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

George, Jan-Peter; Schueler, Silvio; Grabner, Michael; Karanitsch-Ackerl, Sandra; Mayer, Konrad; Stierschneider, Michael; Weißenbacher, Lambert; Loo, Marcela van

doi:10.1002/ece3.7654

Cited by 5 publications

(6 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The gene flow from warm and humid regions (EL and CN) to the cold and arid regions (NE and NW) was greater than the gene flow in the opposite direction, which was beneficial for increasing the genetic diversity of A. viridiflora in the cold and arid environments and enhancing its local adaptability. This result is in accord with studies on different populations of Silene ciliata ,Pseudotsuga menziesii and Eperua falcata (Brousseau, Fine, Dreyer, Vendramin, & Scotti, 2021;George et al, 2021;Morente-López et al, 2021). The G-phoCS results showed that A. viridifloradifferentiated into two lineages, NL and CW, 6.52 Mya.…”

Section: Demographic History and Gene Flow Among A Viridiflorasupporting

confidence: 91%

Genome and transcriptome variation in Aquilegia viridiflora underlies the adaptive evolution to the environment in the early stage of speciation

Zhang,

Wang,

Zhang

et al. 2024

Preprint

View full text Add to dashboard Cite

The elucidation of adaptive evolution mechanisms in the early stage of speciation is important for understanding the origin and evolution of species. Aquilegia viridiflora is in the early stage of speciation, has a wide distribution range, and shows obvious phenotypic variation among its different populations. In this study, to analyze the adaptive evolution mechanism of phenotypic differences in the early stages of speciation, we analyzed the phenotypes, genomes, and transcriptomes of different populations of A. viridiflora. Our results indicated that A. viridiflora originated in northwestern China, and the uplift of the northeastern Qinghai–Tibet Plateau in the late Miocene may have caused its differentiation. Aqcoe5G459400 was a key gene in the early stage of A. viridiflora speciation. Its expression was reduced in environments with large temperature differences between day and night, causing A. viridiflora to develop larger flowers and enhancing its attractiveness to pollinators. Our research revealed the genetic basis of the adaptive evolution of the phenotype in the early stage of speciation and provides new evidence of the pattern of speciation via adaptative radiation in columbine.

show abstract

Section: Demographic History and Gene Flow Among A Viridiflorasupporting

confidence: 91%

Genome and transcriptome variation in Aquilegia viridiflora underlies the adaptive evolution to the environment in the early stage of speciation

Zhang,

Wang,

Zhang

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…3) is not in line with this knowledge. The subdivision into ecotypes that belong to both, the coastal and interior variety of Pseudotsuga menziesii on a small range, such as in British Columbia where we find populations of all ecotypes, indeed happens in a transition zone where we can expect a lot of substructure in populations [57,66]. This becomes evident when allowing for more clusters in SI, Fig.…”

Section: Differentiation Of Ecotypesmentioning

confidence: 85%

“…Our ecotypic classification is determined by the interplay of three climatic factors throughout the range of Douglas-fir that might have been responsible for part of the genotypic adaptations in its biogeographic history [66]. These predictors constrain ecotype identification by prior knowledge that is taken from the literature [13].…”

Section: Differentiation Of Ecotypesmentioning

confidence: 99%

“…Rehfeldt et al [30], only survival responses matter for the results presented here. Lab research in Douglas-fir seedlings of coastal vs interior provenance found differences in some phenotypic traits, such as growth rates [66], but failed to find difference in others, such as twig water potential response to drought, in CO 2 assimilation or stomatal conductance, despite differences in root and leave terpene concentrations [17]. The classification of Douglasfir populations into six ecotypes by similar responses is somewhat a simplification, as intra-specific variation in adaptation is continuous [13].…”

Section: Differentiation Of Ecotypesmentioning

confidence: 99%

See 1 more Smart Citation

Identifying potential provenances for climate-change adaptation using spatially variable coefficient models

Wesselkamp,

Roberts,

Dormann

2024

BMC Ecol Evo

View full text Add to dashboard Cite

Background Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified. Results The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches. Conclusion While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.

show abstract

“…Nevertheless, the available 16‐Gbp assembly is rather fragmented (N50 scaffold = 340.7 kbp) and highly repetitive. Therefore, as a proxy to the prohibitive time and costs of genotyping by whole genome resequencing, a genotyping platform based on Douglas‐fir exome capture has been established (George et al ., 2021 ; Thistlethwaite et al ., 2017 ). Restriction site‐associated DNA sequencing (RADseq) could be another approach (Konar et al ., 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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

Vu,

Cao,

Hofmann

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

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

show abstract

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

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 5 publications

References 84 publications

Genome and transcriptome variation in Aquilegia viridiflora underlies the adaptive evolution to the environment in the early stage of speciation

Genome and transcriptome variation in Aquilegia viridiflora underlies the adaptive evolution to the environment in the early stage of speciation

Identifying potential provenances for climate-change adaptation using spatially variable coefficient models

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

Contact Info

Product

Resources

About