Roles of the Environment in Plant Life-History Trade-offs

Variation in plant life-history and functional traits at between- and within-species levels has key ecological consequences, in which environmental settings impose strong selective pressures and play a vital role throughout life cycles. Our general notion for plant life-history strategies may be that, relative to tall, long-lived plants, short-lived species have features of small stature, small-seededness, rapid growth, and low seedling survival (k- versus r-selection). Rate of evolution may be an important agent of selection and annals evolve more rapidly than perennial congeners. These empirical observations prompt a suite of enticing questions, such as how do life-history traits interplay with functional trait at late stages of regeneration? what are the primary trade-offs in a cohort of key life-history traits that may have undergone stabilizing selection? and how do environmental filters differently affect adaptive trait variation in annuals and perennials? In this chapter, we intend to address aforementioned questions via assembling our updated knowledge with emphasis on seed mass and temporal and spatial dimensions of seed dispersal. Through such synthesis, we wish to raise awareness about life-history trade-offs and provide a holistic understanding of the extent to which climate change is likely to impact plant adaptation and eco-evolutionary trajectories of life-history phenotypes

Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca

Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce (Picea glauca) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm.Inst. de Recursos BiológicosFil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: El-Dien, Omnia Gamal. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá. Alexandria University. Faculty of Pharmacy. Pharmacognosy Department; EgiptoFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; CanadáFil: Klapste, Jaroslav. Czech University of Life Sciences Prague. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República Checa. Scion (New Zealand Forest Research Institute Ltd.); Nueva ZelandaFil: El-Kassaby, Yousry A. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unido

Genomic diversity evaluation of populus trichocarpa germplasm for rare variant genetic association studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenomerelationship. In order to explain most of the observed heritability of a phenotypic trait, asufficient number of individuals and a large set of genetic variants must be examined. Thedevelopment of high-throughput technologies and cost-efficient resequencing of completegenomes have enabled the genome-wide identification of genetic variation at large scale.As such, almost all existing genetic variation becomes available, and it is now possible toidentify rare genetic variants in a population sample. Rare genetic variants that were usuallyfiltered out in most genetic association studies are the most numerous genetic variationsacross genomes and hold great potential to explain a significant part of the missingheritability observed in association studies. Rare genetic variants must be identified withhigh confidence, as they can easily be confounded with sequencing errors. In this study,we used a pre-filtered data set of 1,014 purePopulus trichocarpaentire genomes toidentify rare and common small genetic variants across individual genomes. We comparedvariant calls betweenPlatypusandHaplotypeCallerpipelines, and we further applied strictqualityfilters for improved genetic variant identification. Finally, we only retained geneticvariants that were identified by both variant callers increasing calling confidence. Based onthese shared variants and after stringent qualityfiltering, we found high genomic diversity inP. trichocarpagermplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance ofgenomic diversity and the potential of rare defective genetic variants in explaining asignificant portion ofP. trichocarpa's phenotypic variability in association genetics. Theultimate goal is to associate both rare and common alleles with poplar's wood quality traitsto support selective breeding for an improved bioenergy feedstock

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

Background The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with similar to 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesiiMirb. (Franco)) and Interior spruce (Picea glauca(Moench) Voss xPicea engelmanniiParry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200-50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F(1)families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada. Results As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000-15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size. Conclusions Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits

Exogenous 6-BA inhibited hypocotyl elongation under darkness in Picea crassifolia Kom revealed by transcriptome profiling

Hypocotyl elongation is an important process in plant growth and development, and is under hormonal regulatory signaling pathways. In our study, exogenous 6-BA significantly inhibited Picea crassifolia hypocotyl elongation more than ethylene in the dark, indicating the existence of different regulatory strategies in conifers, therefore, the P. crassifolia transcriptome was studied to explore the responsive genes and their regulatory pathways for exogenous N6-benzyladenine (6-BA) inhibition of hypocotyl elongation using RNA-Sequencing approach. We present the first transcriptome assembly of P. crassifolia obtained from 24.38 Gb clean data. With lowly-expressed and short contigs excluded, the assembly contains roughly 130,612 unigenes with an N50 length of 1,278 bp. Differential expression analysis found 3,629 differentially expressed genes (DEGs) and found that the differential expression fold of genes was mainly concentrated between 2 and 8 (1 ≤ log2FoldChange ≤ 3). Functional annotation showed that the GO term with the highest number of enriched genes (83 unigenes) was the shoot system development (GO: 0048367) and the KEGG category, plant hormone signal transduction (ko04075), was enriched 30 unigenes. Further analysis revealed that several cytokinin dehydrogenase genes (PcCTD1, PcCTD3 and PcCTD6) catabolized cytokinins, while xyloglucan endotransglucosylase hydrolase gene (PcXTH31), WALLS ARE THIN 1-like gene (PcWAT1-1) and Small auxin-induced gene (PcSAUR15) were strongly repressed thus synergistically completing the inhibition of hypocotyl elongation in P. crassifolia. Besides, PcbHLH149, PcMYB44 and PcERF14 were predicted to be potential core TFs that may form a multi-layered regulatory network with the above proteins for the regulation of hypocotyl growth

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

Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees

Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program

Tree improvement programs often focus on improving productivity-related traits; however, under present climate change scenarios, climate change-related (adaptive) traits should also be incorporated into such programs. Therefore, quantifying the genetic variation and correlations among productivity and adaptability traits, and the importance of genotype by environment interactions, including defense compounds involved in biotic and abiotic resistance, is essential for selecting parents for the production of resilient and sustainable forests. Here, we estimated quantitative genetic parameters for 15 growth, wood quality, drought resilience, and monoterpene traits for Picea glauca (Moench) Voss (white spruce). We sampled 1,540 trees from three open-pollinated progeny trials, genotyped with 467,224 SNP markers using genotyping-by-sequencing (GBS). We used the pedigree and SNP information to calculate, respectively, the average numerator and genomic relationship matrices, and univariate and multivariate individual-tree models to obtain estimates of (co)variance components. With few site-specific exceptions, all traits examined were under genetic control. Overall, higher heritability estimates were derived from the genomic- than their counterpart pedigree-based relationship matrix. Selection for height, generally, improved diameter and water use efficiency, but decreased wood density, microfibril angle, and drought resistance. Genome-based correlations between traits reaffirmed the pedigree-based correlations for most trait pairs. High and positive genetic correlations between sites were observed (average 0.68), except for those pairs involving the highest elevation, warmer, and moister site, specifically for growth and microfibril angle. These results illustrate the advantage of using genomic information jointly with productivity and adaptability traits, and defense compounds to enhance tree breeding selection for changing climate.Instituto de Recursos BiológicosFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Klutsch, Jenifer G. University of Alberta; Department of Renewable Resources; CanadaFil: Sebastian-Azcona, Jaime. University of Alberta; Department of Renewable Resources; CanadaFil: Ratchiffe, Blaise. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Xiaojing, Wei. University of Alberta; Department of Renewable Resources; CanadaFil: Da Ros, Letitia. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Yang, Liu. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados UnidosFil: Benowicz, Andy. Alberta Agriculture and Forestry. Forest Stewardship and Trade Branch; CanadáFil: Sadoway, Shane. Blue Ridge Lumber Inc.; CanadáFil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Erbilgin, Nadir. University of Alberta; Department of Renewable Resources; CanadaFil: Thomas, Barb R. University of Alberta; Department of Renewable Resources; CanadaFil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canad

Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine

14 páginas.- 4 figuras.- 1 tabla.- 101 referencias.- Supplementary material is available online at Evolution (https://academic.oup.com/evolut/qpad004) . A correction has been published: Evolution, Volume 77, Issue 4, 1 April 2023, Page 1174, https://doi.org/10.1093/evolut/qpad030 Issue Section: Correction This is a correction to: Yang Liu, Nadir Erbilgin, Eduardo Pablo Cappa, Charles Chen, Blaise Ratcliffe, Xiaojing Wei, Jennifer G Klutsch, Aziz Ullah, Jaime Sebastian Azcona, Barb R Thomas, Yousry A El-Kassaby, Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine, Evolution, 2023; qpad004, https://doi.org/10.1093/evolut/qpad004 In the originally published version of this manuscript, the images for Figures 3 and 4 were erroneously transposed. The images are now in their correct position to align with their respective legends. The Funding section was erroneously removed, and its details situated at the end of the Acknowledgements section. Funding details are now situated within the replaced Funding section. The publisher would like to apologise for the errors introduced here. The errors have been corrected in the article online.The environment could alter growth and resistance tradeoffs in plants by affecting the ratio of resource allocation to various competing traits. Yet, how and why functional tradeoffs change over time and space is poorly understood particularly in long-lived conifer species. By establishing four common-garden test sites for five lodgepole pine populations in western Canada, combined with genomic sequencing, we revealed the decoupling pattern and genetic underpinnings of tradeoffs between height growth, drought resistance based on δ13C and dendrochronology, and metrics of pest resistance based on pest suitability ratings. Height and δ13C correlation displayed a gradient change in magnitude and/or direction along warm-to-cold test sites. All cold test sites across populations showed a positive height and δ13C relationship. However, we did not observe such a clinal correlation pattern between height or δ13C and pest suitability. Further, we found that the study populations exhibiting functional tradeoffs or synergies to various degrees in test sites were driven by non-adaptive evolutionary processes rather than adaptive evolution or plasticity. Finally, we found positive genetic relationships between height and drought or pest resistance metrics and probed five loci showing potential genetic tradeoffs between northernmost and the other populations. Our findings have implications for deciphering the ecological, evolutionary, and genetic bases of the decoupling of functional tradeoffs due to environmental change.This work was funded by Genome Canada, Genome Alberta through Alberta Economic Trade and evelopment, Genome British Columbia, the University of Alberta, the University of Calgary, the University of Cambridge, and the Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture (CE200100015).Peer reviewe

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed