scholarly journals The genetic architecture of local adaptation I: The genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map

2014 ◽  
Author(s):  
Christopher J Friedline ◽  
Brandon M Lind ◽  
Erin M Hobson ◽  
Douglas E Harwood ◽  
Annette Delfino Mix ◽  
...  
Keyword(s):  
Linkage Map ◽  
Loblolly Pine ◽  
Tree Species ◽  
Genetic Architecture ◽  
Evolutionary Dynamics ◽  
Forest Tree ◽  
Linkage Maps ◽  
Adaptive Genetic Variation ◽  
Sequencing Technologies ◽  
Pinus Balfouriana

Explaining the origin and evolutionary dynamics of the genetic architecture of adaptation is a major research goal of evolutionary genetics. Despite controversy surrounding success of the attempts to accomplish this goal, a full understanding of adaptive genetic variation necessitates knowledge about the genomic location and patterns of dispersion for the genetic components affecting fitness-related phenotypic traits. Even with advances in next generation sequencing technologies, the production of full genome sequences for non-model species is often cost prohibitive, especially for tree species such as pines where genome size often exceeds 20 to 30 Gbp. We address this need by constructing a dense linkage map for fox- tail pine (Pinus balfouriana Grev. & Balf.), with the ultimate goal of uncovering and explaining the origin and evolutionary dynamics of adaptive genetic variation in natural populations of this forest tree species. We utilized megagametophyte arrays (n = 76?95 megagametophytes/tree) from four maternal trees in combination with double-digestion restriction site associated DNA sequencing (ddRADseq) to produce a consensus linkage map covering 98.58% of the foxtail pine genome, which was estimated to be 1276 cM in length (95% CI: 1174cM to 1378cM). A novel bioinformatic approach using iterative rounds of marker ordering and imputation was employed to produce single-tree linkage maps (507?17066 contigs/map; lengths: 1037.40?1572.80 cM). These linkage maps were collinear across maternal trees, with highly correlated marker orderings (Spearman's ρ > 0.95). A consensus linkage map derived from these single-tree linkage maps contained 12 linkage groups along which 20 655 contigs were non-randomly distributed across 901 unique positions (n = 23 contigs/position), with an average spacing of 1.34 cM between adjacent positions. Of the 20 655 contigs positioned on the consensus linkage map, 5627 had enough sequence similarity to contigs contained within the most recent build of the loblolly pine (P. taeda L.) genome to identify them as putative homologs containing both genic and non-genic loci. Importantly, all 901 unique positions on the consensus linkage map had at least one contig with putative homology to loblolly pine. When combined with the other biological signals that predominate in our data (e.g., correlations of recombination fractions across single trees), we show that dense linkage maps for non-model forest tree species can be efficiently constructed using next generation sequencing technologies. We subsequently discuss the usefulness of these maps as community-wide resources and as tools with which to test hypotheses about the genetic architecture of adaptation.

scholarly journals Fate of forest tree biotechnology facing climate change

2021 ◽  
Vol 70 (1) ◽  
pp. 117-136
Author(s):  
M. R. Ahuja
Keyword(s):  
Climate Change ◽  
Somatic Embryogenesis ◽  
Loblolly Pine ◽  
Tree Species ◽  
Forest Tree ◽  
Future Climate Change ◽  
Forest Trees ◽  
Forest Tree Species ◽  
Tree Biotechnology

Abstract Woody plants have been cultured in vitro since the 1930s. After that time much progress has been made in the culture of tissues, organs, cells, and protoplasts in tree species. Tree biotechnology has been making strides in clonal propagation by organogenesis and somatic embryogenesis. These regeneration studies have paved the way for gene transfer in forest trees. Transgenics from a number of forest tree species carrying a variety of recombinant genes that code for herbicide tolerance, pest resistance, lignin modification, increased woody bio-mass, and flowering control have been produced by Agrobacterium-mediated and biolistic methods, and some of them are undergoing confined field trials. Although relatively stable transgenic clones have been produced by genetic transformation in trees using organogenesis or somatic embryogenesis, there were also unintended unstable genetic events. In order to overcome the problems of randomness of transgene integration and instability reported in Agrobacterium-mediated or biolistically transformed plants, site-specific transgene insertion strategies involving clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) platform offer prospects for precise genome editing in plants. Nevertheless, it is important to monitor phenotypic and genetic stability of clonal material, not just under greenhouse conditions, but also under natural field conditions. Genetically modified poplars have been commercialized in China, and eucalypts and loblolly pine are expected to be released for commercial deployment in USA. Clonal forestry and transgenic forestry have to cope with rapid global climate changes in the future. Climate change is impacting species distributions and is a significant threat to biodiversity. Therefore, it is important to deploy Strategies that will assist the survival and evolution of forest tree species facing rapid climate change. Assisted migration (managed relocation) and biotechnological approaches offer prospects for adaptation of forest trees to climate change.

scholarly journals Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

2022 ◽  
Vol 12 ◽  
Author(s):  
Isabel García-García ◽  
Belén Méndez-Cea ◽  
David Martín-Gálvez ◽  
José Ignacio Seco ◽  
Francisco Javier Gallego ◽  
...  
Keyword(s):  
Climate Change ◽  
Tree Species ◽  
State Of The Art ◽  
Forest Tree ◽  
Epigenetic Modifications ◽  
Sequencing Technologies ◽  
Induced Stress ◽  
Generation Times ◽  
Reference Genomes ◽  
Sessile Organisms

Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.

scholarly journals Phylogenomic approaches reveal how a climatic inversion and glacial refugia shape patterns of diversity in an African rain forest tree species

2019 ◽  
Author(s):  
Andrew J. Helmstetter ◽  
Biowa E. N. Amoussou ◽  
Kevin Bethune ◽  
Narcisse G. Kandem ◽  
Romain Glèlè Kakaï ◽  
...  
Keyword(s):  
Tree Species ◽  
Rain Forest ◽  
Tropical Rain Forest ◽  
Evolutionary Dynamics ◽  
Central Africa ◽  
Glacial Refugia ◽  
Forest Tree ◽  
Ancestral Population ◽  
Forest Tree Species ◽  
The North

AbstractThe world’s second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity close to the equator at the level of a climatic inversion. Here, we take a phylogeographic approach using 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We show for the first time that the North-South divide is the result of a single major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggest that differences in ecological niche of populations distributed either side of this inversion may have contributed to this phylogenetic discontinuity. We find evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.

scholarly journals A National Multi-Scale Assessment of Regeneration Deficit as an Indicator of Potential Risk of Forest Genetic Variation Loss

Forests ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 19
Author(s):  
Kevin M. Potter ◽  
Kurt Riitters
Keyword(s):  
At Risk ◽  
Genetic Variation ◽  
Tree Species ◽  
Boreal Forests ◽  
The United States ◽  
Forest Tree ◽  
National Forest Inventory ◽  
Adaptive Genetic Variation ◽  
Seed Zones ◽  
Plot Network

Genetic diversity is essential because it provides a basis for adaptation and resilience to environmental stress and change. The fundamental importance of genetic variation is recognized by its inclusion in the Montréal Process sustainability criteria and indicators for temperate and boreal forests. The indicator that focuses on forest species at risk of losing genetic variation, however, has been difficult to address in a systematic fashion. We combined two broad-scale datasets to inform this indicator for the United States: (1) tree species occurrence data from the national Forest Inventory and Analysis (FIA) plot network and (2) climatically and edaphically defined provisional seed zones, which are proxies for among-population adaptive variation. Specifically, we calculated the estimated proportion of small trees (seedlings and saplings) relative to all trees for each species and within seed zone sub-populations, with the assumption that insufficient regeneration could lead to the loss of genetic variation. The threshold between sustainable and unsustainable proportions of small trees reflected the expectation of age–class balance at the landscape scale. We found that 46 of 280 U.S. forest tree species (16.4%) may be at risk of losing genetic variation. California and the Southeast encompassed the most at-risk species. Additionally, 39 species were potentially at risk within at least half of the seed zones in which they occurred. Seed zones in California and the Southwest had the highest proportions of tree species that may be at risk. The results could help focus conservation and management activities to prevent the loss of adaptive genetic variation within tree species.

Improved AFLP analysis of tree species

2000 ◽  
Vol 30 (10) ◽  
pp. 1608-1616 ◽  
Author(s):  
M T Cervera ◽  
D Remington ◽  
J -M Frigerio ◽  
V Storme ◽  
B Ivens ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Tree Species ◽  
Prunus Persica ◽  
Genome Mapping ◽  
Woody Species ◽  
Forest Tree ◽  
Aflp Analysis ◽  
Tree Genetics ◽  
Pinus Taeda L

Amplified fragment length polymorphism (AFLP) is a high-throughput, molecular-marker technique that is used increasingly in a variety of genetic analyses. Here, the conditions for carrying out AFLP analysis have been established for different tree species, including both angiosperm and gymnosperm trees, with genome sizes ranging from 0.54 to 38 pg DNA/2C. Specific parameters have been determined to provide informative and reproducible AFLP fingerprints of peach (Prunus persica L.), eucalypt, oak, poplar, and loblolly pine (Pinus taeda L.). Typically, 80-130 amplified DNA fragments (i.e., loci analyzed per primer combination) were obtained. Subsequently, these AFLP conditions were evaluated for intra- and inter-specific genetic variability studies as well as for genome mapping purposes of woody species. This work demonstrates that AFLP is a powerful tool in forest tree genetics.

scholarly journals A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shan-Shan Zhou ◽  
Xue-Mei Yan ◽  
Kai-Fu Zhang ◽  
Hui Liu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Age Determination ◽  
Genome Plasticity ◽  
Ltr Retrotransposons ◽  
Functional Variation ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Plant Groups ◽  
Functional Implications ◽  
Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

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