Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae)

Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts

The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.

The enigma of genetic adaptation in a panmictic pine

This article is a Commentary on Bruxaux et al. (2024), 243: 1231–1246.

Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla

BACKGROUND

Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla.

RESULTS

We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions.

CONCLUSIONS

Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.

Maritime Pine Rootstock Genotype Modulates Gene Expression Associated with Stress Tolerance in Grafted Stems

Climate change-induced hazards, such as drought, threaten forest resilience, particularly in vulnerable regions such as the Mediterranean Basin. Maritime pine (Pinus pinaster Aiton), a model species in Western Europe, plays a crucial role in the Mediterranean forest due to its genetic diversity and ecological plasticity. This study characterizes transcriptional profiles of scion and rootstock stems of four P. pinaster graft combinations grown under well-watered conditions. Our grafting scheme combined drought-sensitive and drought-tolerant genotypes for scions (GAL1056: drought-sensitive scion; and Oria6: drought-tolerant scion) and rootstocks (R1S: drought-sensitive rootstock; and R18T: drought-tolerant rootstock). Transcriptomic analysis revealed expression patterns shaped by genotype provenance and graft combination. The accumulation of differentially expressed genes (DEGs) encoding proteins, involved in defense mechanisms and pathogen recognition, was higher in drought-sensitive scion stems and also increased when grafted onto drought-sensitive rootstocks. DEGs involved in drought tolerance mechanisms were identified in drought-tolerant genotypes as well as in drought-sensitive scions grafted onto drought-tolerant rootstocks, suggesting their establishment prior to drought. These mechanisms were associated with ABA metabolism and signaling. They were also involved in the activation of the ROS-scavenging pathways, which included the regulation of flavonoid and terpenoid metabolisms. Our results reveal DEGs potentially associated with the conifer response to drought and point out differences in drought tolerance strategies. These findings suggest genetic trade-offs between pine growth and defense, which could be relevant in selecting more drought-tolerant Pinus pinaster trees.

Adaptive potential of maritime pine under contrasting environments

BACKGROUND

Predicting the adaptability of forest tree populations under future climates requires a better knowledge of both the adaptive significance and evolvability of measurable key traits. Phenotypic plasticity, standing genetic variation and degree of phenotypic integration shape the actual and future population genetic structure, but empirical estimations in forest tree species are still extremely scarce. We analysed 11 maritime pine populations covering the distribution range of the species (119 families and 8 trees/family, ca. 1300 trees) in a common garden experiment planted at two sites with contrasting productivity. We used plant height as a surrogate of fitness and measured five traits (mean and plasticity of carbon isotope discrimination, specific leaf area, needle biomass, Phenology growth index) related to four different strategies (acquisitive economics, photosynthetic organ size, growth allocation and avoidance of water stress).

RESULTS

Estimated values of additive genetic variation would allow adaptation of the populations to future environmental conditions. Overall phenotypic integration and selection gradients were higher at the high productivity site, while phenotypic integration within populations was higher at the low productivity site. Response to selection was related mainly to photosynthetic organ size and drought-avoidance mechanisms rather than to water use efficiency. Phenotypic plasticity of water use efficiency could be maladaptive, resulting from selection for height growth.

CONCLUSIONS

Contrary to the expectations in a drought tolerant species, our study suggests that variation in traits related to photosynthetic organ size and acquisitive investment of resources drive phenotypic selection across and within maritime pine populations. Both genetic variation and evolvability of key adaptive traits were considerably high, including plasticity of water use efficiency. These characteristics would enable a relatively fast micro-evolution of populations in response to the ongoing climate changes. Moreover, differentiation among populations in the studied traits would increase under the expected more productive future Atlantic conditions.

Genetic adaptations in the population history of Arabidopsis thaliana

A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.

Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.

Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech

Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.

Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine

How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.

Heat-Priming during Somatic Embryogenesis Increased Resilience to Drought Stress in the Generated Maritime Pine (Pinus pinaster) Plants

Drought stress is becoming the most important factor of global warming in forests, hampering the production of reproductive material with improved resilience. Previously, we reported that heat-priming maritime pine (Pinus pinaster) megagametophytes during SE produced epigenetic changes that generated plants better adapted to subsequent heat stress. In this work, we tested, in an experiment performed under greenhouse conditions, whether heat-priming will produce cross-tolerance to mild drought stress (30 days) in 3-year-old priming-derived plants. We found that they maintain constitutive physiological differences as compared to controls, such as higher proline, abscisic acid, starch, and reduced glutathione and total protein contents, as well as higher ΦPSII yield. Primed plants also displayed a constitutive upregulation of the WRKY transcription factor and the Responsive to Dehydration 22 (RD22) genes, as well as of those coding for antioxidant enzymes (APX, SOD, and GST) and for proteins that avoid cell damage (HSP70 and DHNs). Furthermore, osmoprotectants as total soluble sugars and proteins were early accumulated in primed plants during the stress. Prolongated water withdrawal increased ABA accumulation and negatively affected photosynthesis in all plants but primed-derived plants recovered faster than controls. We concluded that high temperature pulses during somatic embryogenesis resulted in transcriptomic and physiological changes in maritime pine plants that can increase their resilience to drought stress, since heat-primed plants exhibit permanent activation of mechanisms for cell protection and overexpression of stress pathways that pre-adapt them to respond more efficiently to soil water deficit.

Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks

Improving our knowledge of how past climate-driven selection has acted on present-day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction-site-associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen-mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate-driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought-prone environments even in a context of very high rates of gene flow among populations.

Harnessing tree-ring phenotypes to disentangle gene by environment interactions and their climate dependencies in a circum-Mediterranean pine

BACKGROUND AND AIMS

Understanding the genetic basis of adaptation and plasticity in trees constitutes a knowledge gap. We linked dendrochronology and genomics [single nucleotide polymorphisms (SNPs)] for a widespread conifer (Pinus halepensis Mill.) to characterize intraspecific growth differences elicited by climate.

METHODS

The analysis comprised 20-year tree-ring series of 130 trees structured in 23 populations evaluated in a common garden. We tested for genotype by environment interactions (G × E) of indexed ring width (RWI) and early- to latewood ratios (ELI) using factorial regression, which describes G × E as differential gene sensitivity to climate.

KEY RESULTS

The species' annual growth was positively influenced by winter temperature and spring moisture and negatively influenced by previous autumn precipitation and warm springs. Four and five climate factors explained 10 % (RWI) and 16 % (ELI) of population-specific interannual variability, respectively, with populations from drought-prone areas and with uneven precipitation experiencing larger growth reductions during dry vegetative periods. Furthermore, four and two SNPs explained 14 % (RWI) and 10 % (ELI) of interannual variability among trees, respectively. Two SNPs played a putative role in adaptation to climate: one identified from transcriptome sequencing of P. halepensis and another involved in response regulation to environmental stressors.

CONCLUSIONS

We highlight how tree-ring phenotypes, obtained from a common garden experiment, combined with a candidate-gene approach allow the quantification of genetic and environmental effects determining adaptation for a conifer with a large and complex genome.