Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir

Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns

Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long-lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44-year-old Douglas-fir trees (Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness-related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega-sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long-terminal repeats of retroelements are involved in growth-associated DNA methylation regulation (both hyper- and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth.

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies

Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.

Genome Wide Association Study Identifies Candidate Genes Related to the Earlywood Tracheid Properties in Picea crassifolia Kom

Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate genome-wide association study methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western USA, coast redwood and giant sequoia, using 10 drought-related physiological and anatomical traits and genome-wide sequence-capture single nucleotide polymorphisms. Population-level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter, and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress, and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype-environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir (Pseudotsuga menziesii)

Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.