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Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions. PLoS One 2023; 18:e0277797. [PMID: 36795783 PMCID: PMC9934357 DOI: 10.1371/journal.pone.0277797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/03/2022] [Indexed: 02/17/2023] Open
Abstract
Environmental responses are critical for plant growth and survival under different climate conditions. To elucidate the underlying biological mechanisms of environmental responses in Japanese cedar (Cryptomeria japonica D. Don), the annual transcriptome dynamics of common clonal trees (Godai1) planted at three different climate sites (Yamagata, Ibaraki, and Kumamoto Prefectures) were analyzed using microarrays. Both principal component analysis (PCA) and hierarchical clustering of the microarray data indicated the transition to dormant transcriptome status occurred earlier and the transition to active growth status later in the colder region. Interestingly, PCA also indicated that the transcriptomes of trees grown under three different conditions were similar during the growth period (June to September), whereas the transcriptomes differed between sites during the dormant period (January to March). In between-site comparisons, analyses of the annual expression profiles of genes for sites 'Yamagata vs. Kumamoto', 'Yamagata vs. Ibaraki', and 'Ibaraki vs. Kumamoto' identified 1,473, 1,137, and 925 targets exhibiting significantly different expression patterns, respectively. The total of 2,505 targets that exhibited significantly different expression patterns in all three comparisons may play important roles in enabling cuttings to adapt to local environmental conditions. Partial least-squares regression analysis and Pearson correlation coefficient analysis revealed that air temperature and day length were the dominant factors controlling the expression levels of these targets. GO and Pfam enrichment analyses indicated that these targets include genes that may contribute to environmental adaptation, such as genes related to stress and abiotic stimulus responses. This study provided fundamental information regarding transcripts that may play an important role in adaptation to environmental conditions at different planting sites.
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Vuosku J, Martz F, Hallikainen V, Rautio P. Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:1050903. [PMID: 36570907 PMCID: PMC9780549 DOI: 10.3389/fpls.2022.1050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.
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Affiliation(s)
- Jaana Vuosku
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Françoise Martz
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
| | - Ville Hallikainen
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
| | - Pasi Rautio
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
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3
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Response of Poplar Leaf Transcriptome to Changed Management and Environmental Conditions in Pure and Mixed with Black Locust Stands. FORESTS 2022. [DOI: 10.3390/f13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mixed cropping in short rotation coppice can be an alternative to monocultures. To design optimized mixtures, field trials are needed. Poplar, as an economically important and fast-growing species, and black locust, as a nitrogen-fixing species, are promising candidates for such studies. RNA sequencing (RNA-seq) was used to monitor effects of mixed and pure cultivations on the gene expression of poplar along with growth measurements during 2017 and 2018. Both biomass production and leaf transcriptomes revealed a strong competition pressure of black locust and the abiotic environment on poplar trees. Gene expression differed between the two study sites and pure and mixed stands. Shading effects from black locust caused the downregulation of photosynthesis and upregulation of shade avoidance genes in mixed stands in 2017. As a result of higher light availability after cutting black locust, plant organ development genes were upregulated in mixed stands in 2018. Drought conditions during the summer of 2018 and competition for water between the two species caused the upregulation of drought stress response genes in mixed stands and at the unfavorable growing site. Further investigations are required to discover the mechanisms of interspecific competition and to develop stand designs, which could increase the success and productivity of mixed plantations.
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De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes (Basel) 2021; 12:110. [PMID: 33477542 PMCID: PMC7831106 DOI: 10.3390/genes12010110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Benjamin Wilhite
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Daniela Puiu
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - John Bradley St. Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA;
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Steven L. Salzberg
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Brian Allen
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
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5
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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7
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Fréchette E, Chang CYY, Ensminger I. Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming. GLOBAL CHANGE BIOLOGY 2020; 26:5217-5234. [PMID: 32396692 DOI: 10.1111/gcb.15150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
In higher-latitude trees, temperature and photoperiod control the beginning and end of the photosynthetically active season. Elevated temperature (ET) has advanced spring warming and delayed autumn cooling while photoperiod remains unchanged. We assessed the effects of warming on the length of the photosynthetically active season of three provenances of Pinus strobus L. seedlings from different latitudes, and evaluated the accuracy of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI) for tracking the predicted variation in spring and autumn phenology of photosynthesis among provenances. Seedlings from northern, local and southern P. strobus provenances were planted in a temperature-free-air-controlled enhancement (T-FACE) experiment and exposed to ET (+1.5/3°C; day/night). Over 18 months, we assessed photosynthetic phenology by measuring chlorophyll fluorescence, gas exchange, leaf spectral reflectance and pigment content. During autumn, all seedlings regardless of provenance followed the same sequence of phenological events with the initial downregulation of photosynthesis, followed by the modulation of non-photochemical quenching and associated adjustments of zeaxanthin pool sizes. However, the timing of autumn downregulation differed between provenances, with delayed onset in the southern provenance (SP) and earlier onset in the northern relative to the local provenance, indicating that photoperiod at the provenance origin is a dominant factor controlling autumn phenology. Experimental warming further delayed the downregulation of photosynthesis during autumn in the SP. A provenance effect during spring was also observed but was generally not significant. The vegetation indices PRI and CCI were both effective at tracking the seasonal variations of energy partitioning in needles and the differences of carotenoid pigments indicative of the stress status of needles. These results demonstrate that PRI and CCI can be useful tools for monitoring conifer phenology and for the remote monitoring of the length of the photosynthetically active season of conifers in a changing climate.
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Affiliation(s)
- Emmanuelle Fréchette
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Christine Yao-Yun Chang
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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8
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Nose M, Kurita M, Tamura M, Matsushita M, Hiraoka Y, Iki T, Hanaoka S, Mishima K, Tsubomura M, Watanabe A. Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species. PLoS One 2020; 15:e0229843. [PMID: 32150571 PMCID: PMC7062269 DOI: 10.1371/journal.pone.0229843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/15/2020] [Indexed: 11/29/2022] Open
Abstract
Seasonal phenomena in plants are primarily affected by day length and temperature. The shoot transcriptomes of trees grown in the field and a controlled-environment chamber were compared to characterize genes that control annual rhythms and the effects of day length- and temperature-regulated genes in the gymnosperm Japanese cedar (Cryptomeria japonica D. Don), which exhibits seasonally indeterminate growth. Annual transcriptome dynamics were clearly demonstrated by principal component analysis using microarray data obtained under field-grown conditions. Analysis of microarray data from trees grown in a controlled chamber identified 2,314 targets exhibiting significantly different expression patterns under short-day (SD) and long-day conditions, and 2,045 targets exhibited significantly different expression patterns at 15°C (LT; low temperature) versus 25°C. Interestingly, although growth was suppressed under both SD and LT conditions, approximately 80% of the SD- and LT-regulated targets differed, suggesting that each factor plays a unique role in the annual cycle. The top 1,000 up-regulated targets in the growth/dormant period in the field coincided with more than 50% of the SD- and LT-regulated targets, and gene co-expression network analysis of the annual transcriptome indicated a close relationship between the SD- and LT-regulated targets. These results indicate that the respective effects of day length and temperature interact to control annual transcriptome dynamics. Well-known upstream genes of signaling pathways responsive to environmental conditions, such as the core clock (LHY/CjLHYb and CCA1/CjLHYa) and PEBP family (MFT) genes, exhibited unique expression patterns in Japanese cedar compared with previous reports in other species, suggesting that these genes control differences in seasonal regulation mechanisms between species. The results of this study provide new insights into seasonal regulation of transcription in Japanese cedar.
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Affiliation(s)
- Mine Nose
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Manabu Kurita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Michinari Matsushita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Yuichiro Hiraoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Taiichi Iki
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - So Hanaoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Atsushi Watanabe
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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9
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Alakärppä E, Salo HM, Valledor L, Cañal MJ, Häggman H, Vuosku J. Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5293-5305. [PMID: 30113688 DOI: 10.1093/jxb/ery292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Heikki M Salo
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Maria Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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10
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Kost MA, Perales HR, Wijeratne S, Wijeratne AJ, Stockinger E, Mercer KL. Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico. BMC Genomics 2017; 18:707. [PMID: 28886704 PMCID: PMC5591509 DOI: 10.1186/s12864-017-4005-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Background Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. Results Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico. We collected landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between landrace co-expression module expression values and environmental parameters of landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses. Conclusions These findings indicate that natural selection may influence the transcriptomes of crop landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4005-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Kost
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Hugo R Perales
- El Colegio de la Frontera Sur, Departmento de Agroecología, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Saranga Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA
| | - Asela J Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA.,Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, OH, USA.
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11
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Stinziano JR, Way DA. Autumn photosynthetic decline and growth cessation in seedlings of white spruce are decoupled under warming and photoperiod manipulations. PLANT, CELL & ENVIRONMENT 2017; 40:1296-1316. [PMID: 28102913 DOI: 10.1111/pce.12917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
Climate warming is expected to increase the seasonal duration of photosynthetic carbon fixation and tree growth in high-latitude forests. However, photoperiod, a crucial cue for seasonality, will remain constant, which may constrain tree responses to warming. We investigated the effects of temperature and photoperiod on weekly changes in photosynthetic capacity, leaf biochemistry and growth in seedlings of a boreal evergreen conifer, white spruce [Picea glauca (Moench) Voss]. Warming delayed autumn declines in photosynthetic capacity, extending the period when seedlings had high carbon uptake. While photoperiod was correlated with photosynthetic capacity, short photoperiods did not constrain the maintenance of high photosynthetic capacity under warming. Rubisco concentration dynamics were affected by temperature but not photoperiod, while leaf pigment concentrations were unaffected by treatments. Respiration rates at 25 °C were stimulated by photoperiod, although respiration at the growth temperatures was increased in warming treatments. Seedling growth was stimulated by increased photoperiod and suppressed by warming. We demonstrate that temperature is a stronger control on the seasonal timing of photosynthetic down-regulation than is photoperiod. Thus, while warming can stimulate carbon uptake in boreal conifers, the extra carbon may be directed towards respiration rather than biomass, potentially limiting carbon sequestration under climate change.
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Affiliation(s)
- Joseph R Stinziano
- Department of Biology, University of Western Ontario, 1151 Richmond St., London, Ontario, Canada, N6A 5B6
| | - Danielle A Way
- Department of Biology, University of Western Ontario, 1151 Richmond St., London, Ontario, Canada, N6A 5B6
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
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12
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Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics 2017; 18:558. [PMID: 28738815 PMCID: PMC5525293 DOI: 10.1186/s12864-017-3916-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. RESULTS We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. CONCLUSIONS Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Peter C Dolan
- University of Minnesota - Morris, Morris, MN, 56267, USA
| | - Sanjuro Jogdeo
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David B Neale
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - J Bradley St Clair
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
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13
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Wang G, Weng L, Li M, Xiao H. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato. Int J Mol Sci 2017; 18:E475. [PMID: 28257093 PMCID: PMC5372491 DOI: 10.3390/ijms18030475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.
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Affiliation(s)
- Guixiang Wang
- University of Chinese Academy of Sciences, 19A Yuquan Rd., Beijing 100049, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Lin Weng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Meng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
| | - Han Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), 300 Fenglin Rd., Shanghai 200032, China.
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14
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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15
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Hamilton JA, El Kayal W, Hart AT, Runcie DE, Arango-Velez A, Cooke JEK. The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). TREE PHYSIOLOGY 2016; 36:1432-1448. [PMID: 27449791 DOI: 10.1093/treephys/tpw061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Timely responses to environmental cues enable the synchronization of phenological life-history transitions essential for the health and survival of north-temperate and boreal tree species. While photoperiodic cues will remain persistent under climate change, temperature cues may vary, contributing to possible asynchrony in signals influencing developmental and physiological transitions essential to forest health. Understanding the relative contribution of photoperiod and temperature as determinants of the transition from active growth to dormancy is important for informing adaptive forest management decisions that consider future climates. Using a combination of photoperiod (long = 20 h or short = 8 h day lengths) and temperature (warm = 22 °C/16 °C and cool = 8 °C/4 °C day/night, respectively) treatments, we used microscopy, physiology and modeling to comprehensively examine hallmark traits of the growth-dormancy transition-including bud formation, growth cessation, cold hardiness and gas exchange-within two provenances of white spruce [Picea glauca (Moench) Voss] spanning a broad latitude in Alberta, Canada. Following exposure to experimental treatments, seedlings were transferred to favorable conditions, and the depth of dormancy was assessed by determining the timing and ability of spruce seedlings to resume growth. Short photoperiods promoted bud development and growth cessation, whereas longer photoperiods extended the growing season through the induction of lammas growth. In contrast, cool temperatures under both photoperiodic conditions delayed bud development. Photoperiod strongly predicted the development of cold hardiness, whereas temperature predicted photosynthetic rates associated with active growth. White spruce was capable of attaining endodormancy, but its release was environmentally determined. Dormancy depth varied substantially across experimental treatments suggesting that environmental cues experienced within one season could affect growth in the following season, which is particularly important for a determinate species such as white spruce. The joint influence of these environmental cues points toward the importance of including local constant photoperiod and shifting temperature cues into predictive models that consider how climate change may affect northern forests.
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Affiliation(s)
- Jill A Hamilton
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Walid El Kayal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Ashley T Hart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Adriana Arango-Velez
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- Department of Forestry and Horticulture, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
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16
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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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17
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Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, Liepe KJ, Hamann A, Holliday JA, Whitlock MC, Rieseberg LH, Aitken SN. Convergent local adaptation to climate in distantly related conifers. Science 2016; 353:1431-1433. [DOI: 10.1126/science.aaf7812] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023]
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18
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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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19
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Verta JP, Landry CR, MacKay J. Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations. THE NEW PHYTOLOGIST 2016; 211:159-171. [PMID: 26891783 DOI: 10.1111/nph.13888] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Regulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long-lived such as in the case of conifer trees. We developed an RNA sequencing (RNA-seq)-based approach for both expression-quantitative trait locus (eQTL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) eQTLs. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self-fertilized white spruce (Picea glauca) individual to dissect eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs linked to the expressed genes was particularly complex, consisting of cis-acting, trans-acting and, surprisingly, compensatory cis-trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTLs were under compensation, indicating that close linkage between compensatory cis-trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid-diploid eQTL analysis in spruce revealed that compensatory cis-trans eQTLs segregate within populations and evolve in close genetic linkage.
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Affiliation(s)
- Jukka-Pekka Verta
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Département de Biologie, Université Laval, Québec, QC, Canada G1V 0A6
| | - John MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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20
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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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21
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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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22
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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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24
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Cañas RA, Feito I, Fuente-Maqueda JF, Ávila C, Majada J, Cánovas FM. Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats. BMC Genomics 2015; 16:909. [PMID: 26545587 PMCID: PMC4636790 DOI: 10.1186/s12864-015-2177-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/31/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. RESULTS An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. CONCLUSIONS Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.
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Affiliation(s)
- Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
| | - Isabel Feito
- Sección Forestal, SERIDA, Finca Experimental La Mata, 33825, Grado, Principado de Asturias, Spain.
| | | | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
| | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental La Mata, 33825, Grado, Principado de Asturias, Spain.
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto Andaluz de Biotecnología, Universidad de Málaga, Campus Universitario de Teatinos s/n, 29071, Málaga, Spain.
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25
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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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26
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Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea. Heredity (Edinb) 2015; 115:153-64. [PMID: 25806545 PMCID: PMC4815442 DOI: 10.1038/hdy.2015.19] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 01/16/2023] Open
Abstract
Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.
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27
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Arango-Velez A, González LMG, Meents MJ, El Kayal W, Cooke BJ, Linsky J, Lusebrink I, Cooke JEK. Influence of water deficit on the molecular responses of Pinus contorta × Pinus banksiana mature trees to infection by the mountain pine beetle fungal associate, Grosmannia clavigera. TREE PHYSIOLOGY 2014; 34:1220-39. [PMID: 24319029 PMCID: PMC4277265 DOI: 10.1093/treephys/tpt101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/08/2013] [Indexed: 05/14/2023]
Abstract
Conifers exhibit a number of constitutive and induced mechanisms to defend against attack by pests and pathogens such as mountain pine beetle (Dendroctonus ponderosae Hopkins) and their fungal associates. Ecological studies have demonstrated that stressed trees are more susceptible to attack by mountain pine beetle than their healthy counterparts. In this study, we tested the hypothesis that water deficit affects constitutive and induced responses of mature lodgepole pine × jack pine hybrids (Pinus contorta Dougl. ex Loud. var. latifolia Engelm. ex S. Wats. × Pinus banksiana Lamb.) to inoculation with the mountain pine beetle fungal associate Grosmannia clavigera (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield. The degree of stress induced by the imposed water-deficit treatment was sufficient to reduce photosynthesis. Grosmannia clavigera-induced lesions exhibited significantly reduced dimensions in water-deficit trees relative to well-watered trees at 5 weeks after inoculation. Treatment-associated cellular-level changes in secondary phloem were also observed. Quantitative RT-PCR was used to analyze transcript abundance profiles of 18 genes belonging to four families classically associated with biotic and abiotic stress responses: aquaporins (AQPs), dehydration-responsive element binding (DREB), terpene synthases (TPSs) and chitinases (CHIs). Transcript abundance profiles of a TIP2 AQP and a TINY-like DREB decreased significantly in fungus-inoculated trees, but not in response to water deficit. One TPS, Pcb(+)-3-carene synthase, and the Class II CHIs PcbCHI2.1 and PcbCHI2.2 showed increased expression under water-deficit conditions in the absence of fungal inoculation, while another TPS, Pcb(E)-β-farnesene synthase-like, and two CHIs, PcbCHI1.1 and PcbCHI4.1, showed attenuated expression under water-deficit conditions in the presence of fungal inoculation. The effects were observed both locally and systemically. These results demonstrate that both constitutive and induced carbon- and nitrogen-based defenses are affected by water deficit, suggesting potential consequences for mountain pine beetle dynamics, particularly in novel environments.
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Affiliation(s)
- Adriana Arango-Velez
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Leonardo M Galindo González
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Miranda J Meents
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Walid El Kayal
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Barry J Cooke
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, Canada T6H 3S5
| | - Jean Linsky
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Inka Lusebrink
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada T6E 2E3
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
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28
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Harfouche A, Meilan R, Altman A. Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement. TREE PHYSIOLOGY 2014; 34:1181-98. [PMID: 24695726 DOI: 10.1093/treephys/tpu012] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed.
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Affiliation(s)
- Antoine Harfouche
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907-2061, USA
| | - Arie Altman
- Faculty of Agricultural, Food and Environmental Quality Sciences, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
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29
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Avia K, Kärkkäinen K, Lagercrantz U, Savolainen O. Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris). THE NEW PHYTOLOGIST 2014; 204:159-170. [PMID: 24942643 DOI: 10.1111/nph.12901] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.
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Affiliation(s)
- Komlan Avia
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Katri Kärkkäinen
- Finnish Forest Research Institute, METLA, University of Oulu, PO Box 413, FIN-90014, Oulu, Finland
| | - Ulf Lagercrantz
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752, 36, Uppsala, Sweden
| | - Outi Savolainen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
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30
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Zhou L, Bawa R, Holliday JA. Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Mol Ecol 2014; 23:2486-99. [PMID: 24750333 DOI: 10.1111/mec.12752] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5'-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
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Affiliation(s)
- L Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
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31
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Yeaman S, Hodgins KA, Suren H, Nurkowski KA, Rieseberg LH, Holliday JA, Aitken SN. Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii). THE NEW PHYTOLOGIST 2014; 203:578-591. [PMID: 24750196 DOI: 10.1111/nph.12819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
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Affiliation(s)
- Sam Yeaman
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- School of Biological Sciences, Monash University, Building 18, Melbourne, Vic., 3800, Australia
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Kristin A Nurkowski
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, 6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA, 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 203:535-553. [PMID: 24750093 DOI: 10.1111/nph.12815] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/14/2014] [Indexed: 05/02/2023]
Abstract
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst]. PLoS One 2014; 9:e95306. [PMID: 24810273 PMCID: PMC4014479 DOI: 10.1371/journal.pone.0095306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/26/2014] [Indexed: 11/20/2022] Open
Abstract
The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.
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De La Torre AR, Roberts DR, Aitken SN. Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow. Mol Ecol 2014; 23:2046-59. [PMID: 24597663 PMCID: PMC4228761 DOI: 10.1111/mec.12710] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 02/27/2014] [Accepted: 02/28/2014] [Indexed: 01/12/2023]
Abstract
The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21,000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both Fst outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.
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Affiliation(s)
- Amanda R De La Torre
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, Canada; Department of Ecology and Environmental Science, Umeå University, Linneaus väg 6, SE-901 87, Umeå, Sweden
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Changes in metabolite profiles in Norway spruce shoot tips during short-day induced winter bud development and long-day induced bud flush. Metabolomics 2014. [PMID: 0 DOI: 10.1007/s11306-014-0646-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 201:1263-1276. [PMID: 24491114 DOI: 10.1111/nph.12601] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 05/18/2023]
Abstract
• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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De La Torre AR, Wang T, Jaquish B, Aitken SN. Adaptation and exogenous selection in a Picea glauca × Picea engelmannii hybrid zone: implications for forest management under climate change. THE NEW PHYTOLOGIST 2014; 201:687-699. [PMID: 24200028 PMCID: PMC4285121 DOI: 10.1111/nph.12540] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/30/2013] [Indexed: 05/04/2023]
Abstract
The nature of selection responsible for the maintenance of the economically and ecologically important Picea glauca × Picea engelmannii hybrid zone was investigated. Genomic, phenotypic and climatic data were used to test assumptions of hybrid zone maintenance and to model future scenarios under climate change. Genome-wide estimates of admixture based on a panel of 86 candidate gene single nucleotide polymorphisms were combined with long-term quantitative data on growth and survival (over 20 yr), as well as one-time assessments of bud burst and bud set phenology, and cold hardiness traits. A total of 15,498 individuals were phenotyped for growth and survival. Our results suggest that the P. glauca × P. engelmannii hybrid zone is maintained by local adaptation to growing season length and snowpack (exogenous selection). Hybrids appeared to be fitter than pure species in intermediate environments, which fits expectations of the bounded hybrid superiority model of hybrid zone maintenance. Adaptive introgression from parental species has probably contributed to increased hybrid fitness in intermediate habitats. While P. engelmannii ancestry is higher than P. glauca ancestry in hybrid populations, on average, selective breeding in managed hybrid populations is shifting genomic composition towards P. glauca, potentially pre-adapting managed populations to warmer climates.
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Affiliation(s)
- Amanda R De La Torre
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Sciences, University of British Columbia3041–2424 Main Mall, Vancouver, BC, V6T1Z4, Canada
- Department of Ecology and Environmental Sciences, Umeå UniversityLinneaus väg 6, SE-901 87, Umeå, Sweden
- Author for correspondence:Amanda R. De La Torre, Tel: +46 090 7865475,
| | - Tongli Wang
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Sciences, University of British Columbia3041–2424 Main Mall, Vancouver, BC, V6T1Z4, Canada
| | - Barry Jaquish
- Kalamalka Forestry Centre, Tree Improvement Branch, BC Ministry of Forests, Lands & Natural Resource Operations3401 Reservoir Rd, Vernon, BC, V1B2C7, Canada
| | - Sally N Aitken
- Centre for Forest Conservation Genetics, Department of Forest and Conservation Sciences, University of British Columbia3041–2424 Main Mall, Vancouver, BC, V6T1Z4, Canada
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Mosca E, González-Martínez SC, Neale DB. Environmental versus geographical determinants of genetic structure in two subalpine conifers. THE NEW PHYTOLOGIST 2014; 201:180-192. [PMID: 24102203 DOI: 10.1111/nph.12476] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
| | | | - David B Neale
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
- Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA
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Qiu Z, Wan L, Chen T, Wan Y, He X, Lu S, Wang Y, Lin J. The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling. THE NEW PHYTOLOGIST 2013; 199:708-19. [PMID: 23638988 DOI: 10.1111/nph.12301] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/27/2013] [Indexed: 05/03/2023]
Abstract
Chinese fir (Cunninghamia lanceolata), a commercially important tree for the timber and pulp industry, is widely distributed in southern China and northern Vietnam, but its large and complex genome has hindered the development of genomic resources. Few efforts have focused on analysis of the modulation of transcriptional networks in vascular cambium during the transition from active growth to dormancy in conifers. Here, we used Illumina sequencing to analyze the global transcriptome alterations at the different stages of vascular cambium development in Chinese fir. By analyzing dynamic changes in the transcriptome of vascular cambium based on our RNA sequencing (RNA-Seq) data at the dormant, reactivating and active stages, many potentially interesting genes were identified that encoded putative regulators of cambial activity, cell division, cell expansion and cell wall biosynthesis and modification. In particular, the genes involved in transcriptional regulation and hormone signaling were highlighted to reveal their biological importance in the cambium development and wood formation. Our results reveal the dynamics of transcriptional networks and identify potential key components in the regulation of vascular cambium development in Chinese fir, which will contribute to the in-depth study of cambial differentiation and wood-forming candidate genes in conifers.
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Affiliation(s)
- Zongbo Qiu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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40
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Collakova E, Klumas C, Suren H, Myers E, Heath LS, Holliday JA, Grene R. Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC PLANT BIOLOGY 2013; 13:72. [PMID: 23631437 PMCID: PMC3651351 DOI: 10.1186/1471-2229-13-72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 03/19/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cold acclimation in woody perennials is a metabolically intensive process, but coincides with environmental conditions that are not conducive to the generation of energy through photosynthesis. While the negative effects of low temperatures on the photosynthetic apparatus during winter have been well studied, less is known about how this is reflected at the level of gene and metabolite expression, nor how the plant generates primary metabolites needed for adaptive processes during autumn. RESULTS The MapMan tool revealed enrichment of the expression of genes related to mitochondrial function, antioxidant and associated regulatory activity, while changes in metabolite levels over the time course were consistent with the gene expression patterns observed. Genes related to thylakoid function were down-regulated as expected, with the exception of plastid targeted specific antioxidant gene products such as thylakoid-bound ascorbate peroxidase, components of the reactive oxygen species scavenging cycle, and the plastid terminal oxidase. In contrast, the conventional and alternative mitochondrial electron transport chains, the tricarboxylic acid cycle, and redox-associated proteins providing reactive oxygen species scavenging generated by electron transport chains functioning at low temperatures were all active. CONCLUSIONS A regulatory mechanism linking thylakoid-bound ascorbate peroxidase action with "chloroplast dormancy" is proposed. Most importantly, the energy and substrates required for the substantial metabolic remodeling that is a hallmark of freezing acclimation could be provided by heterotrophic metabolism.
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Affiliation(s)
- Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Curtis Klumas
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Haktan Suren
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Elijah Myers
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
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41
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Hamilton JA, Lexer C, Aitken SN. Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone. THE NEW PHYTOLOGIST 2013; 197:927-938. [PMID: 23228022 DOI: 10.1111/nph.12055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/18/2012] [Indexed: 06/01/2023]
Abstract
Differential patterns of introgression between species across ecological gradients provide a fine-scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments. Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis-Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms. Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long-term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes. This study provides a fine-scale analysis of locus-specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christian Lexer
- Department of Biology, Unit of Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
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Mackay J, Dean JFD, Plomion C, Peterson DG, Cánovas FM, Pavy N, Ingvarsson PK, Savolainen O, Guevara MÁ, Fluch S, Vinceti B, Abarca D, Díaz-Sala C, Cervera MT. Towards decoding the conifer giga-genome. PLANT MOLECULAR BIOLOGY 2012; 80:555-69. [PMID: 22960864 DOI: 10.1007/s11103-012-9961-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/24/2012] [Indexed: 05/21/2023]
Abstract
Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.
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Affiliation(s)
- John Mackay
- Center for Forest Research, Institute for Integrative and Systems Biology, Université Laval, Québec, Québec G1V 0A6, Canada
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Hamilton JA, Lexer C, Aitken SN. Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis × P. glauca). Mol Ecol 2012; 22:827-41. [DOI: 10.1111/mec.12007] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/26/2012] [Accepted: 07/26/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Jill A. Hamilton
- Centre for Forest Conservation Genetics and Department of Forest Sciences; University of British Columbia; 3041-2424 Main Mall Vancouver; BC; Canada; 1Z4
| | - Christian Lexer
- Unit of Ecology and Evolution, Department of Biology; University of Fribourg; Chemin du Musee 10, CH-1700 Fribourg; Switzerland
| | - Sally N. Aitken
- Centre for Forest Conservation Genetics and Department of Forest Sciences; University of British Columbia; 3041-2424 Main Mall Vancouver; BC; Canada; 1Z4
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Porth I, White R, Jaquish B, Alfaro R, Ritland C, Ritland K. Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce. PLoS One 2012; 7:e44397. [PMID: 22973444 PMCID: PMC3433439 DOI: 10.1371/journal.pone.0044397] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 08/06/2012] [Indexed: 01/01/2023] Open
Abstract
In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce.
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Affiliation(s)
- Ilga Porth
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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45
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Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, Verta JP, Giguère I, Bomal C, Bohlmann J, MacKay J. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 2012; 13:434. [PMID: 22931377 PMCID: PMC3534630 DOI: 10.1186/1471-2164-13-434] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/11/2012] [Indexed: 12/22/2022] Open
Abstract
Background Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.
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Affiliation(s)
- Elie Raherison
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, Canada, G1V 0A6
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Holliday JA, Suren H, Aitken SN. Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proc Biol Sci 2012; 279:1675-83. [PMID: 22113032 PMCID: PMC3297444 DOI: 10.1098/rspb.2011.1805] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 10/31/2011] [Indexed: 11/12/2022] Open
Abstract
Gene flow and effective population size (N(e)) should depend on a population's position within its range: those near the edges are expected to have smaller N(e) and lower relative emigration rates, whereas those nearer the centre should have larger N(e) and higher relative emigration rates. In species with continuous ranges, this phenomenon may limit the ability of peripheral populations to respond to divergent selection. Here, we employ Sitka spruce as a model to test these predictions. We previously genotyped 339 single nucleotide polymorphisms (SNPs) in 410 individuals from 13 populations, and used these data to identify putative targets of divergent selection, as well as to explore the extent to which central-peripheral structure may impede adaptation. Fourteen SNPs had outlier F(ST) estimates suggestive of divergent selection, of which nine were previously associated with phenotypic variation in adaptive traits (timing of autumn budset and cold hardiness). Using coalescent simulations, we show that populations from near the centre of the range have higher effective populations sizes than those from the edges, and that central populations contribute more migrants to marginal populations than the reverse. Our results suggest that while divergent selection appears to have shaped allele frequencies among populations, asymmetrical movement of alleles from the centre to the edges of the species range may affect the adaptive capacity of peripheral populations. In southern peripheral populations, the movement of cold-adapted alleles from the north represents a significant impediment to adaptation under climate change, while in the north, movement of warm-adapted alleles from the south may enhance adaptation.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Dauwe R, Holliday JA, Aitken SN, Mansfield SD. Metabolic dynamics during autumn cold acclimation within and among populations of Sitka spruce (Picea sitchensis). THE NEW PHYTOLOGIST 2012; 194:192-205. [PMID: 22248127 DOI: 10.1111/j.1469-8137.2011.04027.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
• Autumnal cold acclimation in conifers is a complex process, the timing and extent of which vary widely along latitudinal gradients for many tree species and reflect local adaptation to climate. Although previous studies have detailed some aspects of the metabolic remodelling that accompanies cold acclimation in conifers, little is known about global metabolic dynamics, or how these changes vary among phenotypically divergent populations. • Using untargeted GC-MS metabolite profiling, we monitored metabolic dynamics during autumnal cold acclimation in three populations of Sitka spruce from the southern, central, and northern portions of the species range, which differ in both the timing and extent of cold acclimation. • Latitudinal variation was evident in the nature, intensity, and timing of metabolic events. Early development of strong freezing tolerance in the northern population was associated with a transient accumulation of amino acids. By late autumn, metabolic profiles were highly similar between the northern and central populations, whereas profiles for the southern population were relatively distinct. • Our results provide insight into the metabolic architecture of latitudinal adaptive variation in autumn acclimation and show that different mechanisms are the basis of early October cold hardiness and autumn-acclimated cold hardiness.
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Affiliation(s)
- Rebecca Dauwe
- Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, V6T 1Z4, Vancouver, BC, Canada
| | - Jason A Holliday
- Department of Forest Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, V6T 1Z4, Vancouver, BC, Canada
| | - Sally N Aitken
- Department of Forest Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, V6T 1Z4, Vancouver, BC, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, V6T 1Z4, Vancouver, BC, Canada
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Galindo González LM, El Kayal W, Ju CJT, Allen CCG, King-Jones S, Cooke JEK. Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy. PLANT, CELL & ENVIRONMENT 2012; 35:682-701. [PMID: 21988609 DOI: 10.1111/j.1365-3040.2011.02444.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca[Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree's overwintering preparations. For example, genes associated with carbon-based defences such as terpenoids were down-regulated, while many genes associated with protein-based defences and other stress mitigation mechanisms were up-regulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree's adaptive response to overwintering.
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Eckert AJ, Wegrzyn JL, Cumbie WP, Goldfarb B, Huber DA, Tolstikov V, Fiehn O, Neale DB. Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. THE NEW PHYTOLOGIST 2012; 193:890-902. [PMID: 22129444 DOI: 10.1111/j.1469-8137.2011.03976.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Jill L Wegrzyn
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - W Patrick Cumbie
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Barry Goldfarb
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Dudley A Huber
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Vladimir Tolstikov
- Metabolomics Core Facility, Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Oliver Fiehn
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
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Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). FRONTIERS IN PLANT SCIENCE 2012; 3:241. [PMID: 23112803 PMCID: PMC3482696 DOI: 10.3389/fpls.2012.00241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/10/2012] [Indexed: 05/18/2023]
Abstract
Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location.
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Affiliation(s)
- Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- *Correspondence: Ruth Grene, Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA. e-mail:
| | - Curtis Klumas
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
| | - Haktan Suren
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
- Department of Forest Resources and Environmental Conservation, Virginia TechBlacksburg, VA, USA
| | - Kuan Yang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
| | - Elijah Myers
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
- Department of Computer Science, Virginia TechBlacksburg, VA, USA
| | - Lenwood S. Heath
- Department of Computer Science, Virginia TechBlacksburg, VA, USA
| | - Jason A. Holliday
- Department of Forest Resources and Environmental Conservation, Virginia TechBlacksburg, VA, USA
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