Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds

Technological advances in genomics and bioinformatics made it possible to study the genetic structure of breeds and understand genome changes caused by selection over generations. Our objective was to evaluate selection signatures (SS) in Nelore, Gir, and Red Sindhi cattle from Brazil and the Asian continent to identify divergent variants due to the history of formation and selection of populations, with a focus on the SS of animals from Brazil. Extended haplotype homozygosities between populations (XP-EHH), the ratio of site-specific extended haplotype homozygosity between populations (Rsb), and the allelic fixation index (Fst) were used to detect SS. Considering a window size of 50-kb, a non-sliding window approach was used to define SS regions. A total of 62, 57, and 72 genes were co-located within SS regions for Nelore, Gir, and Red Sindhi, respectively, and used to perform functional analyses per breed. Most genes were associated with productive and reproductive traits, while others were related to thermotolerance, the immune system, temperament, and coat color. The identified SS demonstrate how animal breeding programs shape the genetic makeup of these breeds to meet production system requirements, given that animals from Brazil and the Asian continent have undergone different selection processes. The identification of genes related to thermotolerance, temperament, and the immune system suggests specific alleles have enabled animals to adapt to environmental conditions and selection criteria in Brazil. Understanding SS can support breeding strategies for Nelore, Gir, and Red Sindhi cattle, contributing to enhanced resistance, adaptation, and productivity to meet food production demands.

Genomics highlight an underestimation of phenology sensitivity to the urban heat island effect

The phenological timing of leaf out in temperate forests is a critical transition point each year that alters the global climate system, which in turn, feeds back to plants, driving leaf out to occur nearly 3 d earlier per decade as temperatures rise. To improve predictions of leaf out timing, urban heat islands (UHIs) or densely developed areas that are hotter than surrounding undeveloped regions are often used to approximate warming via space-for-time substitutions (i.e., rural-to-urban temperature gradients). However, more than just environment changes along these gradients-urban regions are highly managed systems with limited-to-no within species diversity. We demonstrate here that recent observations that UHI gradients underpredict leaf out response to temperature when compared to temperature gradients through time is likely because both genetics and environment are changing across rural-to-urban gradients, whereas only environment is changing through time. We tested this hypothesis using genomic, phenological, and temperature data of northern red oak (Quercus rubra) over several years between an urban and rural site. Across our gradient, models that included just temperature predicted moderate advancement of leaf out. However, if we account for the genetic diversity of our trees in our model, leaf out phenology is predicted to advance significantly more in response to temperature. We demonstrate that this stronger relationship between phenological timing and climate is because urban trees have reduced genetic diversity as they are planted from limited stock by humans and, moreover, are most closely related to individuals at the rural site that leaf out later on average.

Local adaptation, genetic diversity and key environmental interactions in a collection of novel red clover germplasm

Red clover (Trifolium pratense L.) is known for its large taproot, nitrogen fixation capabilities and production of forage high in protein and digestibility. It has the potential to strengthen temperate pastural systems against future adverse climatic events by providing higher biomass during periods of water deficit. Being outcrossing and self-incompatible, red clover is a highly heterozygous species. If evaluated and utilized correctly, this genetic diversity can be harnessed to develop productive, persistent cultivars. In this study, we selected 92 geographically diverse red clover novel germplasm populations for assessment in multi-location, multi-year field trials and for genetic diversity and genetic relationship characterization using pooled genotyping-by-sequencing (GBS). Through the development of integrated linear mixed models based on genomic, phenotypic, and environmental information we assessed variance components and genotype-by-environment (G x E) interactions for eight physiological and morphological traits. Key interactions between environmental variables and plant performance were also evaluated using a common garden site at Lincoln. We found that the genetic structure of the 92 populations was highly influenced by country of origin. The expected heterozygosity within populations ranged between 0.08 and 0.17 and varied with geographical origin. For the eight physiological and morphological traits measured there was high narrow-sense heritability (h2 > 0.70). The influence of environmental variables, such as mean precipitation, temperature and isothermality of the original collection locations, on plant and trait performance in the local field trials was also highlighted. Along with the identification of genes associated with these bioclimatic variables that could be used as genetic markers for selection in future breeding programs. Our study identifies the importance of diverse germplasm when adding genetic variation into breeding programs. It also identifies efficient evaluation methods and key climatic variables that should be considered when developing adaptive red clover cultivars.

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns

Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Identification of the xyloglucan endotransglycosylase/hydrolase genes and the role of PagXTH12 in drought resistance in poplar

The xyloglucan endotransglycosylase/hydrolase (XTH) gene family plays a crucial role in plant cell wall remodeling, facilitating growth and structural changes. However, the divergence of paralogous genes among different species of Populus remains inadequately understood. This study investigates the phylogenetic relationships and expression characteristics of XTH genes in two Populus species: Populus trichocarpa and Populus alba × P. glandulosa '84K'. Forty-one XTHs were identified in P. trichocarpa and 38 and 33 members in the subgenome A and G of '84K' poplar, respectively. Gene expression analysis demonstrated differences among paralogous genes within the same subgenome and between orthologous genes across species, likely influenced by variations in promoter regions. Notably, XTH12 showed a specific response to drought stress among various abiotic stresses. In a population of 549 Populus individuals, functional SNPs in XTH12's coding region did not affect its conserved ExDxE catalytic site, highlighting its irreplaceable function. Furthermore, validation through qRT-PCR and ProPagXTH12::GUS activity, alongside PagXTH12-overexpression poplar lines, substantiated the role of PagXTH12 in modulating the balance between plant biomass and drought resistance. Overall, this research provides valuable insights into the biological functions of XTHs in plant environmental adaptability and offers strategies for targeted regulation of tree growth and stress resistance.

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar (Populus trichocarpa). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

Intraspecific variability in plant and soil chemical properties in a common garden plantation of the energy crop Populus

Optimizing crops for synergistic soil carbon (C) sequestration can enhance CO2 removal in food and bioenergy production systems. Yet, in bioenergy systems, we lack an understanding of how intraspecies variation in plant traits correlates with variation in soil biogeochemistry. This knowledge gap is exacerbated by both the heterogeneity and difficulty of measuring belowground traits. Here, we provide initial observations of C and nutrients in soil and root and stem tissues from a common garden field site of diverse, natural variant, Populus trichocarpa genotypes-established for aboveground biomass-to-biofuels research. Our goal was to explore the value of such field sites for evaluating genotype-specific effects on soil C, which ultimately informs the potential for optimizing bioenergy systems for both aboveground productivity and belowground C storage. To do this, we investigated variation in chemical traits at the scale of individual trees and genotypes and we explored correlations among stem, root, and soil samples. We observed substantial variation in soil chemical properties at the scale of individual trees and specific genotypes. While correlations among elements were observed both within and among sample types (soil, stem, root), above-belowground correlations were generally poor. We did not observe genotype-specific patterns in soil C in the top 10 cm, but we did observe genotype associations with soil acid-base chemistry (soil pH and base cations) and bulk density. Finally, a specific phenotype of interest (high vs low lignin) was unrelated to soil biogeochemistry. Our pilot study supports the usefulness of decade-old, genetically-variable, Populus bioenergy field test plots for understanding plant genotype effects on soil properties. Finally, this study contributes to the advancement of sampling methods and baseline data for Populus systems in the Pacific Northwest, USA. Further species- and region-specific efforts will enhance C predictability across scales in bioenergy systems and, ultimately, accelerate the identification of genotypes that optimize yield and carbon storage.

Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus

Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.

Rare variations within the serine/arginine-rich splicing factor PtoRSZ21 modulate stomatal size to determine drought tolerance in Populus

Rare variants contribute significantly to the 'missing heritability' of quantitative traits. The genome-wide characteristics of rare variants and their roles in environmental adaptation of woody plants remain unexplored. Utilizing genome-wide rare variant association study (RVAS), expression quantitative trait loci (eQTL) mapping, genetic transformation, and molecular experiments, we explored the impact of rare variants on stomatal morphology and drought adaptation in Populus. Through comparative analysis of five world-wide Populus species, we observed the influence of mutational bias and adaptive selection on the distribution of rare variants. RVAS identified 75 candidate genes correlated with stomatal size (SS)/stomatal density (SD), and a rare haplotype in the promoter of serine/arginine-rich splicing factor PtoRSZ21 emerged as the foremost association signal governing SS. As a positive regulator of drought tolerance, PtoRSZ21 can recruit the core splicing factor PtoU1-70K to regulate alternative splicing (AS) of PtoATG2b (autophagy-related 2). The rare haplotype PtoRSZ21hap2 weakens binding affinity to PtoMYB61, consequently affecting PtoRSZ21 expression and SS, ultimately resulting in differential distribution of Populus accessions in arid and humid climates. This study enhances the understanding of regulatory mechanisms that underlie AS induced by rare variants and might provide targets for drought-tolerant varieties breeding in Populus.

Biotechnology and Genomic Approaches to Mitigating Disease Impacts on Forest Health

Outbreaks of insects and diseases are part of the natural disturbance regime of all forests. However, introduced pathogens have had outsized impacts on many dominant forest tree species over the past century. Mitigating these impacts and restoring these species are dilemmas of the modern era. Here, we review the ecological and economic impact of introduced pathogens, focusing on examples in North America. We then synthesize the successes and challenges of past biotechnological approaches and discuss the integration of genomics and biotechnology to help mitigate the effects of past and future pathogen invasions. These questions are considered in the context of the transgenic American chestnut, which is the most comprehensive example to date of how biotechnological tools have been used to address the impacts of introduced pathogens on naïve forest ecosystems.

Genetic differentiation across a steep and narrow environmental gradient: Quantitative genetic and genomic insights into Lake Superior populations of Quercus rubra

Adaptive differentiation of traits and underlying loci can occur at a small geographical scale if natural selection is stronger than countervailing gene flow and drift. We investigated this hypothesis using coupled quantitative genetic and genomic approaches for a wind-pollinated tree species, Quercus rubra, along the steep, narrow gradient of the Lake Superior coast that encompasses four USDA Hardiness Zones within 100 km. For the quantitative genetic component of this study, we examined phenotypic differentiation among eight populations in a common garden, measuring seed mass, germination, height, stem diameter, leaf number, specific leaf area and survival. For the genomic component, we quantified genetic differentiation for 26 populations from the same region using RAD-seq. Because hybridisation with Quercus ellipsoidalis occurs in other parts of the species' range, we included two populations of this congener for comparison. In the common garden study, we found a strong signal of population differentiation that was significantly associated with at least one climate factor for nine of 10 measured traits. In contrast, we found no evidence of genomic differentiation among populations based on FST or any other measures. However, both distance-based and genotype-environment association analyses identified loci showing the signature of selection, with one locus in common across five analyses. This locus was associated with the minimum temperature of the coldest month, a factor that defines the climate zones and was also significant in the common garden analyses. In addition, we documented introgression from Q. ellipsoidalis into Q. rubra, with rates of introgression correlated with the climate gradient. In sum, this study reveals signatures of selection at the quantitative trait and genomic level consistent with climate adaptation, a pattern that is more often documented at a much broader geographical scale, especially in long-lived wind-pollinated species.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Genotyping SNPs in lignin biosynthesis gene (CAD1) and transcription factors (MYB1 and MYB2) exhibits association with wood density in teak (Tectona grandis L.f.)

BACKGROUND

Teak (Tectona grandis L.f.), an important source of tropical timber with immense economic value, is a highly outcrossing forest tree species. 150 unrelated accessions of teak (Tectona grandis L.f.) plus trees assembled as clones at National Teak Germplasm Bank, Chandrapur, Maharashtra, India was investigated for association mapping of candidate lignin biosynthesis gene (CAD1) and transcription factors (MYB1 and MYB2).

METHODS AND RESULTS

The CAD1, MYB1 and MYB2 were amplified using specifically designed primers. The amplified sequences were then sequenced and genotyped for 112 SNPs/11 indels. We evaluated the association between SNPs and wood density in teak accessions using GLM and MLM statistical models, with Bonferroni correction applied. The teak accessions recorded an average wood density of 416.69 kg.m-3 (CV 4.97%) and comprised of three loosely structured admixed sub-populations (K = 3), containing 72.05% genetic variation within sub-populations with low intragenic LD (0-21% SNP pairs) at P < 0.05 and high LD decay (33-934 bp) at R2 = 0.1. GLM and MLM models discounting systematic biases (Q and K matrices) to avoid false discovery revealed five loci at rare variants (MAF 0.003) and three loci at common variants (MAF 0.05) to be significantly (P < 0.05) associated with the wood density. However, the stringent Bonferroni correction (4.06-7.04 × 10-4) yielded only a single associated locus (B1485C/A) from exon of MYB1 transcription factor, contributing to about 10.35% phenotypic variation in wood density trait.

CONCLUSION

Scored SNP locus (B1485C/A) can be developed as a molecular probe for selection of improved planting stock with proven wood density trait for a large-scale teak plantation.

Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur

BACKGROUND

Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change.

RESULTS

Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change.

CONCLUSIONS

The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.

Populus cathayana genome and population resequencing provide insights into its evolution and adaptation

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.

The Euphrates Poplar Responses to Abiotic Stress and Its Unique Traits in Dry Regions of China (Xinjiang and Inner Mongolia): What Should We Know?

At the moment, drought, salinity, and low-temperature stress are ubiquitous environmental issues. In arid regions including Xinjiang and Inner Mongolia and other areas worldwide, the area of tree plantations appears to be rising, triggering tree growth. Water is a vital resource in the agricultural systems of countries impacted by aridity and salinity. Worldwide efforts to reduce quantitative yield losses on Populus euphratica by adapting tree plant production to unfavorable environmental conditions have been made in response to the responsiveness of the increasing control of water stress. Although there has been much advancement in identifying the genes that resist abiotic stresses, little is known about how plants such as P. euphratica deal with numerous abiotic stresses. P. euphratica is a varied riparian plant that can tolerate drought, salinity, low temperatures, and climate change, and has a variety of water stress adaptability abilities. To conduct this review, we gathered all available information throughout the Web of Science, the Chinese National Knowledge Infrastructure, and the National Center for Biotechnology Information on the impact of abiotic stress on the molecular mechanism and evolution of gene families at the transcription level. The data demonstrated that P. euphratica might gradually adapt its stomatal aperture, photosynthesis, antioxidant activities, xylem architecture, and hydraulic conductivity to endure extreme drought and salt stress. Our analyses will give readers an understanding of how to manage a gene family in desert trees and the influence of abiotic stresses on the productivity of tree plants. They will also give readers the knowledge necessary to improve biotechnology-based tree plant stress tolerance for sustaining yield and quality trees in China's arid regions.

Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.

Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials

Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.

Natural variation in the prolyl 4-hydroxylase gene PtoP4H9 contributes to perennial stem growth in Populus

Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.

Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa

Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.

Admixture mapping and selection scans identify genomic regions associated with stomatal patterning and disease resistance in hybrid poplars

Variation in fitness components can be linked in some cases to variation in key traits. Metric traits that lie at the intersection of development, defense, and ecological interactions may be expected to experience environmental selection, informing our understanding of evolutionary and ecological processes. Here, we use quantitative genetic and population genomic methods to investigate disease dynamics in hybrid and non-hybrid populations. We focus our investigation on morphological and ecophysiological traits which inform our understanding of physiology, growth, and defense against a pathogen. In particular, we investigate stomata, microscopic pores on the surface of a leaf that regulate gas exchange during photosynthesis and are sites of entry for various plant pathogens. Stomatal patterning traits were highly predictive of disease risk. Admixture mapping identified a polygenic basis of disease resistance. Candidate genes for stomatal and disease resistance map to the same genomic regions and experienced positive selection. Genes with functions to guard cell homeostasis, the plant immune system, components of constitutive defenses, and growth-related transcription factors were identified. Our results indicate positive selection acted on candidate genes for stomatal patterning and disease resistance, potentially acting in concert to structure their variation in naturally formed backcrossing hybrid populations.

Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (a) does not require experimental or image preprocessing, (b) uses the raw RGB images at full resolution, and (c) requires very few samples for training (e.g., just 8 images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (a) methods for fast and accurate image-based feature extraction that require minimal training data and (b) a new population-scale dataset, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

CRISPR/Cas9 mutants delineate roles of Populus FT and TFL1/CEN/BFT family members in growth, dormancy release and flowering

Vegetative and reproductive phase change and phenology are economically and ecologically important traits. Trees typically require several years of growth before flowering and, once mature, seasonal control of the transition to flowering and flower development is necessary to maintain vegetative meristems and for reproductive success. Members of two related gene subfamilies, FLOWERING LOCUST (FT) and TERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN)/BROTHER OF FT AND TFL1 (BFT), have antagonistic roles in flowering in diverse species and roles in vegetative phenology in trees, but many details of their functions in trees have yet to be resolved. Here, we used CRISPR/Cas9 to generate single and double mutants involving the five Populus FT and TFL1/CEN/BFT genes. The ft1 mutants exhibited wild-type-like phenotypes in long days and short days, but after chilling, to release dormancy, they showed delayed bud flush and GA3 could compensate for the ft1 mutation. After rooting and generating some phytomers in tissue culture, both cen1 and cen1ft1 mutants produced terminal as well as axillary flowers, indicating that the cen1 flowering phenotype is independent of FT1. The CEN1 showed distinct circannual expression patterns in vegetative and reproductive tissues and comparison with the expression patterns of FT1 and FT2 suggests that the relative levels of CEN1 compared with FT1 and FT2 regulate multiple phases of vegetative and reproductive seasonal development.

Rapid screening of secondary aromatic metabolites in Populus trichocarpa leaves

BACKGROUND

High-throughput metabolomics analytical methodology is needed for population-scale studies of bioenergy-relevant feedstocks such as poplar (Populus sp.). Here, the authors report the relative abundance of extractable aromatic metabolites in Populus trichocarpa leaves rapidly estimated using pyrolysis-molecular beam mass spectrometry (py-MBMS). Poplar leaves were analyzed in conjunction with and validated by GC/MS analysis of extracts to determine key spectral features used to build PLS models to predict the relative composition of extractable aromatic metabolites in whole poplar leaves.

RESULTS

The Pearson correlation coefficient for the relative abundance of extractable aromatic metabolites based on ranking between GC/MS analysis and py-MBMS analysis of the Boardman leaf set was 0.86 with R² = 0.76 using a simplified prediction approach from select ions in MBMS spectra. Metabolites most influential to py-MBMS spectral features in the Clatskanie set included the following compounds: catechol, salicortin, salicyloyl-coumaroyl-glucoside conjugates, α-salicyloylsalicin, tremulacin, as well as other salicylates, trichocarpin, salicylic acid, and various tremuloidin conjugates. Ions in py-MBMS spectra with the highest correlation to the abundance of extractable aromatic metabolites as determined by GC/MS analysis of extracts, included m/z 68, 71, 77, 91, 94, 105, 107, 108, and 122, and were used to develop the simplified prediction approach without PLS models or a priori measurements.

CONCLUSIONS

The simplified py-MBMS method is capable of rapidly screening leaf tissue for relative abundance of extractable aromatic secondary metabolites to enable prioritization of samples in large populations requiring comprehensive metabolomics that will ultimately inform plant systems biology models and advance the development of optimized biomass feedstocks for renewable fuels and chemicals.

A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Genotype-environment associations to reveal the molecular basis of environmental adaptation

A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.

Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis

In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude. By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62-2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene-Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.

Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus

Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F₁ hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.

High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Background

The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F₁ populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes.

Results

Our mapping approach used probabilistic error correction of the marker data, followed by an iterative approach based on stringent parameters. This approach proved highly effective in producing high-density maps with robust marker orders and realistic map lengths (1285–4674 markers per map, with sizes ranging from c. 1643–2292 cM, and mean marker intervals of 0.7–2.1 cM). Colinearity was high between parental linkage maps, although there was evidence for a large chromosomal rearrangement (affecting ~ 90 cM) in one of the parental maps. In total, 28 QTL were detected for growth (stem diameter) and wood properties (wood density and fibre properties measured by Silviscan) in the QTL discovery population, with 1–3 QTL of small to moderate effect size detected per trait in each parental map. Four of these QTL were validated in a second, unrelated F₁ population. Results from genomic prediction and analyses of genetic architecture were consistent with those from QTL scans, with wood properties generally having moderate to high genomic heritabilities and predictive abilities, as well as somewhat less complex genetic architectures, compared to growth traits.

Conclusions

Despite the economic importance of radiata pine as a plantation forest tree, robust high-density linkage maps constructed from reproducible, sequence-anchored markers have not been published to date. The maps produced in this study will be a valuable resource for several applications, including the selection of marker panels for genomic prediction and anchoring a recently completed de novo whole genome assembly. We also provide the first map-based evidence for a large genomic rearrangement in radiata pine. Finally, results from our QTL scans, genomic prediction, and genetic architecture analyses are informative about the genomic basis of variation in important phenotypic traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08950-6.

Genome Wide Analysis of Family-1 UDP Glycosyltransferases in Populus trichocarpa Specifies Abiotic Stress Responsive Glycosylation Mechanisms

Populus trichocarpa (Black cottonwood) is a dominant timber-yielding tree that has become a notable model plant for genome-level insights in forest trees. The efficient transport and solubility of various glycoside-associated compounds is linked to Family-1 UDP-glycosyltransferase (EC 2.4.1.x; UGTs) enzymes. These glycosyltransferase enzymes play a vital role in diverse plant functions, such as regulation of hormonal homeostasis, growth and development (seed, flower, fiber, root, etc.), xenobiotic detoxification, stress response (salt, drought, and oxidative), and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of the P. trichocarpa genome that identified 191 putative UGTs distributed across all chromosomes (with the exception of chromosome 20) based on 44 conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. Phylogenetic analysis of the 191 Populus UGTs together with 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 16 major groups (A–P). Whole-genome duplication events were the dominant pattern of duplication among UGTs in Populus. A well-conserved intron insertion was detected in most intron-containing UGTs across eight examined eudicots, including Populus. Most of the UGT genes were found preferentially expressed in leaf and root tissues in general. The regulation of putative UGT expression in response to drought, salt and heat stress was observed based on microarray and available RNA sequencing datasets. Up- and down-regulated UGT expression models were designed, based on transcripts per kilobase million values, confirmed their maximally varied expression under drought, salt and heat stresses. Co-expression networking of putative UGTs indicated their maximum co-expression with cytochrome P450 genes involved in triterpenoid biosynthesis. Our results provide an important resource for the identification of functional UGT genes to manipulate abiotic stress responsive glycosylation in Populus.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.

Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait

Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. We examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm²  yr^-1 ) that genotypes invest in, they lose 1.2 to 1.7 units (mg g^-1 NSC) of storage. Across species, for each additional unit of area growth (in cm²  yr^-1 ), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.

Genomic consequences of artificial selection during early domestication of a wood fibre crop

From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.

Current status and trends in forest genomics

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species

Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed Q_ST -F_ST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on Q_ST -F_ST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R² up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.

Multiple dynamic models reveal the genetic architecture for growth in height of Catalpa bungei in the field

Growth in height (GH) is a critical determinant for tree survival and development in forests and can be depicted using logistic growth curves. Our understanding of the genetic mechanism underlying dynamic GH, however, is limited, particularly under field conditions. We applied two mapping models (Funmap and FVTmap) to find quantitative trait loci responsible for dynamic GH and two epistatic models (2HiGWAS and 1HiGWAS) to detect epistasis in Catalpa bungei grown in the field. We identified 13 co-located quantitative trait loci influencing the growth curve by Funmap and three heterochronic parameters (the timing of the inflection point, maximum acceleration and maximum deceleration) by FVTmap. The combined use of FVTmap and Funmap reduced the number of candidate genes by >70%. We detected 76 significant epistatic interactions, amongst which a key gene, COMT14, co-located by three models (but not 1HiGWAS) interacted with three other genes, implying that a novel network of protein interaction centered on COMT14 may control the dynamic GH of C. bungei. These findings provide new insights into the genetic mechanisms underlying the dynamic growth in tree height in natural environments and emphasize the necessity of incorporating multiple dynamic models for screening more reliable candidate genes.

Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections

The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families are shared by the studied four species, and 31 families are species-specific, which might be related to local adaptation. Additionally, multiple miRNA-related single nucleotide polymorphisms (SNPs) were found, indicating that polymorphisms in pre-miRNA hairpins were likely to affect miRNA biogenesis. This study expanded the breadth and depth of miRNA annotations and provided valuable resources for further exploring the diversity and function of poplar miRNAs.

Cross-population selection signatures in Canchim composite beef cattle

Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.

Globally Relaxed Selection and Local Adaptation in Boechera stricta

The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.

Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus

Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.

One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems

A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.

Genomics-Enabled Management of Genetic Resources in Radiata Pine

Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations (N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach.

Identifying and testing marker-trait associations for growth and phenology in three pine species: Implications for genomic prediction

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 single nucleotide polymorphisms (SNPs) from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.

Mutation bias reflects natural selection in Arabidopsis thaliana

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China

The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.

Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F₁ hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.