1
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [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: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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2
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Shu M, Moran EV. Identifying genetic variation associated with environmental gradients and drought-tolerance phenotypes in ponderosa pine. Ecol Evol 2023; 13:e10620. [PMID: 37841219 PMCID: PMC10576020 DOI: 10.1002/ece3.10620] [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: 04/28/2023] [Revised: 09/05/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
As climate changes, understanding the genetic basis of local adaptation in plants becomes an ever more pressing issue. Combining genotype-environment association (GEA) with genotype-phenotype association (GPA) analysis has an exciting potential to uncover the genetic basis of environmental responses. We use these approaches to identify genetic variants linked to local adaptation to drought in Pinus ponderosa. Over 4 million Single Nucleotide Polymorphisms (SNPs) were identified using 223 individuals from across the Sierra Nevada of California. 927,740 (22.3%) SNPs were retained after filtering for proximity to genes and used in our association analyses. We found 1374 associated with five major climate variables, with the largest number (1151) associated with April 1st snowpack. We also conducted a greenhouse study with various drought-tolerance traits measured in first-year seedlings of a subset of the genotyped trees grown in the greenhouse. 796 SNPs were associated with control-condition trait values, while 1149 were associated with responsiveness of these traits to drought. While no individual SNPs were associated with both the environmental variables and the measured traits, several annotated genes were associated with both, particularly those involved in cell wall formation, biotic and abiotic stress responses, and ubiquitination. However, the functions of many of the associated genes have not yet been determined due to the lack of gene annotation information for conifers. Future studies are needed to assess the developmental roles and ecological significance of these unknown genes.
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Affiliation(s)
- Mengjun Shu
- Life and Environmental SciencesUniversity of CaliforniaMercedCaliforniaUSA
| | - Emily V. Moran
- Life and Environmental SciencesUniversity of CaliforniaMercedCaliforniaUSA
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3
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Zhang X, Guo R, Shen R, Landis JB, Jiang Q, Liu F, Wang H, Yao X. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. HORTICULTURE RESEARCH 2023; 10:uhad031. [PMID: 37799629 PMCID: PMC10548413 DOI: 10.1093/hr/uhad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 10/07/2023]
Abstract
A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruinan Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853 USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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Mostert‐O'Neill MM, Tate H, Reynolds SM, Mphahlele MM, van den Berg G, Verryn SD, Acosta JJ, Borevitz JO, Myburg AA. Genomic consequences of artificial selection during early domestication of a wood fibre crop. THE NEW PHYTOLOGIST 2022; 235:1944-1956. [PMID: 35657639 PMCID: PMC9541791 DOI: 10.1111/nph.18297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.
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Affiliation(s)
- Marja M. Mostert‐O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Hannah Tate
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - S. Melissa Reynolds
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Makobatjatji M. Mphahlele
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
- Mondi Forests, Tree Improvement Technology Programme, Trahar Technology Centre – TTCMountain Home Estate, Off Dennis Shepstone Dr.Hilton3245South Africa
| | - Gert van den Berg
- Sappi Forests Research, Shaw Research CentrePO Box 473Howick3290South Africa
| | - Steve D. Verryn
- Creation Breeding Innovations75 Kafue St.Lynnwood Glen0081South Africa
| | - Juan J. Acosta
- Camcore, Department of Forestry and Environmental ResourcesNorth Carolina State UniversityPO Box 7626RaleighNC27695USA
| | - Justin O. Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy BiologyAustralian National UniversityCanberraACT0200Australia
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
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5
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Gene Frequency Shift in Relict Abies pinsapo Forests Associated with Drought-Induced Mortality: Preliminary Evidence of Local-Scale Divergent Selection. FORESTS 2021. [DOI: 10.3390/f12091220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Current climate change constitutes a challenge for the survival of several drought-sensitive forests. The study of the genetic basis of adaptation offers a suitable way to understand how tree species may respond to future climatic conditions, as well as to design suitable conservation and management strategies. Here, we focus on selected genetic signatures of the drought-sensitive relict fir, Abies pinsapo Boiss. Field sampling of 156 individuals was performed in two elevation ecotones, characterized by widespread A. pinsapo decline and mortality. The DNA from dead trees was investigated and compared to living individuals, accounting for different ages and elevations. We studied the genes gated outwardly-rectifying K+ (GORK) channel and Plasma membrane Intrinsic Protein (PIP1) aquaporin, previously related to drought response in plant model species, to test whether drought was the main abiotic factor driving the decline of A. pinsapo forests. A combination of linear regression and factor models were used to test these selection signatures, as well as a fixation index (Fst), used here to analyze the genetic structure. The results were consistent among these approaches, supporting a statistically significant association of the GORK gene with survival in one of the A. pinsapo populations. These results provide preliminary evidence for the potential role of the GORK gene in the resilience to drought of A. pinsapo.
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6
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Bennett KL, McMillan WO, Loaiza JR. The genomic signal of local environmental adaptation in Aedes aegypti mosquitoes. Evol Appl 2021; 14:1301-1313. [PMID: 34025769 PMCID: PMC8127705 DOI: 10.1111/eva.13199] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
Local adaptation is important when predicting arthropod-borne disease risk because of its impacts on vector population fitness and persistence. However, the extent that vector populations are adapted to the environment generally remains unknown. Despite low population structure and high gene flow in Aedes aegypti mosquitoes across Panama, excepting the province of Bocas del Toro, we identified 128 candidate SNPs, clustered within 17 genes, which show a strong genomic signal of local environmental adaptation. This putatively adaptive variation occurred across fine geographical scales with the composition and frequency of candidate adaptive loci differing between populations in wet tropical environments along the Caribbean coast and dry tropical conditions typical of the Pacific coast. Temperature and vegetation were important predictors of adaptive genomic variation in Ae. aegypti with several potential areas of local adaptation identified. Our study lays the foundations of future work to understand whether environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and whether this could either aid or hinder efforts of population control.
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Affiliation(s)
- Kelly L. Bennett
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
| | - W. Owen McMillan
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
| | - Jose R. Loaiza
- Smithsonian Tropical Research InstituteBalboa AnconRepublic of Panama
- Instituto de Investigaciones Científicas y Servicios de Alta TecnologíaPanamáRepublic of Panama
- Programa Centroamericano de Maestría en EntomologíaUniversidad de PanamáPanamáRepublic of Panama
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7
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Westphal D, Mancini AN, Baden AL. Primate landscape genetics: A review and practical guide. Evol Anthropol 2021; 30:171-184. [PMID: 33720482 DOI: 10.1002/evan.21891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/12/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.
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Affiliation(s)
- Darice Westphal
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Andrea L Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA.,Department of Anthropology, Hunter College, New York, New York, USA
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8
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Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-020720-042553] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland 21532, USA
| | - Rachael A. Bay
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
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9
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DeSilva R, Dodd RS. Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients. Ecol Evol 2020; 10:10619-10632. [PMID: 33072284 PMCID: PMC7548164 DOI: 10.1002/ece3.6716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Rainbow DeSilva
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
| | - Richard S Dodd
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
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10
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Napier JD, de Lafontaine G, Hu FS. Exploring genomic variation associated with drought stress in Picea mariana populations. Ecol Evol 2020; 10:9271-9282. [PMID: 32953060 PMCID: PMC7487243 DOI: 10.1002/ece3.6614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/01/2020] [Accepted: 07/08/2020] [Indexed: 01/05/2023] Open
Abstract
Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype-by-environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | - Guillaume de Lafontaine
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of GeologyUniversity of IllinoisUrbanaILUSA
- Department of BiologyWashington UniversitySt. LouisMOUSA
- Department of Earth and Planetary SciencesWashington UniversitySt. LouisMOUSA
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11
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Creech TG, Epps CW, Wehausen JD, Crowhurst RS, Jaeger JR, Longshore K, Holton B, Sloan WB, Monello RJ. Genetic and Environmental Indicators of Climate Change Vulnerability for Desert Bighorn Sheep. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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De La Torre AR, Wilhite B, Neale DB. Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine. Genome Biol Evol 2020; 11:2976-2989. [PMID: 31599932 PMCID: PMC6821164 DOI: 10.1093/gbe/evz220] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 01/21/2023] Open
Abstract
Understanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome resequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant loci and identify their genomic location using our newly constructed ultradense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 821 SNPs showing significant associations with climatic variables or combinations of them based on the consistent results of three different genotype–environment association methods. Our results suggest that adaptation to climate in the species might have occurred by many changes in the frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with groups of environmental variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual environmental variables.
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Affiliation(s)
| | | | - David B Neale
- Department of Plant Sciences, University of California-Davis
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13
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Temperature and Rainfall Are Separate Agents of Selection Shaping Population Differentiation in a Forest Tree. FORESTS 2019. [DOI: 10.3390/f10121145] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Research highlights: We present evidence indicating that covariation of functional traits among populations of a forest tree is not due to genetic constraints, but rather selective covariance arising from local adaptation to different facets of the climate, namely rainfall and temperature. Background and Aims: Traits frequently covary among natural populations. Such covariation can be caused by pleiotropy and/or linkage disequilibrium, but also may arise when the traits are genetically independent as a direct consequence of natural selection, drift, mutation and/or gene flow. Of particular interest are cases of selective covariance, where natural selection directly generates among-population covariance in a set of genetically independent traits. We here studied the causes of population-level covariation in two key traits in the Australian tree Eucalyptus pauciflora. Materials and Methods: We studied covariation in seedling lignotuber size and vegetative juvenility using 37 populations sampled from throughout the geographic and ecological ranges of E. pauciflora on the island of Tasmania. We integrated evidence from multiple sources: (i) comparison of patterns of trait covariation within and among populations; (ii) climate-trait modelling using machine-learning algorithms; and (iii) selection analysis linking trait variation to field growth in an arid environment. Results: We showed strong covariation among populations compared with the weak genetic correlation within populations for the focal traits. Population differentiation in these genetically independent traits was correlated with different home-site climate variables (lignotuber size with temperature; vegetative juvenility with rainfall), which spatially covaried. The role of selection in shaping the population differentiation in lignotuber size was supported by its relationship with fitness measured in the field. Conclusions: Our study highlights the multi-trait nature of adaptation likely to occur as tree species respond to spatial and temporal changes in climate.
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Zhang S, Isabel N, Huang JG, Ren H, Rossi S. Responses of bud-break phenology to daily-asymmetric warming: daytime warming intensifies the advancement of bud break. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2019; 63:1631-1640. [PMID: 31385094 DOI: 10.1007/s00484-019-01776-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
There is evidence that the ongoing climate change is happening through nighttime rather than daytime warming. How such a daily-asymmetric warming modifies plant phenology is still unclear. We investigated the effects of asymmetric warming on bud break by daily monitoring seedlings belonging to 26 black spruce [Picea mariana (Mill.) BSP.] and 15 balsam fir [Abies balsamea (L.) Mill.] provenances from the native range in Canada. Seedlings were subjected to either daytime or nighttime warming in three growth chambers at temperatures ranging between 10 and 24 °C. On average, a warming of 4 °C advanced the timings of bud break in both species by 2.4 days, with the later phases being more sensitive to the treatment. Bud break of both species responded more strongly to daytime warming, with the bud break occurred 1.2 and 3.2 days earlier under daytime than nighttime warming in black spruce and balsam fir, respectively. A marked ecotypic differentiation was only observed in black spruce that originated from provenances distributed broadly across Canada, with seedlings from the warmest provenance completing bud break 8.3 days later than those from the coldest one. However, no significant effect of provenance was observed for balsam fir, the narrowly distributed species. Overall, the above results suggest that a higher temporal resolution such as temperatures during daytime and nighttime, and higher spatial resolution should be taken into account to improve the accuracy of phenological model predictions under global change scenarios. Phenological models based on daily average temperature should take into account the diverging impacts of asymmetric warming on plant phenology. Our findings may indicate that the influence of warming on plant phenology may be less dramatic than expected.
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Affiliation(s)
- Shaokang Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Jian-Guo Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Hai Ren
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Sergio Rossi
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, G7H 2B1, Canada
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15
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Hopley T, Byrne M. Gene Flow and Genetic Variation Explain Signatures of Selection across a Climate Gradient in Two Riparian Species. Genes (Basel) 2019; 10:genes10080579. [PMID: 31370268 PMCID: PMC6723506 DOI: 10.3390/genes10080579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022] Open
Abstract
Many species occur across environmental gradients and it is expected that these species will exhibit some signals of adaptation as heterogeneous environments and localized gene flow may facilitate local adaptation. While riparian zones can cross climate gradients, many of which are being impacted by climate change, they also create microclimates for the vegetation, reducing environmental heterogeneity. Species with differing distributions in these environments provide an opportunity to investigate the importance of genetic connectivity in influencing signals of adaptation over relatively short geographical distance. Association analysis with genomic data was used to compare signals of selection to climate variables in two species that have differing distributions along a river traversing a climate gradient. Results demonstrate links between connectivity, standing genetic variation, and the development of signals of selection. In the restricted species, the combination of high gene flow in the middle and lower catchment and occurrence in a microclimate created along riverbanks likely mitigated the development of selection to most climatic variables. In contrast the more widely distributed species with low gene flow showed a stronger signal of selection. Together these results strengthen our knowledge of the drivers and scale of adaptation and reinforce the importance of connectivity across a landscape to maintain adaptive potential of plant species.
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Affiliation(s)
- Tara Hopley
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
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16
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Acosta JJ, Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davis JM, Holliday JA, Kirst M. Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii. Genome Biol Evol 2019; 11:508-520. [PMID: 30689841 PMCID: PMC6385631 DOI: 10.1093/gbe/evz016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.
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Affiliation(s)
- Juan J Acosta
- School of Forest Resources and Conservation, University of Florida.,University of Florida Genetics Institute, University of Florida.,Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida
| | - Leandro G Neves
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,RAPiD Genomics, Gainesville, FL
| | | | | | - John M Davis
- School of Forest Resources and Conservation, University of Florida
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,University of Florida Genetics Institute, University of Florida
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17
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Momigliano P, Jokinen H, Calboli F, Aro E, Merilä J. Cryptic temporal changes in stock composition explain the decline of a flounder ( Platichthys spp.) assemblage. Evol Appl 2019; 12:549-559. [PMID: 30828373 PMCID: PMC6383698 DOI: 10.1111/eva.12738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 01/15/2023] Open
Abstract
Unobserved diversity, such as undetected genetic structure or the presence of cryptic species, is of concern for the conservation and management of global biodiversity in the face of threatening anthropogenic processes. For instance, unobserved diversity can lead to overestimation of maximum sustainable yields and therefore to overharvesting of the more vulnerable stock components within unrecognized mixed-stock fisheries. We used DNA from archival (otolith) samples to reconstruct the temporal (1976-2011) genetic makeup of two mixed-stock flounder fisheries in the Åland Sea (AS) and the Gulf of Finland (GoF). Both fisheries have hitherto been managed as a single stock of European flounders (Platichthys flesus), but were recently revealed to target two closely related species: the pelagic-spawning P. flesus and the newly described, demersal-spawning P. solemdali. While the AS and GoF fisheries were assumed to consist exclusively of P. solemdali, P. flesus dominated the GoF flounder assemblage (87% of total) in 1983, had disappeared (0%) by 1993, and remained in low proportions (10%-11%) thereafter. In the AS, P. solemdali dominated throughout the sampling period (>70%), and P. flesus remained in very low proportions after 1983. The disappearance of P. flesus from the GoF coincides in time with a dramatic (~60%) decline in commercial landings and worsening environmental conditions in P. flesus' northernmost spawning ground, the Eastern Gotland Basin, in the preceding 4-6 years. These results are compatible with the hypothesis that P. flesus in the GoF is a sink population relying on larval subsidies from southern spawning grounds and the cause of their disappearance is a cessation of larval supply. Our results highlight the importance of uncovering unobserved genetic diversity and studying spatiotemporal changes in the relative contribution of different stock components, as well as the underlying environmental causes, to manage marine resources in the age of rapid anthropogenic change.
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Affiliation(s)
- Paolo Momigliano
- Ecological Genetics Research Unit, Research Program in Organismal and Evolutionary BiologyUniversity of HelsinkiHelsinkiFinland
| | - Henri Jokinen
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Federico Calboli
- Ecological Genetics Research Unit, Research Program in Organismal and Evolutionary BiologyUniversity of HelsinkiHelsinkiFinland
- Department of BiologyUniversity of LeuvenLeuvenBelgium
| | - Eero Aro
- Finnish Game and Fisheries Research InstituteHelsinkiFinland
- Present address:
Puolipäivänkatu 4 A 6, FI‐00160HelsinkiFinland
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Program in Organismal and Evolutionary BiologyUniversity of HelsinkiHelsinkiFinland
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18
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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19
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Henriques D, Wallberg A, Chávez-Galarza J, Johnston JS, Webster MT, Pinto MA. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 2018; 8:11145. [PMID: 30042407 PMCID: PMC6057950 DOI: 10.1038/s41598-018-29469-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
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Affiliation(s)
- Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal.
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20
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Stival Sena J, Giguère I, Rigault P, Bousquet J, Mackay J. Expansion of the dehydrin gene family in the Pinaceae is associated with considerable structural diversity and drought-responsive expression. TREE PHYSIOLOGY 2018; 38:442-456. [PMID: 29040752 DOI: 10.1093/treephys/tpx125] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
Temperatures are expected to increase over the next century in all terrestrial biomes and particularly in boreal forests, where drought-induced mortality has been predicted to rise. Genomics research is helping to develop hypotheses regarding the molecular basis of drought tolerance and recent work proposed that the osmo-protecting dehydrin proteins have undergone a clade-specific expansion in the Pinaceae, a major group of conifer trees. The objectives of this study were to identify all of the putative members of the gene family, trace their evolutionary origin, examine their structural diversity and test for drought-responsive expression. We identified 41 complete dehydrin coding sequences in Picea glauca, which is four times more than most angiosperms studied to date, and more than in pines. Phylogenetic reconstructions indicated that the family has undergone an expansion in conifers, with parallel evolution implicating the sporadic resurgence of certain amino acid sequence motifs, and a major duplication giving rise to a clade specific to the Pinaceae. A variety of plant dehydrin structures were identified with variable numbers of the A-, E-, S- and K-segments and an N-terminal (N1) amino acid motif including assemblages specific to conifers. The expression of several of the spruce dehydrins was tissue preferential under non-stressful conditions or responded to water stress after 7-18 days without watering, reflecting changes in osmotic potential. We found that dehydrins with N1 K2 and N1 AESK2 sequences were the most responsive to the lack of water. Together, the family expansion, drought-responsive expression and structural diversification involving loss and gain of amino acid motifs suggests that subfunctionalization has driven the diversification seen among dehydrin gene duplicates. Our findings clearly indicate that dehydrins represent a large family of candidate genes for drought tolerance in spruces and in other Pinaceae that may underpin adaptability in spatially and temporally variable environments.
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Affiliation(s)
- Juliana Stival Sena
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - Isabelle Giguère
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - Philippe Rigault
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec QC G1S 1E7, Canada
| | - Jean Bousquet
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - John Mackay
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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21
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Shih KM, Chang CT, Chung JD, Chiang YC, Hwang SY. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir ( Keteleeria davidiana var. formosana). FRONTIERS IN PLANT SCIENCE 2018; 9:92. [PMID: 29449860 PMCID: PMC5799944 DOI: 10.3389/fpls.2018.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 05/05/2023]
Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
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Affiliation(s)
- Kai-Ming Shih
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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22
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Moran E, Lauder J, Musser C, Stathos A, Shu M. The genetics of drought tolerance in conifers. THE NEW PHYTOLOGIST 2017; 216:1034-1048. [PMID: 28895167 DOI: 10.1111/nph.14774] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/27/2017] [Indexed: 05/20/2023]
Abstract
Contents 1034 I. 1034 II. 1035 III. 1037 IV. 1038 V. 1042 VI. 1043 VII. 1045 References 1045 SUMMARY: As temperatures warm and precipitation patterns shift as a result of climate change, interest in the identification of tree genotypes that will thrive under more arid conditions has grown. In this review, we discuss the multiple definitions of 'drought tolerance' and the biological processes involved in drought responses. We describe the three major approaches taken in the study of genetic variation in drought responses, the advantages and shortcomings of each, and what each of these approaches has revealed about the genetic basis of adaptation to drought in conifers. Finally, we discuss how a greater knowledge of the genetics of drought tolerance may aid forest management, and provide recommendations for how future studies may overcome the limitations of past approaches. In particular, we urge a more direct focus on survival, growth and the traits that directly predict them (rather than on proxies, such as water use efficiency), combining research approaches with complementary strengths and weaknesses, and the inclusion of a wider range of taxa and life stages.
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Affiliation(s)
- Emily Moran
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
| | | | - Cameron Musser
- Yale School of Forestry & Environmental Studies, 195 Prospect Street, New Haven, CT, 06511, USA
| | | | - Mengjun Shu
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
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23
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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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Landscape genomics analysis of Achyranthes bidentata reveal adaptive genetic variations are driven by environmental variations relating to ecological habit. POPUL ECOL 2017. [DOI: 10.1007/s10144-017-0599-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Miao CY, Li Y, Yang J, Mao RL. Landscape genomics reveal that ecological character determines adaptation: a case study in smoke tree (Cotinus coggygria Scop.). BMC Evol Biol 2017; 17:202. [PMID: 28835216 PMCID: PMC5569454 DOI: 10.1186/s12862-017-1055-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/18/2017] [Indexed: 01/08/2023] Open
Abstract
Background The adaptive evolution of species response to environment are the key issues in molecular ecology and evolutionary biology. The direction of adaptive differentiation of species in regions lacking strong selection pressure is usually diverse. However, the driving mechanism of the diverse adaptive differentiation for regional species is still undetermined to date. In this study, we used landscape genomics modelling to infer the adaptive evolution of Cotinus coggygria in China’s warm-temperate zone. Results Using fifteen natural populations and nine start codon targeted (SCoT) markers, a total of 1131 unambiguous loci were yielded. Our results showed two genetic groups existed in the fifteen natural populations of C. coggygria, which is due to the divergent selection driven by six environmental factors. Environmental association analyses revealed the environmental variables related to precipitation were associated with high numbers of environment-associated loci. Conclusions Our results indicated that the ecological characters of C. coggygria, i.e. avoiding wetness and tolerating drought, determine its adaptive evolution. This study provides a reference that ecological character determines the adaptive evolution of species in regions lacking strong selection pressure. Electronic supplementary material The online version of this article (10.1186/s12862-017-1055-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cai-Yun Miao
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jie Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Run-Li Mao
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
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Perrin M, Rossi S, Isabel N. Synchronisms between bud and cambium phenology in black spruce: early-flushing provenances exhibit early xylem formation. TREE PHYSIOLOGY 2017; 37:593-603. [PMID: 28338976 DOI: 10.1093/treephys/tpx019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
Bud and cambial phenology represent the adaptation of species to the local environment that allows the growing season to be maximized while minimizing the risk of frost for the developing tissues. The temporal relationship between the apical and radial meristems can help in the understanding of tree growth as a whole process. The aim of this study was to compare cambial phenology in black spruce (Picea mariana (Mill.) B.S.P.) provenances classified as early and late bud flushing. The different phases of cambial phenology were assessed on wood microcores sampled weekly from April to October in 2014 and 2015 from 61 trees growing in a provenance trial in Quebec, Canada. Trees showing an early bud flush also exhibited early reactivation of xylem differentiation, although an average difference of 12 days for buds corresponded to small although significant differences of 4 days for xylem. Provenances with early bud flush had an early bud set and completed xylem formation earlier than late bud flush provenances. No significant difference in the period of xylem formation and total growth was observed between the flushing classes. Our results demonstrate that the ecotype differentiation of black spruce provenances represented by the phenological adaptation of buds to the local climate corresponds to specific growth dynamics of the xylem.
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Affiliation(s)
- Magali Perrin
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Sergio Rossi
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec, QC, Canada
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Lenz PRN, Beaulieu J, Mansfield SD, Clément S, Desponts M, Bousquet J. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana). BMC Genomics 2017; 18:335. [PMID: 28454519 PMCID: PMC5410046 DOI: 10.1186/s12864-017-3715-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/21/2017] [Indexed: 11/11/2022] Open
Abstract
Background Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, which is especially relevant for the genetic improvement of boreal conifers characterized by long breeding cycles. In the present study, we tested GS in an advanced-breeding population of the boreal black spruce (Picea mariana [Mill.] BSP) for growth and wood quality traits, and concurrently examined factors affecting GS model accuracy. Results The study relied on 734 25-year-old trees belonging to 34 full-sib families derived from 27 parents and that were established on two contrasting sites. Genomic profiles were obtained from 4993 Single Nucleotide Polymorphisms (SNPs) representative of as many gene loci distributed among the 12 linkage groups common to spruce. GS models were obtained for four growth and wood traits. Validation using independent sets of trees showed that GS model accuracy was high, related to trait heritability and equivalent to that of conventional pedigree-based models. In forward selection, gains per unit of time were three times higher with the GS approach than with conventional selection. In addition, models were also accurate across sites, indicating little genotype-by-environment interaction in the area investigated. Using information from half-sibs instead of full-sibs led to a significant reduction in model accuracy, indicating that the inclusion of relatedness in the model contributed to its higher accuracies. About 500 to 1000 markers were sufficient to obtain GS model accuracy almost equivalent to that obtained with all markers, whether they were well spread across the genome or from a single linkage group, further confirming the implication of relatedness and potential long-range linkage disequilibrium (LD) in the high accuracy estimates obtained. Only slightly higher model accuracy was obtained when using marker subsets that were identified to carry large effects, indicating a minor role for short-range LD in this population. Conclusions This study supports the integration of GS models in advanced-generation tree breeding programs, given that high genomic prediction accuracy was obtained with a relatively small number of markers due to high relatedness and family structure in the population. In boreal spruce breeding programs and similar ones with long breeding cycles, much larger gain per unit of time can be obtained from genomic selection at an early age than by the conventional approach. GS thus appears highly profitable, especially in the context of forward selection in species which are amenable to mass vegetative propagation of selected stock, such as spruces.
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Affiliation(s)
- Patrick R N Lenz
- Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Government of Canada, 1055 du PEPS, P.O. Box 10380, Québec, Québec, G1V 4C7, Canada. .,Canada Research Chair in Forest Genomics, Institute of Systems and Integrative Biology and Centre for Forest Research, Université Laval, 1030, Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada.
| | - Jean Beaulieu
- Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Government of Canada, 1055 du PEPS, P.O. Box 10380, Québec, Québec, G1V 4C7, Canada.,Canada Research Chair in Forest Genomics, Institute of Systems and Integrative Biology and Centre for Forest Research, Université Laval, 1030, Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Forest Sciences Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sébastien Clément
- Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Government of Canada, 1055 du PEPS, P.O. Box 10380, Québec, Québec, G1V 4C7, Canada
| | - Mireille Desponts
- Ministère des Forêts, de la Faune et des Parcs, Gouvernement du Québec, Direction de la recherche forestière, 2700 rue Einstein, Québec, Québec, G1P 3W8, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Institute of Systems and Integrative Biology and Centre for Forest Research, Université Laval, 1030, Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
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Steane DA, Mclean EH, Potts BM, Prober SM, Stock WD, Stylianou VM, Vaillancourt RE, Byrne M. Evidence for adaptation and acclimation in a widespread eucalypt of semi-arid Australia. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw051] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, 4556, Australia
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - Elizabeth H. Mclean
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Suzanne M. Prober
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - William D. Stock
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - Vanessa M. Stylianou
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
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Ren J, Chen L, Jin X, Zhang M, You FM, Wang J, Frenkel V, Yin X, Nevo E, Sun D, Luo MC, Peng J. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides. FRONTIERS IN PLANT SCIENCE 2017; 8:258. [PMID: 28352272 PMCID: PMC5348526 DOI: 10.3389/fpls.2017.00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 05/06/2023]
Abstract
Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
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Affiliation(s)
- Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, China
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Xiaoli Jin
- Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, China
| | - Miaomiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipeg, MB, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Vladimir Frenkel
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Xuegui Yin
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Dongfa Sun
- Department of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Junhua Peng
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
- The State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co. Ltd.Wuhan, China
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Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon. Genome Biol Evol 2017; 9:253-265. [PMID: 28391293 PMCID: PMC5381606 DOI: 10.1093/gbe/evw290] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
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Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
- CSIRO Land and Water, Wembley, Western Australia, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Elizabeth H. McLean
- CSIRO Land and Water, Wembley, Western Australia, Australia
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
| | - Lesley Collins
- Faculty of Health Science, Universal College of Learning, Palmerston North, New Zealand
| | - Barbara R. Holland
- School of Physical Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - William D. Stock
- Centre for Ecosystem Management, School of Natural Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
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Hughes KA, Leips J. Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses. Ann N Y Acad Sci 2017; 1389:76-91. [PMID: 27936291 PMCID: PMC5318229 DOI: 10.1111/nyas.13256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022]
Abstract
Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.
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Affiliation(s)
- Kimberly A. Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
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Yang J, Miao CY, Mao RL, Li Y. Landscape Population Genomics of Forsythia ( Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species. FRONTIERS IN PLANT SCIENCE 2017; 8:481. [PMID: 28424728 PMCID: PMC5380681 DOI: 10.3389/fpls.2017.00481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/20/2017] [Indexed: 05/06/2023]
Abstract
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F. suspensa exist resulting from divergent selection driven by seven environmental variables. A total of 26 outlier loci were identified by both BayeScan and FDIST2, 23 of which were environment-associated loci (EAL). Environmental association analysis revealed that the environmental variables related to the ecological habitats of F. suspensa are associated with high numbers of EAL. Results of EAL characterization in F. suspensa are consistent with the hypothesis that ecological habitats determine the adaptive evolution of this species. Moreover, a model of species adaptation to environmental variables was proposed in this study. The adaptation model was used to further evaluate the adaptation status of F. suspensa to environmental variables. This study will be useful to help us in understanding the adaptive evolution of species in regions lacking strong selection pressure.
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Jordan R, Dillon SK, Prober SM, Hoffmann AA. Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box). THE NEW PHYTOLOGIST 2016; 212:992-1006. [PMID: 27440730 DOI: 10.1111/nph.14084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/31/2016] [Indexed: 05/22/2023]
Abstract
In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.
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Affiliation(s)
- Rebecca Jordan
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Rd, Parkville, Vic, 3010, Australia
- CSIRO Land and Water, 147 Underwood Ave, Floreat, WA, 6014, Australia
| | - Shannon K Dillon
- CSIRO Agriculture, Clunies Ross Street, Black Mountain, ACT, 2601, Australia
| | - Suzanne M Prober
- CSIRO Land and Water, 147 Underwood Ave, Floreat, WA, 6014, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Rd, Parkville, Vic, 3010, Australia
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McAssey EV, Corbi J, Burke JM. Range-wide phenotypic and genetic differentiation in wild sunflower. BMC PLANT BIOLOGY 2016; 16:249. [PMID: 27829377 PMCID: PMC5103407 DOI: 10.1186/s12870-016-0937-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and also determined the extent of population structure across the range of this species. We then used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation. RESULTS Traits including flowering time, plant height, and seed oil composition (i.e., percentage of saturated fatty acids) were significantly correlated with latitude, and thus differentiated northern vs. southern populations. Average pairwise FST was found to be 0.21, and a STRUCTURE analysis identified two significant clusters that largely separated northern and southern individuals. The significant FST outliers included a SNP in HaFT2, a flowering time gene that has been previously shown to co-localize with flowering time QTL, and which exhibits a known cline in gene expression. CONCLUSIONS Latitudinal differentiation in both phenotypic traits and SNP allele frequencies is observed across wild sunflower populations in central North America. Such differentiation may play an important adaptive role across the range of this species, and could facilitate adaptation to a changing climate.
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Affiliation(s)
- Edward V. McAssey
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA 30602 USA
| | - Jonathan Corbi
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Miller Plant Sciences Building, Athens, GA 30602 USA
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Nadeau S, Meirmans PG, Aitken SN, Ritland K, Isabel N. The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines. Ecol Evol 2016; 6:8649-8664. [PMID: 28035257 PMCID: PMC5192886 DOI: 10.1002/ece3.2550] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023] Open
Abstract
Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and FST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.
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Affiliation(s)
- Simon Nadeau
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada; Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Sally N Aitken
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Nathalie Isabel
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada
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Song Z, Zhang M, Li F, Weng Q, Zhou C, Li M, Li J, Huang H, Mo X, Gan S. Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites. Sci Rep 2016; 6:34941. [PMID: 27748400 PMCID: PMC5066178 DOI: 10.1038/srep34941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations.
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Affiliation(s)
- Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- Baoshan University, Yuanzheng Road, Baoshan 678000, China
| | - Miaomiao Zhang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Fagen Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Chanpin Zhou
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Jie Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
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Hess M, Wildhagen H, Junker LV, Ensminger I. Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. BMC Genomics 2016; 17:682. [PMID: 27565139 PMCID: PMC5002200 DOI: 10.1186/s12864-016-3022-6] [Citation(s) in RCA: 19] [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: 09/24/2015] [Accepted: 08/16/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). RESULTS Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction. CONCLUSIONS The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.
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Affiliation(s)
- Moritz Hess
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Institute for Biology III, Faculty of Biology, Albert Ludwigs University Freiburg, Schänzlestrasse 1, D-79104 Freiburg i. Brsg., Germany
- Present Address: Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Obere Zahlbacher Strasse 69, 55131 Mainz, Germany
| | - Henning Wildhagen
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Present Address: Department of Forest Botany and Tree Physiology, Büsgen-Institute, Georg-August-University Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
| | - Laura Verena Junker
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
| | - Ingo Ensminger
- Forest Research Institute of Baden-Württemberg (FVA), Wonnhaldestrasse 4, D-79100 Freiburg i. Brsg., Germany
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6 Canada
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Christmas MJ, Biffin E, Breed MF, Lowe AJ. Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species. Mol Ecol 2016; 25:4216-33. [DOI: 10.1111/mec.13750] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/27/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Matthew J. Christmas
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
| | - Ed Biffin
- State Herbarium of South Australia Hackney Road Adelaide SA 5000 Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
| | - Andrew J. Lowe
- Environment Institute and School of Biological Sciences The University of Adelaide North Terrace SA 5005 Australia
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Brousseau L, Postolache D, Lascoux M, Drouzas AD, Källman T, Leonarduzzi C, Liepelt S, Piotti A, Popescu F, Roschanski AM, Zhelev P, Fady B, Vendramin GG. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe. PLoS One 2016; 11:e0158216. [PMID: 27392065 PMCID: PMC4938419 DOI: 10.1371/journal.pone.0158216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. METHODS A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). RESULTS HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. CONCLUSION Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.
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Affiliation(s)
- Louise Brousseau
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Dragos Postolache
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Andreas D. Drouzas
- School of Biology, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Cristina Leonarduzzi
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Palermo, National 3. Research Council—Corso Calatafimi, 414—I-90129, Palermo (PA), Italy
| | - Sascha Liepelt
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Flaviu Popescu
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Anna M. Roschanski
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank Collections North, Inselstrasse 9, D-23999 Malchow/Poel, Germany
| | - Peter Zhelev
- University of Forestry, 10, Kl. Ohridsky Blvd., 1797 Sofia, Bulgaria
| | - Bruno Fady
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
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Yang AH, Wei N, Fritsch PW, Yao XH. AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect. FRONTIERS IN PLANT SCIENCE 2016; 7:698. [PMID: 27303414 PMCID: PMC4880593 DOI: 10.3389/fpls.2016.00698] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/06/2016] [Indexed: 05/27/2023]
Abstract
Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.
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Affiliation(s)
- Ai-Hong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Na Wei
- Department of Ecology and Evolutionary Biology, University of MichiganAnn Arbor, MI, USA
| | | | - Xiao-Hong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
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Wang T, Wang Z, Xia F, Su Y. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China. Sci Rep 2016; 6:25031. [PMID: 27113970 PMCID: PMC4844950 DOI: 10.1038/srep25031] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.
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Affiliation(s)
- Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Wang
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Xia
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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42
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Roschanski AM, Csilléry K, Liepelt S, Oddou-Muratorio S, Ziegenhagen B, Huard F, Ullrich KK, Postolache D, Vendramin GG, Fady B. Evidence of divergent selection for drought and cold tolerance at landscape and local scales inAbies albaMill. in the French Mediterranean Alps. Mol Ecol 2016; 25:776-94. [DOI: 10.1111/mec.13516] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 11/20/2015] [Accepted: 12/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Anna M. Roschanski
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | - Katalin Csilléry
- INRA, UR629; Ecologie des Forêts Méditerranéennes (URFM); Avignon Cedex 9 84914 France
| | - Sascha Liepelt
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | | | - Birgit Ziegenhagen
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | | | - Kristian K. Ullrich
- Cell Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | - Dragos Postolache
- Scuola Superiore Sant'Anna; Piazza Martiri della Libertà 33 Pisa 56127 Italy
- Institute of Biosciences and Bioresources; National Research Council (CNR); Via Madonna del Piano 10 Sesto Fiorentino (Firenze) 50019 Italy
- National Institute of Forest Research and Development (INCDS); Simeria Research Station; Str. Biscaria 1 Simeria 335900 Romania
| | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council (CNR); Via Madonna del Piano 10 Sesto Fiorentino (Firenze) 50019 Italy
| | - Bruno Fady
- INRA, UR629; Ecologie des Forêts Méditerranéennes (URFM); Avignon Cedex 9 84914 France
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43
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Prunier J, Verta JP, MacKay JJ. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. THE NEW PHYTOLOGIST 2016; 209:44-62. [PMID: 26206592 DOI: 10.1111/nph.13565] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/14/2015] [Indexed: 05/21/2023]
Abstract
Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - John J MacKay
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
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Liu Y, Müller K, El-Kassaby YA, Kermode AR. Changes in hormone flux and signaling in white spruce (Picea glauca) seeds during the transition from dormancy to germination in response to temperature cues. BMC PLANT BIOLOGY 2015; 15:292. [PMID: 26680643 PMCID: PMC4683703 DOI: 10.1186/s12870-015-0638-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/05/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Seeds use environmental cues such as temperature to coordinate the timing of their germination, allowing plants to synchronize their life history with the seasons. Winter chilling is of central importance to alleviate seed dormancy, but very little is known of how chilling responses are regulated in conifer seeds. White spruce (Picea glauca) is an important conifer species of boreal forests in the North American taiga. The recent sequencing and assembly of the white spruce genome allows for comparative gene expression studies toward elucidating the molecular mechanisms governing dormancy alleviation by moist chilling. Here we focused on hormone metabolite profiling and analyses of genes encoding components of hormone signal transduction pathways, to elucidate changes during dormancy alleviation and to help address how germination cues such as temperature and light trigger radicle emergence. RESULTS ABA, GA, and auxin underwent considerable changes as seeds underwent moist chilling and during subsequent germination; likewise, transcripts encoding hormone-signaling components (e.g. ABI3, ARF4 and Aux/IAA) were differentially regulated during these critical stages. During moist chilling, active IAA was maintained at constant levels, but IAA conjugates (IAA-Asp and IAA-Glu) were substantially accumulated. ABA concentrations decreased during germination of previously moist-chilled seeds, while the precursor of bioactive GA1 (GA53) accumulated. We contend that seed dormancy and germination may be partly mediated through the changing hormone concentrations and a modulation of interactions between central auxin-signaling pathway components (TIR1/AFB, Aux/IAA and ARF4). In response to germination cues, namely exposure to light and to increased temperature: the transfer of seeds from moist-chilling to 30 °C, significant changes in gene transcripts and protein expression occurred during the first six hours, substantiating a very swift reaction to germination-promoting conditions after seeds had received sufficient exposure to the chilling stimulus. CONCLUSIONS The dormancy to germination transition in white spruce seeds was correlated with changes in auxin conjugation, auxin signaling components, and potential interactions between auxin-ABA signaling cascades (e.g. the transcription factor ARF4 and ABI3). Auxin flux adds a new dimension to the ABA:GA balance mechanism that underlies both dormancy alleviation by chilling, and subsequent radicle emergence to complete germination by warm temperature and light stimuli.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Kerstin Müller
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Allison R Kermode
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
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Prunier J, Tessier G, Bousquet J, MacKay J. From genotypes to phenotypes: expression levels of genes encompassing adaptive SNPs in black spruce. PLANT CELL REPORTS 2015; 34:2111-2125. [PMID: 26260097 DOI: 10.1007/s00299-015-1855-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Measuring transcript levels for adaptive genes revealed polymorphisms having cis -effect upon gene expression levels related to phenotype variation in a black spruce natural population. Trees growing in temperate and boreal regions must acclimate to changes in climatic factors such as low winter temperatures to survive to seasonal variations. Common garden studies have shown that genetic variation in quantitative traits helps species to survive and adapt to environmental changes and local conditions. Twenty-four genes carrying SNPs were previously associated with genetic adaptation in black spruce (Picea mariana [Mill.] BSP). The objectives of this study were to investigate the potential role of these genes in regulation of winter acclimation and adaptation by studying their patterns of expression as a function of the physiological stage during the annual growth cycle, tissue type, and their SNP genotypic class. Considerable variability in gene expression was observed between different vegetative tissues or organs, and between physiological stages. The genes were expressed predominantly in tissues that could be linked more directly to winter acclimation and adaptation. The expression levels of several of the genes were significantly related to variation in tree height growth or budset timing and expression level variation related to SNP genotypic classes was observed in four of the genes. An interaction between genotypic classes and physiological stages was also observed for some genes, indicating genotypes with different reaction norms in terms of gene expression.
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Affiliation(s)
- Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada.
| | - Guillaume Tessier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
| | - John MacKay
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for System and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, G1V0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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Porth I, Klápště J, McKown AD, La Mantia J, Guy RD, Ingvarsson PK, Hamelin R, Mansfield SD, Ehlting J, Douglas CJ, El-Kassaby YA. Evolutionary Quantitative Genomics of Populus trichocarpa. PLoS One 2015; 10:e0142864. [PMID: 26599762 PMCID: PMC4658102 DOI: 10.1371/journal.pone.0142864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/27/2015] [Indexed: 11/23/2022] Open
Abstract
Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We also provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species’ potential adaptive capacity to future climatic scenarios.
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Affiliation(s)
- Ilga Porth
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval, Québec, QC, G1V 0A6 Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Genetics and Physiology of Forest Trees, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Athena D. McKown
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jonathan La Mantia
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Corn, Soybean and Wheat Quality Research Unit, United States Department of Agriculture, Wooster, Ohio, 44691 United States of America
| | - Robert D. Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden
| | - Richard Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shawn D. Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Carl J. Douglas
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- * E-mail:
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Hornoy B, Pavy N, Gérardi S, Beaulieu J, Bousquet J. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. Genome Biol Evol 2015; 7:3269-85. [PMID: 26560341 PMCID: PMC4700950 DOI: 10.1093/gbe/evv218] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources.
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Affiliation(s)
- Benjamin Hornoy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
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Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J, Bousquet J. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Mol Ecol Resour 2015; 16:588-98. [PMID: 26391535 DOI: 10.1111/1755-0998.12468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 06/30/2015] [Accepted: 08/21/2015] [Indexed: 11/29/2022]
Abstract
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - France Gagnon
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Astrid Deschênes
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Brian Boyle
- Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Natural Resources Canada, Canadian Wood Fibre Centre, 1055 Rue du P.E.P.S., PO Box 10380, Station Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 2015; 16:574-87. [PMID: 26358548 DOI: 10.1111/1755-0998.12464] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022]
Abstract
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
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Affiliation(s)
- C Plomion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J Bartholomé
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - I Lesur
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,HelixVenture, F-33700, Mérignac, France
| | - C Boury
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | | | - H Lagraulet
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - F Ehrenmann
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - L Bouffier
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J M Gion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,UMR AGAP, CIRAD, F-33612, Cestas, France
| | - D Grivet
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M de Miguel
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - N de María
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M T Cervera
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
| | - F Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
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