high mortality. Here we review what has been learned about the genetic structure within tanoak since SOD has caused disease epidemics in the species. We review published work on genetic structure at the species level and provide some re-analyses of these data that show divergence across the geographic range. We also review recently published data on genetic structure at a fine spatial scale that provides some guidelines for the selection of trees as seed sources. Finally, we interpret a range of seed provenancing strategies in the light of our knowledge of tanoak genetic diversity.

Comparative transcriptomics among four white pine species

Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

Morphology, Physiology, Genetics, Enigmas, and Status of an Extremely Rare Tree: Mutant Tanoak

Abstract Important physical characteristics, morphological attributes, physiological functions, and genetic properties of mutant tanoak, Notholithocarpus densiflorus f. attenuato-dentatus (Fagaceae), and normal tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh, were studied on the Challenge Experimental Forest in Yuba Co., California in an attempt to explain the cause of the mutation and to determine where in the tree it was manifest. Leaves, stomata, trichomes, foliar nutrients, photosynthesis, transpiration, internal moisture stress, DNA, and genetics (metabolonics) all were examined in detail. In some instances, the plant part or the process favored the mutant; in others, the normal tanoak exceeded. Susceptibility to Phytophthora ramorum, the sudden oak death pathogen (SOD) was similar. No all-encompassing functional difference for either type was indicated, other than the size and shape of the leaves and the metabolites in them. We know the two tanoak types differ genetically, but more complete genomic analysis is needed to pinpoint the cause of the mutation. Some thought-provoking enigmas concerning the morphology and physiology of tanoak are presented along with the status (number of plants and location) of the rare mutant.