Performing Department
(N/A)
Non Technical Summary
Drought and fire already are increasing in the Western United States, with consequences forCalifornia's economically and culturally valuable oak rangelands. These agroecosystems face further climatic changes over the next century that are projected to cause substantial loss of oaks and the services they provide that supportcattle, sheep and pig production. Even where oak distributions are predicted to remain stable, some populations may not have the necessary local adaptations to persist in new climates. Therefore, the relatively novel strategy of 'assisted gene flow,' or moving genetic material from historically warmer to newly warming sites may increase oakresilience to climate change.However,more information is needed on how and where genetics impact oak drought tolleranceand whether transplanted individuals will be viability in sites that are far from their origin. Using the widespread, foundational blue oak (Quercus douglasii) as a focal species, the proposed research will increase our knowledge on whether different populations of oaks have different degrees of drought tollerance, how their genetics vary across the distribution, and the whether transplants ofindividuals from historically warmer and drier sitescan survive incurrently more cooler and wetter that are projected to become warmer and drier in the future. We build on existing greenhouse studies and field common garden experimentsthat provide a proof-of-concept, and an established network of rangeland manager partners. This work connects to the BNRE program priorities in its development and evaluation of new conservation and restoration practices that will promote the long-term sustainability of oak rangelands with climate change. These approaches could also apply to other climate-threatened hardwood agroecosystems.
Animal Health Component
0%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
(N/A)
Goals / Objectives
Improve understanding of genetic structure across the blue oak distribution and identify populations with likely drought-adaptive variants.Create models to guide best practices for genetic climate adaptation strategiesExpand protections for blue oak genetic resourcesConduct outreach to increase knowledge of how genetic resource could improve climate change resilience on oak rangelands.
Project Methods
Seedling performance: During two summer field seasons we will surveyexistingfield common gardens.Samples will be dried in an oven at 40 degrees C and stored in individual paper bags with desiccantto preserve phytochemicals for use in the proposed leaf defense chemistry analyses.Leaf defense chemistry will be contracted to be performed at UC Davis. Phenolic compounds will be extracted, and flavonoids, condensed tannins (proanthocyanidins), hydrolyzable tannins, and hydroxycinnamic acid precursors (lignins) will be quantified.Environmental data: To model the influence of environmental factors on seedling performance we will use regional historical (1950-1980) and recent (2018-present) climate data from the publicly-available 270 by 270 m resolution, downscaled Basin Characterization Model (Flint and Flint 2021). To determine site-scale fire influences, we will use data on wildfire in the region from CalFire and from local land manager interviews to determine which plantings have burned.Modeling seedling performance: We will use mixed effect models to explore the influence of climatic distance between current planting-site and historical source-site climate on seedling performance measures (logistic models for survival and linear models for growth). We will first model all sites together, regardless of whether they burned within our study period, to evaluate an interaction between climatic distance and fire on seedling performance.We will use linear models to explore whether leaf defense compounds (total phenolics and compound groups) correlate with observed leaf herbivory and disease patterns and plant growth rates. These traits co-vary somewhat with climate. We will use mixed models, as mentioned above (ARIMA) to explore the relationship between leaf defense compounds and historical source-site climate.Phenotype characterization: To develop phenotypes and scores for genome wide association study (GWAS) input, we will categorize highly drought-adaptive and low drought-adaptive individuals from a previousgreenhouse drydown experiment in multiple ways. Based on the seedling responses to experimental drought, we will score 1) above- and below-ground biomass, and then accounting for biomass, we will score obtained 2) Fv/Fm measures and 3) desiccation rates during drydown. We will also develop a holistic drought response phenotype score (1-5) for each seedling, with the slowest desiccation and highest Fv/Fm under drydown scoring highest. Leaf tissue from one adult tree in one of the UC System Natural Reserves (Blue Oak Ranch Reserve, located in the central part of the speciesdistribution) will be lightly sequenced and mapped to existing oak reference genetic data toverify that it is not a hybrid. Fresh flash frozen tissue will be split and sent to UC Davis for Pacific BioSciences HiFi long reads library generation (1 SMRT cell), and to UCSC Paleogenomics Laboratory for Omni-C library generation for Hi-C chromatin proximity sequencing (100m paired short reads on an Illumina NextSeq 2000). Young leaves, young acorns, roots and catkins from the reference tree will be flash frozen and sent to UC Berkeley for reference transcripts using the PacBio Sequel II system, supplemented by Illumina 2x150 bp data. We will generate transcriptomes and annotate the blue oak genome with the MAKER annotation pipeline that leverages known proteins from other species, AUGUSTUS (Stanke et al. 2006) tode novopredict gene structures, and RNAmmer (Lagesen et al. 2007) to annotate ribosomal RNAs.During the summer of 2023, whole genome resequencing will be done for 90 seedlings (18 seedlings from each of 5 sites) with previously dried leaf samples from the above-described greenhouse drydown experiment, aiming for >20x coverage. We will usefastp(Chen et al. 2018) for quality data filtering, and map remaining readsto our blue oak reference genome usingBWA-MEM(Li and Durbin 2009). We estimate ~4 million SNPs and indels will be found among blue oaks in this study, based on the variation found in other species. We will filter linked variants with Picard Tools and the Genome Analysis Toolkit and Bedtools. We will perform genome wide association on these subsets of plants using PLINK and EMMAX that consider kinship in building models.The highest windows of genomic association with drought phenotypes will be screened for genes and other genomic features to propose candidate alleles under selection and the genomic pathways that regulate drought tolerance. We will also look for previously identified candidate genes in our results such as genes already identified as drought response candidate genes (Mead et al. 2019). Variants and genes of high interest will be confirmed for expression in common garden living plant tissue via RNA-Seq.Overlaying GWAS with population statistics to look for adaptive loci under environmental selection: Because we found Fv/Fm and desiccation measures to be correlated with seed source site climate (Fig 2), we can look for where drought response alleles from GWAS work overlap with genomic islands of relative elevated differentiation (Fst: allele fixation index) between mesic and xeric source climates, which may be under natural selection. A randomly chosen subset of 90 of the greenhouse drydown experiment plants will be analyzed for population structure, hypothesizing that the most mesic and xeric extreme sites will be assigned to different populations. We will bin these into populations or sites with genetic structure, calculate Fst in sliding windows between populations, and calculate the population branch statistic (PBS; Yi et al. 2010) to identify genes with the highest dissimilarity between a certain population or site and two others, suggesting signatures of selection. Results will allow us to estimate where in the environment there are plants that may harbor the most adaptive alleles.We will sample trees from 20 natural populations selected in the consultation above from across the blue oak distribution, that will vary from xeric-edge populations to highly mesic populations, and within populations, stratified across mesic and xeric microenvironments. At each site, we will collect leaves from 8 adult trees per site, with a stratified random sampling design across xeric and mesic microenvironments (N=160). Microenvironments will be identified on-the-ground, e.g., north versus south facing slopes, or channel versus upland environments (methods in McLaughlin et al. 2020).Where seedling recruitment occurs, we also will sample 8 seedlings inorder in the same manner to compare genetic diversity of trees of different generations (N=160).Precise geolocation will be acquired for all trees in order to associate additional environmental metadata as needed. Leaves will be kept cool until returning to the lab, where they will be immediately flash frozen and stored at -80°C until DNA extraction. We will extract DNA, make whole genome libraries, sequence plants to 20x coverage, and then map sequences to our reference genome as before. We will observe the allele frequencies of candidate drought adaptive alleles across the landscape of these 320 new collections, and correlate allelic distributions with environmental features and location.We will expand the pilot PGB with at least 3 new plantings including 8 trees each, representing 8 new lines added to the gene bank. The new plantings will target climate-adaptive genetic resources from threatened populations, as well as individual maternal lines with seedlings that showed particularly high drought tolerance, that are underrepresented in the current PGB plantings.We anticipate 3peer-reviewed publications from this work, and will present our findings at the Society for Ecological Restoration meeting. We also plan to conduct outreach to range management stakeholders by hosting a range management workshop for those interested in oak genetics, climate change, participatory field gene banking or assisted gene flow.