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Xu WQ, Ren CQ, Zhang XY, Comes HP, Liu XH, Li YG, Kettle CJ, Jalonen R, Gaisberger H, Ma YZ, Qiu YX. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1372-1387. [PMID: 38343032 DOI: 10.1111/tpj.16675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/31/2024]
Abstract
Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.
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Affiliation(s)
- Wu-Qin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Chao-Qian Ren
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xin-Yi Zhang
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hans-Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Xin-Hong Liu
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Yin-Gang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | | | - Riina Jalonen
- Bioversity International, Regional Office for Asia, Penang, Malaysia
| | | | - Ya-Zhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Ying-Xiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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Chen B, Wang M, Guo Y, Zhang Z, Zhou W, Cao L, Zhang T, Ali S, Xie L, Li Y, Zinta G, Sun S, Zhang Q. Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana. Mol Ecol 2024:e17356. [PMID: 38634782 DOI: 10.1111/mec.17356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China
| | - Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shahid Ali
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC PLANT BIOLOGY 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
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Affiliation(s)
- E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
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Guillardín L, MacKay JJ. Comparing DNA isolation methods for forest trees: quality, plastic footprint, and time-efficiency. PLANT METHODS 2023; 19:111. [PMID: 37858169 PMCID: PMC10588216 DOI: 10.1186/s13007-023-01086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Genetic and genomic studies are seeing an increase in sample sizes together with a wider range of species investigated in response to environmental change concerns. In turn, these changes may come with challenges including the time and difficulty to isolate nucleic acids (DNA or RNA), the sequencing cost and environmental impacts of the growing amount of plastic waste generated in the process. Pseudotsuga menziesii var. menziesii (Mirbel) Franco (PM), Tsuga heterophylla (Raf.) Sarg. (TH) and Thuja plicata Donn ex D.Don (TP) are conifer species found in diverse woodlands both as natives and naturalized exotics. Our study was carried out whilst investigating their genetics to understand their population structure and potential for adaptation. RESULTS In the present study, we compared two different DNA isolation methods, i.e., spin-column DNeasy plant mini kit (QIAGEN), and temperature-driven enzymatic cocktail Plant DNA Extraction (MicroGEM). The quantity of recovered DNA and the quality of DNA were assessed along with the plastic footprint and time needed for three tree species. Both methods were optimised and proven to provide enough DNA for each studied species. The yield of DNA for each method depended on the species: QIAGEN showed higher yield in P. menziesii and T. heterophylla, while T. plicata recovered similar amount of DNA for both methods. The DNA quality was investigated using DNA barcoding techniques by confirming species identity and species discrimination. No difference was detected in the PCR amplification of the two barcoding loci, (rbcL and trnH-psbA), and the recovered sequences between DNA isolation methods. Measurement of the plastic use and the processing time per sample indicated that MicroGEM had a 52.64% lower plastic footprint and was 51.8% faster than QIAGEN. CONCLUSIONS QIAGEN gave higher yields in two of the species although both methods showed similar quality results across all species. However, MicroGEM was clearly advantageous to decrease the plastic footprint and improve the time efficiency. Overall, MicroGEM recovers sufficient and reliable DNA to perform common downstream analyses such as PCR and sequencing. Our findings illustrate the benefits of research and efforts towards developing more sustainable methods and techniques to reduce the environmental footprint of molecular analyses.
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Affiliation(s)
- Laura Guillardín
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
| | - John J MacKay
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
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Riehl JFL, Cole CT, Morrow CJ, Barker HL, Bernhardsson C, Rubert‐Nason K, Ingvarsson PK, Lindroth RL. Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen ( Populus tremuloides Michx.). Ecol Evol 2023; 13:e10541. [PMID: 37780087 PMCID: PMC10534199 DOI: 10.1002/ece3.10541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.
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Affiliation(s)
| | | | - Clay J. Morrow
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Hilary L. Barker
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Present address:
Office of Student SuccessWisconsin Technical College SystemMadisonWisconsinUSA
| | - Carolina Bernhardsson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
- Present address:
Department of Organismal Biology, Center for Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Kennedy Rubert‐Nason
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Present address:
Division of Natural SciencesUniversity of Maine at Fort KentFort KentMaineUSA
| | - Pär K. Ingvarsson
- Department of Plant BiologySwedish University of Agricultural Sciences, Uppsala BioCenterUppsalaSweden
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Stettinius A, Holmes H, Zhang Q, Mehochko I, Winters M, Hutchison R, Maxwell A, Holliday J, Vlaisavljevich E. DNA release from plant tissue using focused ultrasound extraction (FUSE). APPLICATIONS IN PLANT SCIENCES 2023; 11:e11510. [PMID: 36818781 PMCID: PMC9934592 DOI: 10.1002/aps3.11510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/18/2023]
Abstract
PREMISE Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis. METHODS FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (Castanea dentata), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), and chestnut oak (Quercus montana). RESULTS We observed that FUSE can extract high quantities of DNA in 9-15 min, compared to the 30 min required for control DNA extraction methods. FUSE extracted DNA quantities of 24.33 ± 6.51 ng/mg and 35.32 ± 9.21 ng/mg from American chestnut and red maple, respectively, while control methods yielded 6.22 ± 0.87 ng/mg and 11.51 ± 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing. DISCUSSION These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.
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Affiliation(s)
- Alexia Stettinius
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Hal Holmes
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
- Conservation X LabsSeattleWashingtonUSA
| | - Qian Zhang
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Isabelle Mehochko
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | | | - Ruby Hutchison
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Adam Maxwell
- Department of UrologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jason Holliday
- Department of Forest Resources and Environmental ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Eli Vlaisavljevich
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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Feng Y, Zheng K, Lin X, Huang J. Plant growth, physiological variation and homological relationship of Cyclocarya species in ex situ conservation. CONSERVATION PHYSIOLOGY 2022; 10:coac016. [PMID: 35539008 PMCID: PMC9082347 DOI: 10.1093/conphys/coac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/25/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Natural forests of Cyclocarya paliurus have been seriously damaged because of the extreme demand for leaf medicinal uses, making conservation of this valuable, medicinal woody species necessary. Because of geographical differentiation and diverse adaptability, in this study we analysed the variations in plant growth and physiological response to environmental factors at a resource plantation of ex situ conservation and determined the homological relationships between local provenance (from Fujian Province, FJ) and introduced provenances showing high-survival rate and better growth (from Zhejiang, Hubei, Guizhou and Jiangxi Province). Our results suggested the following: (i) Plant growth: FJ had the highest plant height but not the largest basal diameter in comparison to that of other provenances. (ii) Physiological responses during the growth periods: water content in leaf of FJ had similar change with that of other provenances, except for the provenance from Guizhou Province; total soluble sugar content in leaf of FJ was more than that of other provenances; calcium content in leaf of all provenances was higher as compared to K, Mg and Na; the highest activity among four kinds of antioxidant enzymes in all provenances was superoxide dismutase, then was polyphenol oxidase and peroxidase, finally was catalase; and total flavonoid among three kinds of secondary metabolites in all provenances showed the greatest content, followed by polysaccharides and total triterpenoid. (iii) Relation analysis: plant growth and physiological responses related with environmental factors, especially temperature and precipitation. (iv) Homological relationships: leaf characteristics among six provenances varied in colour, area and common petiole length, but not the shape of leaf base or apex. Cyclocarya paliurus distributed in Fujian Province showed a very close homological relationship with that distributed in Zhejiang Province by simple sequence repeat. These findings will provide knowledge on physiological response to environmental factors and aid to select suitable provenances for Cyclocarya cultivation.
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Affiliation(s)
| | - Kailing Zheng
- Quanzhou Institute of Agricultural Science, Chidian Town, Jinjiang City, Fujian Province, 362000, China
| | - Xiulian Lin
- Horticulture Department, Huizhou Engineering Vocational College, Xiaojinkou Street, Guangdong Province, 561023, China
| | - Junpo Huang
- School of Resource and Environmental Science, Quanzhou Normal University, Donghai Street, Quanzhou City, Fujian Province, 362000, China
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Neophytou C, Heer K, Milesi P, Peter M, Pyhäjärvi T, Westergren M, Rellstab C, Gugerli F. Genomics and adaptation in forest ecosystems. TREE GENETICS & GENOMES 2022; 18:12. [PMID: 35210985 PMCID: PMC8828617 DOI: 10.1007/s11295-022-01542-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 05/11/2023]
Abstract
UNLABELLED Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of "Genomics and Adaptation in Forest Ecosystems" brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11295-022-01542-1.
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Affiliation(s)
- Charalambos Neophytou
- Institute of Silviculture, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Str. 82, A-1190, Vienna, Austria
| | - Katrin Heer
- Albert-Ludwigs Universität Freiburg, Forest Genetics, Bertoldstraße 17, D-79098 Freiburg, Germany
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE 752 36 and ScilifeLab, Uppsala, Sweden
| | - Martina Peter
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, FI-00014 Helsinki, Finland
| | | | - Christian Rellstab
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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12
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Feng L, Du FK. Landscape Genomics in Tree Conservation Under a Changing Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:822217. [PMID: 35283901 PMCID: PMC8908315 DOI: 10.3389/fpls.2022.822217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 05/11/2023]
Abstract
Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Fang K. Du,
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13
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Guevara-Escudero M, Osorio AN, Cortés AJ. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102022. [PMID: 34685832 PMCID: PMC8541610 DOI: 10.3390/plants10102022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 05/18/2023]
Abstract
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.
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Affiliation(s)
- Melisa Guevara-Escudero
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Angy N. Osorio
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Andrés J. Cortés
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
- Main Address: Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia
- Correspondence:
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14
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Mugula BB, Kiboi SK, Kanya JI, Egeru A, Okullo P, Curto M, Meimberg H. Knowledge Gaps in Taxonomy, Ecology, Population Distribution Drivers and Genetic Diversity of African Sandalwood ( Osyris lanceolata Hochst. & Steud.): A Scoping Review for Conservation. PLANTS 2021; 10:plants10091780. [PMID: 34579313 PMCID: PMC8465005 DOI: 10.3390/plants10091780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
The increasing demand for ornamental, cosmetic and pharmaceutical products is driving exploitation of plant species globally. Sub-Saharan Africa harbours unique and valuable plant resources and is now a target of plant resource depletion. African Sandalwood (Osyris lanceolata), a multi-purpose and drought-tolerant species, has seen increased exploitation for the last thirty years and is now declared endangered. Initiatives to conserve O. lanceolata are not yet successful in Africa due to poor understanding of the species. This review surveys relevant research on the ecology, taxonomy, population dynamics, genetic diversity and ethnobotany of O. lanceolata, and highlights gaps in the literature for further research. A scoping review of grey literature, scholarly papers and reports was applied with pre-determined criteria to screen relevant information. Review findings indicate O. lanceolata is a globally distributed species with no identified center of origin. In Africa, it ranges from Algeria to Ethiopia and south to South Africa; in Europe it occurs in the Iberian Peninsula and Balearic Islands; in Asia from India to China, and also on Socotra. The species has a confusing taxonomy, with unresolved issues in nomenclature, country range distribution, extensive synonymisation and variation in growth form (shrub or tree). The species population is reported to be declining in Africa, but information on population dynamics across its entire range of distribution is anecdotal. Additionally, ecological factors influencing spatial distribution and survival of the species remain unknown. A variety of uses are reported for O. lanceolata globally, including: cultural; medicinal and food; dye; perfumery; timber; ethnoveterinary and phytoremediation. Key research areas and implications for conservation of O. lanceolata in Sub-Saharan Africa are proposed.
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Affiliation(s)
- Ben Belden Mugula
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
- Department of Life and Physical Sciences, School of Natural Sciences, Bugema University, Kampala P.O. Box 6529, Uganda
- Correspondence:
| | - Samuel Kuria Kiboi
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
| | - James Ireri Kanya
- School of Biological Sciences, College of Biological and Physical Sciences, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya; (S.K.K.); (J.I.K.)
| | - Anthony Egeru
- College of Environmental and Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Paul Okullo
- National Agricultural Research Organization (NARO), Entebbe P.O. Box 295, Uganda;
| | - Manuel Curto
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Gregor Mendel-Straße 33, A-1180 Vienna, Austria; (M.C.); (H.M.)
- MARE-Marine and Environmental Sciences Centre, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | - Harald Meimberg
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Gregor Mendel-Straße 33, A-1180 Vienna, Austria; (M.C.); (H.M.)
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15
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Liu JJ, Schoettle AW, Sniezko RA, Williams H, Zamany A, Rancourt B. Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family. BMC Genomics 2021; 22:567. [PMID: 34294045 PMCID: PMC8299668 DOI: 10.1186/s12864-021-07885-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/29/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The available transcriptomes of limber pine (Pinus flexilis) allow us to characterize NLR genes and related resistance gene analogs (RGAs) in host resistance against Cronartium ribicola, the causal fungal pathogen of white pine blister rust (WPBR) on five-needle pines throughout the world. We previously mapped a limber pine major gene locus (Cr4) that confers complete resistance to C. ribicola on the Pinus consensus linkage group 8 (LG-8). However, genetic distribution of NLR genes as well as their divergence between resistant and susceptible alleles are still unknown. RESULTS To identify NLR genes at the Cr4 locus, the present study re-sequenced a total of 480 RGAs using targeted sequencing in a Cr4-segregated seed family. Following a call of single nucleotide polymorphisms (SNPs) and genetic mapping, a total of 541 SNPs from 155 genes were mapped across 12 LGs. Three putative NLR genes were newly mapped in the Cr4 region, including one that co-segregated with Cr4. The tight linkage of NLRs with Cr4-controlled phenotypes was further confirmed by bulked segregation analysis (BSA) using extreme-phenotype genome-wide association study (XP-GWAS) for significance test. Local tandem duplication in the Cr4 region was further supported by syntenic analysis using the sugar pine genome sequence. Significant gene divergences have been observed in the NLR family, revealing that diversifying selection pressures are relatively higher in local duplicated genes. Most genes showed similar expression patterns at low levels, but some were affected by genetic background related to disease resistance. Evidence from fine genetic dissection, evolutionary analysis, and expression profiling suggests that two NLR genes are the most promising candidates for Cr4 against WPBR. CONCLUSION This study provides fundamental insights into genetic architecture of the Cr4 locus as well as a set of NLR variants for marker-assisted selection in limber pine breeding. Novel NLR genes were identified at the Cr4 locus and the Cr4 candidates will aid deployment of this R gene in combination with other major/minor genes in the limber pine breeding program.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Anna W. Schoettle
- USDA Forest Service, Rocky Mountain Research Station, 240 West Prospect Road, Fort Collins, CO 80526 USA
| | - Richard A. Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, Oregon, 97424 USA
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Benjamin Rancourt
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
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16
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Lind BM, Lu M, Obreht Vidakovic D, Singh P, Booker TR, Aitken SN, Yeaman S. Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species. Mol Ecol Resour 2021; 22:225-238. [PMID: 34270863 PMCID: PMC9292622 DOI: 10.1111/1755-0998.13474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/18/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022]
Abstract
Despite their suitability for studying evolution, many conifer species have large and repetitive giga‐genomes (16–31 Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost‐saving benefits of pool‐seq and exome‐capture to discover SNPs in two conifer species, Douglas‐fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (r > .948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > .973). Our work addresses bioinformatic challenges in non‐model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool‐seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.
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Affiliation(s)
- Brandon M Lind
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Tom R Booker
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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17
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Cortés AJ, López-Hernández F. Harnessing Crop Wild Diversity for Climate Change Adaptation. Genes (Basel) 2021; 12:783. [PMID: 34065368 PMCID: PMC8161384 DOI: 10.3390/genes12050783] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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18
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von Takach B, Ahrens CW, Lindenmayer DB, Banks SC. Scale-dependent signatures of local adaptation in a foundation tree species. Mol Ecol 2021; 30:2248-2261. [PMID: 33740830 DOI: 10.1111/mec.15894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023]
Abstract
Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.
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Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia.,Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - David B Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program. Sci Rep 2021; 11:4990. [PMID: 33654140 PMCID: PMC7925517 DOI: 10.1038/s41598-021-84566-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7-68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson's correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.
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20
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Hoffmann AA, Miller AD, Weeks AR. Genetic mixing for population management: From genetic rescue to provenancing. Evol Appl 2021; 14:634-652. [PMID: 33767740 PMCID: PMC7980264 DOI: 10.1111/eva.13154] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.
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Affiliation(s)
- Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWarrnamboolVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | - Andrew R. Weeks
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
- cesar Pty LtdParkvilleVic.Australia
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21
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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22
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Do We Need to Identify Adaptive Genetic Variation When Prioritizing Populations for Conservation? CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01327-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don). Sci Rep 2021; 11:1496. [PMID: 33452328 PMCID: PMC7810747 DOI: 10.1038/s41598-020-80688-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022] Open
Abstract
Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) in Cryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterile C. japonica to reduce the pollinosis caused by pollen dispersal from artificial C. japonica forests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with the ms1. All nine breeding materials with the allele ms1 had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene of MS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials of C. japonica with the allele ms1 adapted to the unique environment of each region of the Japanese archipelago.
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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Jaramillo-Correa JP, Bagnoli F, Grivet D, Fady B, Aravanopoulos FA, Vendramin GG, González-Martínez SC. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse. Mol Ecol 2020; 29:4797-4811. [PMID: 33063352 DOI: 10.1111/mec.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene-loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene-loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa ) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
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Affiliation(s)
- Juan P Jaramillo-Correa
- Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francesca Bagnoli
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain
| | - Bruno Fady
- INRAE, Unité de Recherche Écologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Filippos A Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, Department of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
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26
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Cortés AJ, Restrepo-Montoya M, Bedoya-Canas LE. Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate. FRONTIERS IN PLANT SCIENCE 2020; 11:583323. [PMID: 33193532 PMCID: PMC7609427 DOI: 10.3389/fpls.2020.583323] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 05/02/2023]
Abstract
Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, Rionegro, Colombia
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Manuela Restrepo-Montoya
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Larry E. Bedoya-Canas
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
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27
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Brundu G, Pauchard A, Pyšek P, Pergl J, Bindewald AM, Brunori A, Canavan S, Campagnaro T, Celesti-Grapow L, Dechoum MDS, Dufour-Dror JM, Essl F, Flory SL, Genovesi P, Guarino F, Guangzhe L, Hulme PE, Jäger H, Kettle CJ, Krumm F, Langdon B, Lapin K, Lozano V, Le Roux JJ, Novoa A, Nuñez MA, Porté AJ, Silva JS, Schaffner U, Sitzia T, Tanner R, Tshidada N, Vítková M, Westergren M, Wilson JRU, Richardson DM. Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts. NEOBIOTA 2020. [DOI: 10.3897/neobiota.61.58380] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sustainably managed non-native trees deliver economic and societal benefits with limited risk of spread to adjoining areas. However, some plantations have launched invasions that cause substantial damage to biodiversity and ecosystem services, while others pose substantial threats of causing such impacts. The challenge is to maximise the benefits of non-native trees, while minimising negative impacts and preserving future benefits and options.
A workshop was held in 2019 to develop global guidelines for the sustainable use of non-native trees, using the Council of Europe – Bern Convention Code of Conduct on Invasive Alien Trees as a starting point.
The global guidelines consist of eight recommendations: 1) Use native trees, or non-invasive non-native trees, in preference to invasive non-native trees; 2) Be aware of and comply with international, national, and regional regulations concerning non-native trees; 3) Be aware of the risk of invasion and consider global change trends; 4) Design and adopt tailored practices for plantation site selection and silvicultural management; 5) Promote and implement early detection and rapid response programmes; 6) Design and adopt tailored practices for invasive non-native tree control, habitat restoration, and for dealing with highly modified ecosystems; 7) Engage with stakeholders on the risks posed by invasive non-native trees, the impacts caused, and the options for management; and 8) Develop and support global networks, collaborative research, and information sharing on native and non-native trees.
The global guidelines are a first step towards building global consensus on the precautions that should be taken when introducing and planting non-native trees. They are voluntary and are intended to complement statutory requirements under international and national legislation. The application of the global guidelines and the achievement of their goals will help to conserve forest biodiversity, ensure sustainable forestry, and contribute to the achievement of several Sustainable Development Goals of the United Nations linked with forest biodiversity.
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28
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Plomion C, Martin F. Oak genomics is proving its worth. THE NEW PHYTOLOGIST 2020; 226:943-946. [PMID: 32301515 DOI: 10.1111/nph.16560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
| | - Francis Martin
- INRAE, UMR IAM, Centre INRAE-Grand Est, Université de Lorraine, F-54280, Champenoux, France
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29
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Jia K, Zhao W, Maier PA, Hu X, Jin Y, Zhou S, Jiao S, El‐Kassaby YA, Wang T, Wang X, Mao J. Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae). Evol Appl 2020; 13:665-676. [PMID: 32211059 PMCID: PMC7086053 DOI: 10.1111/eva.12891] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 10/30/2019] [Accepted: 11/03/2019] [Indexed: 12/22/2022] Open
Abstract
Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
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Affiliation(s)
- Kai‐Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | | | - Xian‐Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuqing Jin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Shan‐Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Si‐Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yousry A El‐Kassaby
- Department of Forest and Conservation SciencesFaculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Tongli Wang
- Department of Forest and Conservation SciencesFaculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Xiao‐Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Department of Ecology and Environmental ScienceUPSCUmeå UniversityUmeåSweden
| | - Jian‐Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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30
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Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
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Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
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Mahony CR, MacLachlan IR, Lind BM, Yoder JB, Wang T, Aitken SN. Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study. Evol Appl 2020; 13:116-131. [PMID: 31892947 PMCID: PMC6935591 DOI: 10.1111/eva.12871] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/29/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023] Open
Abstract
We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a seedling common garden trial of 281 lodgepole pine (Pinus contorta) populations from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype-associated loci are equivalent or slightly superior to climate data for describing local adaptation in seedling traits, but that climate data are superior to genomic data that have not been selected for phenotypic associations. We also find agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with the experimental traits occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than those indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.
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Affiliation(s)
- Colin R. Mahony
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Ian R. MacLachlan
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Brandon M. Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Jeremy B. Yoder
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Tongli Wang
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Sally N. Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
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Ruiz-Benito P, Vacchiano G, Lines ER, Reyer CP, Ratcliffe S, Morin X, Hartig F, Mäkelä A, Yousefpour R, Chaves JE, Palacios-Orueta A, Benito-Garzón M, Morales-Molino C, Camarero JJ, Jump AS, Kattge J, Lehtonen A, Ibrom A, Owen HJ, Zavala MA. Available and missing data to model impact of climate change on European forests. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2019.108870] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cruz MV, Mori GM, Signori-Müller C, da Silva CC, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, de Souza AP. Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. Sci Rep 2019; 9:19936. [PMID: 31882752 PMCID: PMC6934818 DOI: 10.1038/s41598-019-56469-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/07/2019] [Indexed: 12/21/2022] Open
Abstract
Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (Unesp), São Vicente, SP, 11330-900, Brazil
| | - Caroline Signori-Müller
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, 70803, United States
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, SP, 13083-863, Brazil.
- Center for Molecular Biology and Genetic Engineering, University of Campinas (Unicamp), Campinas, SP, 13083-875, Brazil.
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Cruz MV, Mori GM, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, Souza APD. Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae). Mol Ecol 2019; 29:344-362. [PMID: 31834961 DOI: 10.1111/mec.15330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/31/2022]
Abstract
Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | | | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
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Adaptational lag to temperature in valley oak ( Quercus lobata) can be mitigated by genome-informed assisted gene flow. Proc Natl Acad Sci U S A 2019; 116:25179-25185. [PMID: 31767740 PMCID: PMC6911187 DOI: 10.1073/pnas.1908771116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Climate change over the next century is predicted to cause widespread maladaptation in natural systems. This prediction, as well as many sustainable management and conservation practices, assumes that species are adapted to their current climate. However, this assumption is rarely tested. Using a large-scale common garden experiment combined with genome-wide sequencing, we found that valley oak (Quercus lobata), a foundational tree species in California ecosystems, showed a signature of adaptational lag to temperature, with fastest growth rates occurring at cooler temperatures than populations are currently experiencing. Future warming under realistic emissions scenarios was predicted to lead to further maladaptation to temperature and reduction in growth rates for valley oak. We then identified genotypes predicted to grow relatively fast under warmer temperatures and demonstrated that selecting seed sources based on their genotype has the potential to mitigate predicted negative consequences of future climate warming on growth rates in valley oak. These results illustrate that the belief of local adaptation underlying many management and conservation practices, such as using local seed sources for restoration, may not hold for some species. If contemporary adaptational lag is commonplace, we will need new approaches to help alleviate predicted negative consequences of climate warming on natural systems. We present one such approach, "genome-informed assisted gene flow," which optimally matches individuals to future climates based on genotype-phenotype-environment associations.
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Lu M, Krutovsky KV, Loopstra CA. Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models. J Hered 2019; 110:857-865. [DOI: 10.1093/jhered/esz065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/25/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX
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Allona I, Kirst M, Boerjan W, Strauss S, Sederoff R. Editorial: Forest Genomics and Biotechnology. FRONTIERS IN PLANT SCIENCE 2019; 10:1187. [PMID: 31681350 PMCID: PMC6806019 DOI: 10.3389/fpls.2019.01187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Isabel Allona
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steven Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Ronald Sederoff
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
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Wegrzyn JL, Staton MA, Street NR, Main D, Grau E, Herndon N, Buehler S, Falk T, Zaman S, Ramnath R, Richter P, Sun L, Condon B, Almsaeed A, Chen M, Mannapperuma C, Jung S, Ficklin S. Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. FRONTIERS IN PLANT SCIENCE 2019; 10:813. [PMID: 31293610 PMCID: PMC6603172 DOI: 10.3389/fpls.2019.00813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/05/2019] [Indexed: 05/11/2023]
Abstract
Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Margaret A. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Emily Grau
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Nic Herndon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sean Buehler
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Risharde Ramnath
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Peter Richter
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Lang Sun
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, United States
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Dorant Y, Benestan L, Rougemont Q, Normandeau E, Boyle B, Rochette R, Bernatchez L. Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus) as a case study. Ecol Evol 2019; 9:6606-6623. [PMID: 31236247 PMCID: PMC6580275 DOI: 10.1002/ece3.5240] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost-effective sequencing approaches, namely Pool-seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping-by-sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool-seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool-seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual-based approaches provided more congruent results than Pool-seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost-effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.
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Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Pêches et Océans CanadaInstitut Maurice‐LamontagneMont‐JoliCanada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Plateforme d'analyses génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Rémy Rochette
- Department of BiologyUniversity of New BrunswickSaint JohnCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
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Rey MD, Castillejo MÁ, Sánchez-Lucas R, Guerrero-Sanchez VM, López-Hidalgo C, Romero-Rodríguez C, Valero-Galván J, Sghaier-Hammami B, Simova-Stoilova L, Echevarría-Zomeño S, Jorge I, Gómez-Gálvez I, Papa ME, Carvalho K, Rodríguez de Francisco LE, Maldonado-Alconada AM, Valledor L, Jorrín-Novo JV. Proteomics, Holm Oak ( Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? Int J Mol Sci 2019; 20:ijms20030692. [PMID: 30736277 PMCID: PMC6386906 DOI: 10.3390/ijms20030692] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.
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Affiliation(s)
- María-Dolores Rey
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Ángeles Castillejo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Victor M Guerrero-Sanchez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina López-Hidalgo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina Romero-Rodríguez
- Departamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, Paraguay.
| | - José Valero-Galván
- Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, Ciudad Juarez 32310, Mexico.
| | - Besma Sghaier-Hammami
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, Bulgaria.
| | - Sira Echevarría-Zomeño
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Inmaculada Jorge
- Department of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Isabel Gómez-Gálvez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Eugenia Papa
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Kamilla Carvalho
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | | | - Ana María Maldonado-Alconada
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Santiago Gascón Building, 2nd Floor (Office 2.9), 33006 Oviedo, Spain.
| | - Jesús V Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
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Kardos M, Shafer AB. The Peril of Gene-Targeted Conservation. Trends Ecol Evol 2018; 33:827-839. [DOI: 10.1016/j.tree.2018.08.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 01/01/2023]
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Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR, Abel N, Binai N, Rajashekar B, Bachpai VKW, Pillai C, Dev SA. Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Res 2018; 25:409-419. [PMID: 29800113 PMCID: PMC6105116 DOI: 10.1093/dnares/dsy013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.
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Affiliation(s)
- Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Ramesh Vasudeva
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Swathi Balakrishnan
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Ambothi Rathnasamy Sakthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nicodemus Abel
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nagarajan Binai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Balaji Rajashekar
- Genotypic Technology Private Limited, Bengaluru, Karnataka, India.,Institute of Computer Science, University of Tartu, Estonia
| | - Vijay Kumar Waman Bachpai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Chandrasekhara Pillai
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Suma Arun Dev
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
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Abstract
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera. While these are ‘draft’ genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of each reference genome to the remaining six. In addition, we have re-sequenced a sample of accessions from four Juglans species (including regia). The variation discovered in these surveys comprises a critical resource for experimentation and breeding, as well as a solid complementary annotation. To demonstrate the potential of these resources the structural and sequence variation in and around the polyphenol oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in the domestication of walnuts. The apparently Juglandaceae specific PPO1 duplicate shows accelerated divergence and an excess of amino acid replacement on the lineage leading to accessions of the domesticated nut crop species, Juglans regia and sigillata.
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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46
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Hipp AL, Gonzalez-Martinez SC, Jaramillo-Correa JP. The Evolution of Tree Diversity: Proceedings of the 2016 IUFRO Genomics and Forest Tree Genetics Conference, Phylogenetics and Genomic Evolution Session, Arcachon, France. Genome 2017; 60:v-vi. [PMID: 28885056 DOI: 10.1139/gen-2017-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Andrew L Hipp
- a The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA; The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | | | - Juan P Jaramillo-Correa
- c Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, Mexico City, CDMX 04510, Mexico
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Gugger PF, Liang CT, Sork VL, Hodgskiss P, Wright JW. Applying landscape genomic tools to forest management and restoration of Hawaiian koa ( Acacia koa) in a changing environment. Evol Appl 2017; 11:231-242. [PMID: 29387158 PMCID: PMC5775490 DOI: 10.1111/eva.12534] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023] Open
Abstract
Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa. Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state.
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Affiliation(s)
- Paul F Gugger
- Ecology and Evolutionary Biology University of California Los Angeles CA USA.,Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | | | - Victoria L Sork
- Ecology and Evolutionary Biology University of California Los Angeles CA USA.,Institute of the Environment and Sustainability University of California Los Angeles Los Angeles CA USA
| | - Paul Hodgskiss
- USDA Forest Service Pacific Southwest Research Station Davis CA USA
| | - Jessica W Wright
- USDA Forest Service Pacific Southwest Research Station Davis CA USA
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