scholarly journals Evolutionary quantitative genomics of Populus trichocarpa

2015 ◽  
Author(s):  
Ilga Porth ◽  
Jaroslav Klapste ◽  
Athena D McKown ◽  
Jonathan La Mantia ◽  
Robert D Guy ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Molecular Basis ◽  
Population Genomics ◽  
Populus Trichocarpa ◽  
Detection Methods ◽  
Forest Trees ◽  
Adaptive Traits ◽  
Trait Variation ◽  
Adaptive Trait ◽  
Quantitative Genomics

Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Merging quantitative genetics and population genomics, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin. 29,354 SNPs were investigated employing three different outlier detection methods. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection, and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees. We highlight that important loci underlying adaptive trait variation also show relationship to climate of origin.

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

2014 ◽  
Vol 46 (10) ◽  
pp. 1089-1096 ◽  
Author(s):  
Luke M Evans ◽  
Gancho T Slavov ◽  
Eli Rodgers-Melnick ◽  
Joel Martin ◽  
Priya Ranjan ◽  
...  
Keyword(s):  
Population Genomics ◽  
Populus Trichocarpa ◽  
Adaptive Trait ◽  
Signatures Of Selection ◽  
Trait Associations

scholarly journals Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree

2020 ◽  
Author(s):  
Juliette Archambeau ◽  
Marta Benito Garzón ◽  
Frédéric Barraquand ◽  
Marina de Miguel Vega ◽  
Christophe Plomion ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Data ◽  
Common Garden ◽  
Height Growth ◽  
Forest Trees ◽  
Trait Variation ◽  
Species Ranges ◽  
Adaptive Trait ◽  
Common Gardens ◽  
Plastic Components

AbstractPredicting adaptive-trait variation across species ranges is essential to assess the potential of populations to survive under future environmental conditions. In forest trees, multi-site common gardens have long been the gold standard for separating the genetic and plastic components of trait variation and predicting population responses to new environments. However, relying on common gardens alone limits our ability to extrapolate predictions to populations or sites not included in these logistically expensive and time-consuming experiments. In this study, we aimed to determine whether models that integrate large-scale climatic and genomic data could capture the underlying drivers of tree adaptive-trait variation, and thus improve predictions at large geographical scales. Using a clonal common garden consisting of 34 provenances of maritime pine (523 genotypes and 12,841 trees) planted in five sites under contrasted environments, we compared twelve statistical models to: (i) separate the genetic and plastic components of height growth, a key adaptive trait in forest trees, (ii) identify the relative importance of factors underlying height-growth variation across individuals and populations, and (iii) improve height-growth prediction of unknown observations and provenances. We found that the height-growth plastic component exceeded more than twice the genetic component. The plastic component was likely due to multiple environmental factors, including annual climatic variables, while the genetic component was driven by the confounded effects of past demographic history and provenance adaptation to the climate-of-origin. Distinct gene pools were characterized by different total genetic variance, with broad-sense heritability ranging from 0.104 (95% CIs: 0.065-0.146) to 0.223 (95% CIs: 0.093-0.363), suggesting different potential response to selection along the geographical distribution of maritime pine. When predicting height-growth of new observations, models combining population demographic history, provenance climate-of-origin, and positive-effect height-associated alleles (PEAs; previously identified by GWAs) explained as much variance as models relying directly on the common garden design. Noteworthy, these models explained substantially more variance when predicting height-growth in new provenances, particularly in harsh environments. Predicting quantitative traits of ecological and/or economic importance across species ranges would therefore benefit from integrating ecological and genomic information.

Adaptive trait variation in the federally endangered Lindera melissifolia (Lauraceae), as it relates to genotype and genotype-environment interaction1

2019 ◽  
Vol 146 (3) ◽  
pp. 166
Author(s):  
Tracy S. Hawkins ◽  
Craig S. Echt ◽  
Margaret S. Devall ◽  
Paul B. Hamel ◽  
A. Dan Wilson ◽  
...  
Keyword(s):  
Trait Variation ◽  
Adaptive Trait

scholarly journals Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

2018 ◽  
Author(s):  
Jacob W. Malcom ◽  
Thomas E. Juenger ◽  
Mathew A. Leibold
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Life History ◽  
Molecular Basis ◽  
Life History Traits ◽  
Evolutionary Dynamics ◽  
Daphnia Pulex ◽  
Life History Trait ◽  
Life History Variation ◽  
Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

scholarly journals Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress

2021 ◽  
Vol 7 (12) ◽  
pp. 1024
Author(s):  
Fengxin Dong ◽  
Yihan Wang ◽  
Ming Tang
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Plant Disease Resistance ◽  
Mycorrhizal Fungi ◽  
Populus Trichocarpa ◽  
Gene Expression Pattern ◽  
Oxygen Metabolism ◽  
Resistance Response ◽  
Expression Of Genes ◽  
Plant Pathogen Interaction

Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor–P. trichocarpa–B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes’ expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.

Quantitative Trait Variation, Molecular Basis of

2016 ◽  
pp. 388-394
Author(s):  
F. Seidl ◽  
R. Linder ◽  
I.M. Ehrenreich
Keyword(s):  
Quantitative Trait ◽  
Molecular Basis ◽  
Trait Variation

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

2020 ◽  
pp. PHYTO-08-20-035
Author(s):  
Pauline Hessenauer ◽  
Nicolas Feau ◽  
Upinder Gill ◽  
Benjamin Schwessinger ◽  
Gurcharn S. Brar ◽  
...  
Keyword(s):  
Population Genomics ◽  
Production Systems ◽  
Management Strategies ◽  
Forest Trees ◽  
Forest Production ◽  
Population Genomic ◽  
Genomic Studies ◽  
Pathogen Populations ◽  
Different Characteristics ◽  
Global Food

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

scholarly journals Molecular Basis of Disease Resistance and Perspectives on Breeding Strategies for Resistance Improvement in Crops

2020 ◽  
Vol 13 (10) ◽  
pp. 1402-1419
Author(s):  
Yiwen Deng ◽  
Yuese Ning ◽  
Dong-Lei Yang ◽  
Keran Zhai ◽  
Guo-Liang Wang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Molecular Basis ◽  
Breeding Strategies ◽  
Resistance Improvement
Sign in / Sign up

Export Citation Format

Share Document