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Tumas H, Ilska JJ, Gérardi S, Laroche J, A’Hara S, Boyle B, Janes M, McLean P, Lopez G, Lee SJ, Cottrell J, Gorjanc G, Bousquet J, Woolliams JA, MacKay JJ. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 (BETHESDA, MD.) 2024; 14:jkae020. [PMID: 38366548 PMCID: PMC10989875 DOI: 10.1093/g3journal/jkae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.
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Affiliation(s)
- Hayley Tumas
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Joana J Ilska
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Sebastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Jerome Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Stuart A’Hara
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Mateja Janes
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Paul McLean
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gustavo Lopez
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Steve J Lee
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Joan Cottrell
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gregor Gorjanc
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - John A Woolliams
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - John J MacKay
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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2
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Ullah A, Klutsch JG, Erbilgin N. Complementary roles of two classes of defense chemicals in white spruce against spruce budworm. PLANTA 2024; 259:105. [PMID: 38551685 DOI: 10.1007/s00425-024-04383-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/08/2024] [Indexed: 04/02/2024]
Abstract
MAIN CONCLUSION Monoterpenes and phenolics play distinct roles in defending white spruce trees from insect defoliators. Monoterpenes contribute to the toxicity of the foliage, deterring herbivory, whereas phenolics impede budworm growth. This study demonstrates the complex interplay between monoterpenes and phenolics and their collective influence on the defense strategy of white spruce trees against a common insect defoliator. Long-lived coniferous trees display considerable variations in their defensive chemistry. The impact of these defense phenotype variations on insect herbivores of the same species remains to be thoroughly studied, mainly due to challenges in replicating the comprehensive defense profiles of trees under controlled conditions. This study methodically examined the defensive properties of foliar monoterpenes and phenolics across 80 distinct white spruce families. These families were subsequently grouped into two chemotypes based on their foliar monoterpene concentrations. To understand the separate and combined effects of these classes on tree defenses to the eastern spruce budworm, we conducted feeding experiments using actual defense profiles from representative families. Specifically, we assessed budworm response when exposed to substrates amended with phenolics alone or monoterpenes. Our findings indicate that the ratios and amounts of monoterpenes and phenolics present in the white spruce foliage influence the survival of spruce budworms. Phenotypes associated with complete larval mortality exhibited elevated ratios (ranging from 0.4 to 0.6) and concentrations (ranging from 1143 to 1796 ng mg-1) of monoterpenes. Conversely, families characterized by higher phenolic ratios (ranging from 0.62 to 0.77) and lower monoterpene concentrations (ranging from 419 to 985 ng mg-1) were less lethal to the spruce budworm. Both classes of defense compounds contribute significantly to the overall defensive capabilities of white spruce trees. Monoterpenes appear critical in determining the general toxicity of foliage, while phenolics play a role in slowing budworm development, thereby underscoring their collective importance in white spruce defenses.
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Affiliation(s)
- Aziz Ullah
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada.
| | - Jennifer G Klutsch
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
- Natural Resources Canada, Canadian Forest Service, Edmonton, AB, T6H 3S5, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
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Hung TH, Wu ETY, Zeltiņš P, Jansons Ā, Ullah A, Erbilgin N, Bohlmann J, Bousquet J, Birol I, Clegg SM, MacKay JJ. Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce. BMC Genomics 2024; 25:118. [PMID: 38281030 PMCID: PMC10821269 DOI: 10.1186/s12864-024-09978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/05/2024] [Indexed: 01/29/2024] Open
Abstract
Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1 and Ugt5 genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of βglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.
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Affiliation(s)
- Tin Hang Hung
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Ernest T Y Wu
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Pauls Zeltiņš
- Latvian State Forest Research Institute "Silava", Salaspils, 2169, Latvia
| | - Āris Jansons
- Latvian State Forest Research Institute "Silava", Salaspils, 2169, Latvia
| | - Aziz Ullah
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sonya M Clegg
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - John J MacKay
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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4
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Li Y, Sun H, de Paula Protásio T, Hein PRG, Du B. The mechanisms and prediction of non-structural carbohydrates accretion and depletion after mechanical wounding in slash pine (Pinus elliottii) using near-infrared reflectance spectroscopy. PLANT METHODS 2022; 18:107. [PMID: 36050789 PMCID: PMC9434866 DOI: 10.1186/s13007-022-00939-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The allocation of non-structural carbohydrates (NSCs) plays a critical role in the physiology and metabolism of tree growth and survival defense. However, little is known about the allocation of NSC after continuous mechanical wounding of pine by resin tapping during tree growth. RESULTS Here, we examine the NSC allocation in plant tissues after 3 year lasting resin tapping, and also investigate the use of near-infrared reflectance (NIR) spectroscopy to quantify the NSC, starch and free sugar (e.g., sucrose, glucose, and fructose) concentrations in different plant tissues of slash pine. Spectral measurements on pine needle, branch, trunk phloem, and root were obtained before starch and free sugar concentrations were measured in the laboratory. The variation of NSC, starch and free sugars in different plant tissues after resin tapping was analyzed. Partial least squares regression was applied to calibrate prediction models, models were simulated 100 times for model performance and error estimation. More NSC, starch and free sugars were stored in winter than summer both in tapped and control trees. The position of resin tapping significantly influenced the NSCs allocation in plant tissues: more NSCs were transformed into free sugars for defensive resin synthesis close to the tapping wound rather than induced distal systemic responses. Models for predicting NSC and free sugars of plant tissues showed promising results for the whole tree for fructose (R2CV = 0.72), glucose (R2CV = 0.67), NSCs (R2CV = 0.66) and starch (R2CV = 0.58) estimates based on NIR models. Models for individual plant tissues also showed reasonable predictive ability: the best model for NSCs and starch prediction was found in root. The significance multivariate correlation algorithm for variable selection significantly reduced the number of variables. Important variables were identified, including features at 1021-1290 nm, 1480, 1748, 1941, 2020, 2123 and 2355 nm, which are highly related to NSC, starch, fructose, glucose and sucrose. CONCLUSIONS NIR spectroscopy provided a rapid and cost-effective method to monitor NSC, starch and free sugar concentrations after continuous resin tapping. It can be used for studying the trade-off between growth and production of defensive metabolites.
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Affiliation(s)
- Yanjie Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Honggang Sun
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Thiago de Paula Protásio
- Federal Rural University of Amazonia-UFRA, Campus Parauapebas, Parauapebas, Pará, 68515-000, Brazil
| | | | - Baoguo Du
- Chair of Tree Physiology, Institute of Forest Sciences, AlbertLudwigs-Universitat Freiburg, Georges-Koehler-Allee 53, 79110, Freiburg, Germany
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5
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Cappa EP, Klutsch JG, Sebastian-Azcona J, Ratcliffe B, Wei X, Da Ros L, Liu Y, Chen C, Benowicz A, Sadoway S, Mansfield SD, Erbilgin N, Thomas BR, El-Kassaby YA. Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program. PLoS One 2022; 17:e0264549. [PMID: 35298481 PMCID: PMC8929621 DOI: 10.1371/journal.pone.0264549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/13/2022] [Indexed: 11/18/2022] Open
Abstract
Tree improvement programs often focus on improving productivity-related traits; however, under present climate change scenarios, climate change-related (adaptive) traits should also be incorporated into such programs. Therefore, quantifying the genetic variation and correlations among productivity and adaptability traits, and the importance of genotype by environment interactions, including defense compounds involved in biotic and abiotic resistance, is essential for selecting parents for the production of resilient and sustainable forests. Here, we estimated quantitative genetic parameters for 15 growth, wood quality, drought resilience, and monoterpene traits for Picea glauca (Moench) Voss (white spruce). We sampled 1,540 trees from three open-pollinated progeny trials, genotyped with 467,224 SNP markers using genotyping-by-sequencing (GBS). We used the pedigree and SNP information to calculate, respectively, the average numerator and genomic relationship matrices, and univariate and multivariate individual-tree models to obtain estimates of (co)variance components. With few site-specific exceptions, all traits examined were under genetic control. Overall, higher heritability estimates were derived from the genomic- than their counterpart pedigree-based relationship matrix. Selection for height, generally, improved diameter and water use efficiency, but decreased wood density, microfibril angle, and drought resistance. Genome-based correlations between traits reaffirmed the pedigree-based correlations for most trait pairs. High and positive genetic correlations between sites were observed (average 0.68), except for those pairs involving the highest elevation, warmer, and moister site, specifically for growth and microfibril angle. These results illustrate the advantage of using genomic information jointly with productivity and adaptability traits, and defense compounds to enhance tree breeding selection for changing climate.
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Affiliation(s)
- Eduardo P. Cappa
- Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jennifer G. Klutsch
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | | | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaojing Wei
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Letitia Da Ros
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yang Liu
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Andy Benowicz
- Forest Stewardship and Trade Branch, Alberta Agriculture and Forestry, Edmonton, Alberta, Canada
| | - Shane Sadoway
- Blue Ridge Lumber Inc., West Fraser Mills Ltd, Blue Ridge, Alberta, Canada
| | - Shawn D. Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Barb R. Thomas
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Dou J, Ilina P, Hemming J, Malinen K, Mäkkylä H, Oliveira de Farias N, Tammela P, de Aragão Umbuzeiro G, Räisänen R, Vuorinen T. Effect of Hybrid Type and Harvesting Season on Phytochemistry and Antibacterial Activity of Extracted Metabolites from Salix Bark. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2948-2956. [PMID: 35200036 PMCID: PMC8915259 DOI: 10.1021/acs.jafc.1c08161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Hundreds of different fast-growing Salix hybrids have been developed mainly for energy crops. In this paper, we studied water extracts from the bark of 15 willow hybrids and species as potential antimicrobial additives. Treatment of ground bark in water under mild conditions extracted 12-25% of the dry material. Preparative high-performance liquid chromatography is proven here as a fast and highly efficient tool in the small-scale recovery of raffinose from Salix bark crude extracts for structural elucidation. Less than half of the dissolved material was assigned by chromatographic (gas chromatography and liquid chromatography) and spectroscopic (mass spectrometry and nuclear magnetic resonance spectroscopy) techniques for low-molecular-weight compounds, including mono- and oligosaccharides (sucrose, raffinose, and stachyose) and aromatic phytochemicals (triandrin, catechin, salicin, and picein). The composition of the extracts varied greatly depending on the hybrid or species and the harvesting season. This information generated new scientific knowledge on the variation in the content and composition of the extracts between Salix hybrids and harvesting season depending on the desired molecule. The extracts showed high antibacterial activity on Staphylococcus aureus with a minimal inhibitory concentration (MIC) of 0.6-0.8 mg/mL; however, no inhibition was observed against Escherichia coli, Enterococcus faecalis, and Salmonella typhimurium. MIC of triandrin (i.e., 1.25 mg/mL) is reported for the first time. Although antibacterial triandrin and (+)-catechin were present in extracts, clear correlation between the antibacterial effect and the chemical composition was not established, which indicates that antibacterial activity of the extracts mainly originates from some not yet elucidated substances. Aquatic toxicity and mutagenicity assessments showed the safe usage of Salix water extracts as possible antibacterial additives.
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Affiliation(s)
- Jinze Dou
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
| | - Polina Ilina
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Jarl Hemming
- Johan
Gadolin Process Chemistry Centre, c/o Laboratory of Natural Materials
Technology, Åbo Akademi University, Turku 20500, Finland
| | - Kiia Malinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
| | - Heidi Mäkkylä
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Natália Oliveira de Farias
- Laboratory
of Ecotoxicology and Genotoxicity—LAEG, School of Technology, University of Campinas, Campinas 13083-970, Brazil
| | - Päivi Tammela
- Drug
Research Program, Division of Pharmaceutical Biosciences, Faculty
of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Gisela de Aragão Umbuzeiro
- Laboratory
of Ecotoxicology and Genotoxicity—LAEG, School of Technology, University of Campinas, Campinas 13083-970, Brazil
| | - Riikka Räisänen
- HELSUS
Helsinki Institute of Sustainability Science, Craft Studies, University of Helsinki, Helsinki 00014, Finland
| | - Tapani Vuorinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
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Dou J, Evtuguin DV, Vuorinen T. Structural Elucidation of Suberin from the Bark of Cultivated Willow ( Salix sp.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10848-10855. [PMID: 34514798 DOI: 10.1021/acs.jafc.1c04112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although extractives have been symbolized as major bioactive pharmacological compounds from Salix (Salicaceae) bark, we speculated that these pharmaceutical effects cannot be solely attributed to phenolic components and their derivatives, but the long-chain suberin acids also contribute to their therapeutic effects. Hence, isolation and deconstruction of suberin were conducted, for the first time, to enrich our knowledge about the macromolecular components at the cell wall of willow bark. Saponification was adopted to obtain suberin extracts at a yield of approximately 5 wt % based on the bark of the studied hybrids. Gas chromatography-mass spectrometry allowed qualification and quantification of 23 compounds from the released suberin monomers, from which fatty acids represented majority of the isolated suberin, namely, fatty acid methyl esters (C17-C19); mono-carboxylic acid (C7-C16); alpha, omega-dicarboxylic acid (C7-C16); and omega-hydroxy long-chain fatty acids (C16-C22). Additionally, the lipophilic extractive was dominated by piceol, heptacosane, β-sitosterol, and fatty acids (C16-C28) from the studied hybrids. These findings could boost our integrative approach toward full valorization of willow bark.
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Affiliation(s)
- Jinze Dou
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo FI-00076, Finland
| | - Dmitry V Evtuguin
- CICECO/Department of Chemistry, University of Aveiro, Aveiro 3810-193, Portugal
| | - Tapani Vuorinen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo FI-00076, Finland
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Lirette AO, Despland E. Defensive Traits during White Spruce ( Picea glauca) Leaf Ontogeny. INSECTS 2021; 12:insects12070644. [PMID: 34357304 PMCID: PMC8306798 DOI: 10.3390/insects12070644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/05/2021] [Accepted: 07/11/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Leaves can only toughen after they have finished growing and, as a result, many herbivorous insects specialize in newly developing leaves because softer leaves are easier to chew. The foliage of conifer trees is particularly tough, and so one would expect conifers to invest more defensive chemicals into soft vulnerable growing needles than into tough mature ones. We summarize the literature describing how chemical defenses of foliage change during the growing season in white spruce, an economically important conifer tree. We next report measurements of the toughness of white spruce buds as they swell, burst, and grow into young needles. As expected, buds soften as they swell in spring, but after budburst, needles become tougher until they are similar to previous-year foliage in mid-summer. Leaves grown in the sun are slightly tougher than leaves grown in the shade. However, there was no indication that trees invest more in chemical defense of growing leaves than of mature leaves. Abstract Changes during leaf ontogeny affect palatability to herbivores, such that many insects, including the eastern spruce budworm (Choristoneura fumiferana (Clem.)), are specialist feeders on growing conifer leaves and buds. Developmental constraints imply lower toughness in developing foliage, and optimal defense theory predicts higher investment in chemical defense in these vulnerable yet valuable developing leaves. We summarize the literature on the time course of defensive compounds in developing white spruce (Picea glauca (Moench) Voss) needles and report original research findings on the ontogeny of white spruce needle toughness. Our results show the predicted pattern of buds decreasing in toughness followed by leaves increasing in toughness during expansion, accompanied by opposite trends in water content. Toughness of mature foliage decreased slightly during the growing season, with no significant relationship with water content. Toughness of sun-grown leaves was slightly higher than that of shade-grown leaves. However, the literature review did not support the expected pattern of higher defensive compounds in expanding leaves than in mature leaves, suggesting that white spruce might instead exhibit a fast-growth low-defense strategy.
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Dou J, Heinonen J, Vuorinen T, Xu C, Sainio T. Chromatographic recovery and purification of natural phytochemicals from underappreciated willow bark water extracts. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.118247] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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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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11
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Yang J, Ma L, Jiang W, Yao Y, Tang Y, Pang Y. Comprehensive identification and characterization of abiotic stress and hormone responsive glycosyl hydrolase family 1 genes in Medicago truncatula. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:21-33. [PMID: 33291052 DOI: 10.1016/j.plaphy.2020.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
β-glucosidases (BGLUs) hydrolyze the β-D-glycosidic bond with retention of anomeric configuration. BGLUs were associated with many aspects of plant physiological processes, in particular biotic and abiotic stresses through the activation of phytohormones and defense compounds. However, studies on systematic analysis of the stress- or hormone-responsive BGLU genes in plant are still rare. In this study, total 51 BGLU genes of the glycoside hydrolase family 1 were identified in the genome of the model legume plant Medicago truncatula, and they were classified into five distinct clusters. Sequence alignments revealed several conserved and characteristic motifs among these MtBGLU proteins. Analyses of their putative signal peptides and N-glycosylation site suggested that the majority of MtBGLU members have dual targeting to the vacuole and/or chloroplast. Many regulatory elements possibly related with abiotic stresses and phytohormones were identified in MtBGLU genes. Moreover, Microarray and qPCR analyses showed that these MtBGLU genes exhibited distinct expression patterns in various tissues, and in response to different abiotic stress and hormonal treatments. Notably, MtBGLU21, MtBGLU22, MtBGLU28, and MtBGLU30 in cluster I were dramatically activated by NaCl, PEG, IAA, ABA, SA and GA3 treatments. Collectively, our genome-wide characterization, evolutionary analysis, and expression pattern analysis of MtBGLU genes suggested that BGLU genes play crucial roles in response to various abiotic stresses and hormonal cues in M. truncatula.
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Affiliation(s)
- Junfeng Yang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yu Yao
- The Institute of Medicinal Plant Development, Beijing, 100193, China
| | - Yuhong Tang
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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12
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Beaulieu J, Nadeau S, Ding C, Celedon JM, Azaiez A, Ritland C, Laverdière J, Deslauriers M, Adams G, Fullarton M, Bohlmann J, Lenz P, Bousquet J. Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits. Evol Appl 2020; 13:2704-2722. [PMID: 33294018 PMCID: PMC7691460 DOI: 10.1111/eva.13076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
With climate change, the pressure on tree breeding to provide varieties with improved resilience to biotic and abiotic stress is increasing. As such, pest resistance is of high priority but has been neglected in most tree breeding programs, given the complexity of phenotyping for these traits and delays to assess mature trees. In addition, the existing genetic variation of resistance and its relationship with productivity should be better understood for their consideration in multitrait breeding. In this study, we evaluated the prospects for genetic improvement of the levels of acetophenone aglycones (AAs) in white spruce needles, which have been shown to be tightly linked to resistance to spruce budworm. Furthermore, we estimated the accuracy of genomic selection (GS) for these traits, allowing selection at a very early stage to accelerate breeding. A total of 1,516 progeny trees established on five sites and belonging to 136 full-sib families from a mature breeding population in New Brunswick were measured for height growth and genotyped for 4,148 high-quality SNPs belonging to as many genes along the white spruce genome. In addition, 598 trees were assessed for levels of AAs piceol and pungenol in needles, and 578 for wood stiffness. GS models were developed with the phenotyped trees and then applied to predict the trait values of unphenotyped trees. AAs were under moderate-to-high genetic control (h 2: 0.43-0.57) with null or marginally negative genetic correlations with other traits. The prediction accuracy of GS models (GBLUP) for AAs was high (PAAC: 0.63-0.67) and comparable or slightly higher than pedigree-based (ABLUP) or BayesCπ models. We show that AA traits can be improved and that GS speeds up the selection of improved trees for insect resistance and for growth and wood quality traits. Various selection strategies were tested to optimize multitrait gains.
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Affiliation(s)
- Jean Beaulieu
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Wood Fibre CentreQuébecQCCanada
| | - Chen Ding
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
- Present address:
Western Gulf Forest Tree Improvement ProgramTexas A&M Forest ServiceForest Science LaboratoryCollege StationTXUSA
| | - Jose M. Celedon
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCCanada
| | - Aïda Azaiez
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | - Carol Ritland
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCCanada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Jean‐Philippe Laverdière
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | | | | | - Michele Fullarton
- Forest Development SectionNatural Resources and Energy DevelopmentGovernment of New BrunswickIsland ViewNBCanada
| | - Joerg Bohlmann
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCCanada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
| | - Patrick Lenz
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Wood Fibre CentreQuébecQCCanada
| | - Jean Bousquet
- Canada Research Chair in Forest GenomicsInstitute of Systems and Integrative Biology and Systems, and Centre for Forest ResearchUniversité LavalQuébecQCCanada
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13
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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce. Sci Rep 2020; 10:12711. [PMID: 32728135 PMCID: PMC7391732 DOI: 10.1038/s41598-020-69386-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/07/2020] [Indexed: 11/08/2022] Open
Abstract
The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
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14
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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15
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Lumley LM, Pouliot E, Laroche J, Boyle B, Brunet BMT, Levesque RC, Sperling FAH, Cusson M. Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm ( Choristoneura fumiferana). Ecol Evol 2020; 10:914-927. [PMID: 32015854 PMCID: PMC6988549 DOI: 10.1002/ece3.5950] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.
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Affiliation(s)
- Lisa M. Lumley
- Royal Alberta MuseumEdmontonABCanada
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Esther Pouliot
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
| | | | | | | | | | | | - Michel Cusson
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
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16
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Parent GJ, Méndez‐Espinoza C, Giguère I, Mageroy MH, Charest M, Bauce É, Bohlmann J, MacKay JJ. Hydroxyacetophenone defenses in white spruce against spruce budworm. Evol Appl 2020; 13:62-75. [PMID: 31892944 PMCID: PMC6935585 DOI: 10.1111/eva.12885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/17/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
We review a recently discovered white spruce (Picea glauca) chemical defense against spruce budworm (Choristoneura fumiferana) involving hydroxyacetophenones. These defense metabolites detected in the foliage accumulate variably as the aglycons, piceol and pungenol, or the corresponding glucosides, picein and pungenin. We summarize current knowledge of the genetic, genomic, molecular, and biochemical underpinnings of this defense and its effects on C. fumiferana. We present an update with new results on the ontogenic variation and the phenological window of this defense, including analysis of transcript responses in P. glauca to C. fumiferana herbivory. We also discuss this chemical defense from an evolutionary and a breeding context.
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Affiliation(s)
- Geneviève J. Parent
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
- Institut de biologie intégrative et des systèmesUniversité LavalQuébecQCCanada
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Claudia Méndez‐Espinoza
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
- Institut de biologie intégrative et des systèmesUniversité LavalQuébecQCCanada
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas ForestalesInstituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasCiudad de MéxicoMexico
| | - Isabelle Giguère
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
- Institut de biologie intégrative et des systèmesUniversité LavalQuébecQCCanada
| | - Melissa H. Mageroy
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCCanada
- Norwegian Institute for Bioeconomy ResearchÅsNorway
| | - Martin Charest
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
| | - Éric Bauce
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
| | - Joerg Bohlmann
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCCanada
| | - John J. MacKay
- Département des sciences du bois et de la forêtCentre d’étude de la forêtUniversité LavalQuébecQCCanada
- Institut de biologie intégrative et des systèmesUniversité LavalQuébecQCCanada
- Department of Plant SciencesUniversity of OxfordOxfordUK
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17
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Godbout J, Gros-Louis M, Lamothe M, Isabel N. Going with the flow: Intraspecific variation may act as a natural ally to counterbalance the impacts of global change for the riparian species Populus deltoides. Evol Appl 2020; 13:176-194. [PMID: 31892951 PMCID: PMC6935597 DOI: 10.1111/eva.12854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/16/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022] Open
Abstract
The speed and magnitude of global change will have major impacts on riparian ecosystems, thereby leading to greater forest vulnerability. Assessing species' adaptive capacities to provide relevant information for vulnerability assessments remains challenging, especially for nonmodel species like the North American Populus deltoides W. Bartram ex Marshall. The objective of this study was to understand how genomic diversity of this foundation species was shaped by its environment (climate, soil, and biotic interactions) to gauge its adaptive capacity. We used two complementary approaches to get a full portrait of P. deltoides genetic diversity at both the species and whole-genome ranges. First, we used a set of 93 nuclear and three chloroplastic SNP markers in 946 individuals covering most of the species' natural distribution. Then, to measure the degree of intraspecific divergence at the whole-genome level and to support the outlier and genomic-environment association analyses, we used a sequence capture approach on DNA pools. Three distinct lineages for P. deltoides were detected, and their current distribution was associated with abiotic and biotic variations. The comparison between both cpDNA and ncDNA patterns showed that gene flow between the lineages is unbalanced. The southern and northeastern populations may benefit from the input, through river flow, of novel alleles located upstream to their local gene pools. These alleles could migrate from populations that are already adapted to conditions that fit the predicted climates in the receiving local populations, hotter at the northeastern limit and drier in the Central United States. These "preadapted" incoming alleles may help to cope with maladaptation in populations facing changing conditions.
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Affiliation(s)
- Julie Godbout
- Ministère des Forêts, de la Faune et des Parcs, Direction de la recherche forestièreQuébecQCCanada
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
| | | | - Manuel Lamothe
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
| | - Nathalie Isabel
- Canadian Forest Service, Laurentian Forestry CentreNatural Resources CanadaQuébecQCCanada
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18
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Ramos PAB, Moreirinha C, Silva S, Costa EM, Veiga M, Coscueta E, Santos SAO, Almeida A, Pintado MM, Freire CSR, Silva AMS, Silvestre AJD. The Health-Promoting Potential of Salix spp. Bark Polar Extracts: Key Insights on Phenolic Composition and In Vitro Bioactivity and Biocompatibility. Antioxidants (Basel) 2019; 8:antiox8120609. [PMID: 31801290 PMCID: PMC6943414 DOI: 10.3390/antiox8120609] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 01/15/2023] Open
Abstract
Salix spp. have been exploited for energy generation, along with folk medicine use of bark extracts for antipyretic and analgesic benefits. Bark phenolic components, rather than salicin, have demonstrated interesting bioactivities, which may ensure the sustainable bioprospection of Salix bark. Therefore, this study highlights the detailed phenolic characterization, as well as the in vitro antioxidant, anti-hypertensive, Staphylococcus aureus growth inhibitory effects, and biocompatibility of Salix atrocinerea Brot., Salix fragilis L., and Salix viminalis L. bark polar extracts. Fifteen phenolic compounds were characterized by ultra-high-performance liquid chromatography-ultraviolet detection-mass spectrometry analysis, from which two flavan-3-ols, an acetophenone, five flavanones, and a flavonol were detected, for the first time, as their bark components. Salix bark extracts demonstrated strong free radical scavenging activity (5.58–23.62 µg mL−1 IC50 range), effective inhibition on angiotensin-I converting enzyme (58–84%), and S. aureus bactericidal action at 1250–2500 µg mL−1 (6–8 log CFU mL−1 reduction range). All tested Salix bark extracts did not show cytotoxic potential against Caco-2 cells, as well as S. atrocinerea Brot. and S. fragilis L. extracts at 625 and 1250 µg mL−1 against HaCaT and L929 cells. These valuable findings can pave innovative and safer food, nutraceutical, and/or cosmetic applications of Salix bark phenolic-containing fractions.
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Affiliation(s)
- Patrícia A. B. Ramos
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Catarina Moreirinha
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
| | - Sara Silva
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal; (S.S.); (E.M.C.); (M.V.); (E.C.); (M.M.P.)
| | - Eduardo M. Costa
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal; (S.S.); (E.M.C.); (M.V.); (E.C.); (M.M.P.)
| | - Mariana Veiga
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal; (S.S.); (E.M.C.); (M.V.); (E.C.); (M.M.P.)
| | - Ezequiel Coscueta
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal; (S.S.); (E.M.C.); (M.V.); (E.C.); (M.M.P.)
| | - Sónia A. O. Santos
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
| | - Adelaide Almeida
- Biology Department and CESAM—Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - M. Manuela Pintado
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal; (S.S.); (E.M.C.); (M.V.); (E.C.); (M.M.P.)
| | - Carmen S. R. Freire
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
| | - Artur M. S. Silva
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Armando J. D. Silvestre
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (P.A.B.R.); (C.M.); (S.A.O.S.); (C.S.R.F.); (A.M.S.S.)
- Correspondence: ; Tel.: +351-234-370-711
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19
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Whitehill JG, Bohlmann J. A molecular and genomic reference system for conifer defence against insects. PLANT, CELL & ENVIRONMENT 2019; 42:2844-2859. [PMID: 31042808 PMCID: PMC6852437 DOI: 10.1111/pce.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 05/29/2023]
Abstract
Insect pests are part of natural forest ecosystems contributing to forest rejuvenation but can also cause ecological disturbance and economic losses that are expected to increase with climate change. The white pine or spruce weevil (Pissodes strobi) is a pest of conifer forests in North America. Weevil-host interactions with various spruce (Picea) species have been explored as a genomic and molecular reference system for conifer defence against insects. Interactions occur in two major phases of the insect life cycle. In the exophase, adult weevils are free-moving and display behaviour of host selection for oviposition that is affected by host traits. In the endophase, insects live within the host where mobility and development from eggs to young adults are affected by a complex system of host defences. Genetic resistance exists in several spruce species and involves synergism of constitutive and induced chemical and physical defences that comprise the conifer defence syndrome. Here, we review conifer defences that disrupt the weevil life cycle and mechanisms by which trees resist weevil attack. We highlight molecular and genomic aspects and a possible role for the weevil microbiome. Knowledge of this conifer defence system is supporting forest health strategies and tree breeding for insect resistance.
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Affiliation(s)
| | - Jörg Bohlmann
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of BotanyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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20
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Donkor D, Mirzahosseini Z, Bede J, Bauce E, Despland E. Detoxification of host plant phenolic aglycones by the spruce budworm. PLoS One 2019; 14:e0208288. [PMID: 31095557 PMCID: PMC6522000 DOI: 10.1371/journal.pone.0208288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/28/2019] [Indexed: 11/18/2022] Open
Abstract
This study examines the post-ingestive fate of two host-plant derived small-molecule phenolics (the acetophenones piceol and pungenol) that have previously been shown to be toxic to the outbreaking forest pest, spruce budworm (Choristoneura fumiferana). We test first whether these compounds are transformed during passage through the midgut, and second whether the budworm upregulates activity of the detoxification enzyme glutathione-s-transferase (GST) in response to feeding on these compounds. Insects were reared on either foliage or artificial diet to the fourth instar, when they were transferred individually to one of two treatment diets, either control or phenolic-laced, for approximately 10 days, after which midguts were dissected out and used for Bradford soluble protein and GST enzyme activity analysis. Frass was collected and subjected to HPLC-DAD-MS. HPLC showed that the acetophenones do not autoxidize under midgut pH conditions, but that glucose- and glutathione- conjugates are present in the frass of insects fed the phenolic-laced diet. GST enzyme activity increases in insects fed the phenolic-laced diet, in both neutral pH and alkaline assays. These data show that the spruce budwom exhibits counter-adaptations to plant phenolics similar to those seen in angiosperm feeders, upregulating an important detoxifying enzyme (GST) and partially conjugating these acetophenones prior to elimination, but that these counter-measures are not totally effective at mitigating toxic effects of the ingested compounds in the context of our artifical-diet based laboratory experiment.
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Affiliation(s)
- Dominic Donkor
- Biology Department, Concordia University, Montreal, Canada
| | | | - Jacquie Bede
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Eric Bauce
- Département des sciences du bois et de la forêt, Université Laval, Ste-Foy, Canada
| | - Emma Despland
- Biology Department, Concordia University, Montreal, Canada
- * E-mail:
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21
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Lamara M, Parent GJ, Giguère I, Beaulieu J, Bousquet J, MacKay JJ. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC PLANT BIOLOGY 2018; 18:231. [PMID: 30309315 PMCID: PMC6182838 DOI: 10.1186/s12870-018-1434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Outbreaks of spruce budworm (SBW, Choristoneura fumiferana Clem.) cause major recurrent damage in boreal conifers such as white spruce (Picea glauca [Moench] Voss) and large losses of forest biomass in North America. Although defensive phenolic compounds have recently been linked to chemical resistance against SBW, their genetic basis remains poorly understood in forest trees, especially in conifers. Here, we used diverse association genetics approaches to discover genes and their variants that may control the accumulation of acetophenones, and dissect the genetic architecture of these defence compounds against SBW in white spruce mature trees. RESULTS Out of 4747 single nucleotide polymorphisms (SNPs) from 2312 genes genotyped in a population of 211 unrelated individuals, genetic association analyses identified 35 SNPs in 33 different genes that were significantly associated with the defence traits by using single-locus, multi-locus and multi-trait approaches. The multi-locus approach was particularly effective at detecting SNP-trait associations that explained a large fraction of the phenotypic variance (from 20 to 43%). Significant genes were regulatory including the NAC transcription factor, or they were involved in carbohydrate metabolism, falling into the binding, catalytic or transporter activity functional classes. Most of them were highly expressed in foliage. Weak positive phenotypic correlations were observed between defence and growth traits, indicating little or no evidence of defence-growth trade-offs. CONCLUSIONS This study provides new insights on the genetic architecture of tree defence traits, contributing to our understanding of the physiology of resistance mechanisms to biotic factors and providing a basis for the genetic improvement of the constitutive defence of white spruce against SBW.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | | | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Beaulieu
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - John J. MacKay
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
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22
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Li W, Li H, Xu P, Xie Z, Ye Y, Li L, Li D, Zhang Y, Li L, Zhao Y. Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway. PLANT MOLECULAR BIOLOGY 2018; 98:275-287. [PMID: 30311174 DOI: 10.1007/s11103-018-0779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/17/2018] [Indexed: 05/05/2023]
Abstract
A new synthetic auxin AAL1 with new structure was identified. Different from known auxins, it has weak effects. By AAL1, we found specific amino acids could restore the effects of auxin with similar structure. Auxin, one of the most important phytohormones, plays crucial roles in plant growth, development and environmental response. Although many critical regulators have been identified in auxin signaling pathway, some factors, especially those with weak fine-tuning roles, are still yet to be discovered. Through chemical genetic screenings, we identified a small molecule, Auxin Activity Like 1 (AAL1), which can effectively inhibit dark-grown Arabidopsis thaliana seedlings. Genetic screening identified AAL1 resistant mutants are also hyposensitive to indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). AAL1 resistant mutants such as shy2-3c and ecr1-2 are well characterized as mutants in auxin signaling pathway. Genetic studies showed that AAL1 functions through auxin receptor Transport Inhibitor Response1 (TIR1) and its functions depend on auxin influx and efflux carriers. Compared with known auxins, AAL1 exhibits relatively weak effects on plant growth, with 20 µM and 50 µM IC50 (half growth inhibition chemical concentration) in root and hypocotyl growth respectively. Interestingly, we found the inhibitory effects of AAL1 and IAA could be partially restored by tyrosine and tryptophan respectively, suggesting some amino acids can also affect auxin signaling pathway in a moderate manner. Taken together, our results demonstrate that AAL1 acts through auxin signaling pathway, and AAL1, as a weak auxin activity analog, provides us a tool to study weak genetic interactions in auxin pathway.
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Affiliation(s)
- Wenbo 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, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Haimin 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, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Peng Xu
- 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, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhi Xie
- 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, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yajin Ye
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lingting Li
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Deqiang 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, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yijing Zhang
- 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, Shanghai, 200032, China
| | - Laigeng 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, Shanghai, 200032, China.
| | - Yang Zhao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 68 Wenchang Road, Yunnan, 650000, China.
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23
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Méndez-Espinoza C, Parent GJ, Lenz P, Rainville A, Tremblay L, Adams G, McCartney A, Bauce É, MacKay J. Genetic control and evolutionary potential of a constitutive resistance mechanism against the spruce budworm (Choristoneura fumiferana) in white spruce (Picea glauca). Heredity (Edinb) 2018; 121:142-154. [PMID: 29453424 PMCID: PMC6039516 DOI: 10.1038/s41437-018-0061-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 11/09/2022] Open
Abstract
Insect herbivory may drive evolution by selecting for trees with heritable resistance against defoliation. The spruce budworm (Choristoneura fumiferana, SBW) is a highly damaging forest insect pest that can affect population structure of white spruce (Picea glauca) in North America. Resistance against SBW was recently described in white spruce and was linked to three constitutive resistance biomarkers: the phenolic compounds piceol and pungenol, and expression of a beta-glucosidase encoding gene (Pgβglu-1). We investigated the phenotypic variability and heritability of these resistance biomarkers and of picein, the precursor of piceol, in the foliage of 874 trees belonging to 33 full-sib families and 71 clonal lines under evaluation in seven field locations in Eastern Canada. We aimed to (i) determine their genetic control, (ii) estimate the genetic and phenotypic correlations among defense biomarkers, and (iii) determine whether their constitutive levels are associated with detrimental trade-offs on growth. Quantitative genetics analyses indicated that all four traits are moderately to highly heritable. The full-sib and clonal analyses showed that additive and non-additive genetic effects play major and minor roles, respectively. Positive genetic and phenotypic correlations between resistance biomarkers and primary growth indicated that there is no trade-off between total height and height increment and resistance traits, contradicting the GDBH (Growth Differentiation Balance Hypothesis). Our findings about the predominant additive genetic basis of the resistance biomarkers show that adaptive evolution of white spruce natural populations to resist to SBW is possible and that potentially important gains could also be expected from artificial selection.
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Affiliation(s)
- Claudia Méndez-Espinoza
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada.
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, Av. Progreso 5, Barrio de Santa Catarina, 04010, Ciudad de México, CDMX, Mexico.
| | - Geneviève J Parent
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford, 0X1 3RB, UK
| | - Patrick Lenz
- Canadian Wood Fibre Center, Natural Resources Canada, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Université Laval, Québec, QC, G1V 0A6, Canada
| | - André Rainville
- Ministère des Forêts, de la Faune et des Parcs, Québec, QC, G2K 0G9, Canada
| | - Laurence Tremblay
- Ministère des Forêts, de la Faune et des Parcs, Québec, QC, G2K 0G9, Canada
| | - Greg Adams
- J.D. Irving, Limited, Saint John, NB, E4G 2V5, Canada
| | | | - Éric Bauce
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, G1V 0A6, Canada
| | - John MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford, 0X1 3RB, UK
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24
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Parent GJ, Giguère I, Mageroy M, Bohlmann J, MacKay JJ. Evolution of the biosynthesis of two hydroxyacetophenones in plants. PLANT, CELL & ENVIRONMENT 2018; 41:620-629. [PMID: 29314043 DOI: 10.1111/pce.13134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
Acetophenones are phenolic metabolites of plant species. A metabolic route for the biosynthesis and release of 2 defence-related hydroxyacetophenones in white spruce (Picea glauca) was recently proposed to involve 3 phases: (a) biosynthesis of the acetophenone aglycons catalysed by a currently unknown set of enzymes, (b) formation and accumulation of the corresponding glycosides catalysed by a glucosyltransferase, and (c) release of the aglycons catalysed by a glucosylhydrolase (PgβGLU-1). We tested if this biosynthetic model is conserved across Pinaceae and land plant species. We assayed and surveyed the literature and sequence databases for possible patterns of the presence of the acetophenone aglycons piceol and pungenol and their glucosides, as well as sequences and expression of Pgβglu-1 orthologues. In the Pinaceae, the 3 phases of the biosynthetic model are present and differences in expression of Pgβglu-1 gene orthologues explain some of the interspecific variation in hydroxyacetophenones. The phylogenetic signal in the metabolite phenotypes was low across species of 6 plant divisions. Putative orthologues of PgβGLU-1 do not form a monophyletic group in species producing hydroxyacetophenones. The biosynthetic model for acetophenones appears to be conserved across Pinaceae, whereas convergent evolution has led to the production of acetophenone glucosides across land plants.
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Affiliation(s)
- Geneviève J Parent
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Isabelle Giguère
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec City, Québec, G1V 0A6, Canada
| | - Melissa Mageroy
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Norwegian Institute for Bioeconomy Research, Ås, 1433, Norway
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - John J MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec City, Québec, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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25
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Celedon JM, Yuen MMS, Chiang A, Henderson H, Reid KE, Bohlmann J. Cell-type- and tissue-specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:710-726. [PMID: 28857307 DOI: 10.1111/tpj.13673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/07/2017] [Accepted: 08/22/2017] [Indexed: 05/09/2023]
Abstract
Plant defenses often involve specialized cells and tissues. In conifers, specialized cells of the bark are important for defense against insects and pathogens. Using laser microdissection, we characterized the transcriptomes of cortical resin duct cells, phenolic cells and phloem of white spruce (Picea glauca) bark under constitutive and methyl jasmonate (MeJa)-induced conditions, and we compared these transcriptomes with the transcriptome of the bark tissue complex. Overall, ~3700 bark transcripts were differentially expressed in response to MeJa. Approximately 25% of transcripts were expressed in only one cell type, revealing cell specialization at the transcriptome level. MeJa caused cell-type-specific transcriptome responses and changed the overall patterns of cell-type-specific transcript accumulation. Comparison of transcriptomes of the conifer bark tissue complex and specialized cells resolved a masking effect inherent to transcriptome analysis of complex tissues, and showed the actual cell-type-specific transcriptome signatures. Characterization of cell-type-specific transcriptomes is critical to reveal the dynamic patterns of spatial and temporal display of constitutive and induced defense systems in a complex plant tissue or organ. This was demonstrated with the improved resolution of spatially restricted expression of sets of genes of secondary metabolism in the specialized cell types.
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Affiliation(s)
- Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Angela Chiang
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Hannah Henderson
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Karen E Reid
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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26
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Mageroy MH, Jancsik S, Man Saint Yuen M, Fischer M, Withers SG, Paetz C, Schneider B, Mackay J, Bohlmann J. A Conifer UDP-Sugar Dependent Glycosyltransferase Contributes to Acetophenone Metabolism and Defense against Insects. PLANT PHYSIOLOGY 2017; 175:641-651. [PMID: 28794260 PMCID: PMC5619895 DOI: 10.1104/pp.17.00611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/01/2017] [Indexed: 05/15/2023]
Abstract
Acetophenones are phenolic compounds involved in the resistance of white spruce (Picea glauca) against spruce budworm (Choristoneura fumiferiana), a major forest pest in North America. The acetophenones pungenol and piceol commonly accumulate in spruce foliage in the form of the corresponding glycosides, pungenin and picein. These glycosides appear to be inactive against the insect but can be cleaved by a spruce β-glucosidase, PgβGLU-1, which releases the active aglycons. The reverse glycosylation reaction was hypothesized to involve a family 1 UDP-sugar dependent glycosyltransferase (UGT) to facilitate acetophenone accumulation in the plant. Metabolite and transcriptome profiling over a developmental time course of white spruce bud burst and shoot growth revealed two UGTs, PgUGT5 and PgUGT5b, that glycosylate pungenol. Recombinant PgUGT5b enzyme produced mostly pungenin, while PgUGT5 produced mostly isopungenin. Both UGTs also were active in vitro on select flavonoids. However, the context of transcript and metabolite accumulation did not support a biological role in flavonoid metabolism but correlated with the formation of pungenin in growing shoots. Transcript levels of PgUGT5b were higher than those of PgUGT5 in needles across different genotypes of white spruce. These results support a role of PgUGT5b in the biosynthesis of the glycosylated acetophenone pungenin in white spruce.
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Affiliation(s)
- Melissa H Mageroy
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Norwegian Institute for Bioeconomy Research, NO-1430 As, Norway
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Michael Fischer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T1Z1, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T1Z1, Canada
| | - Christian Paetz
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Bernd Schneider
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - John Mackay
- Department of Wood and Forest Sciences, Université Laval, Quebec City, Quebec G1V0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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27
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Prunier J, Caron S, Lamothe M, Blais S, Bousquet J, Isabel N, MacKay J. Gene copy number variations in adaptive evolution: The genomic distribution of gene copy number variations revealed by genetic mapping and their adaptive role in an undomesticated species, white spruce (Picea glauca). Mol Ecol 2017; 26:5989-6001. [PMID: 28833771 DOI: 10.1111/mec.14337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/26/2017] [Accepted: 08/05/2017] [Indexed: 01/09/2023]
Abstract
Gene copy number variation (CNV) has been associated with phenotypic variability in animals and plants, but a genomewide understanding of their impacts on phenotypes is largely restricted to human and agricultural systems. As such, CNVs have rarely been considered in investigations of the genomic architecture of adaptation in wild species. Here, we report on the genetic mapping of gene CNVs in white spruce, which lacks a contiguous assembly of its large genome (~20 Gb), and their relationships with adaptive phenotypic variation. We detected 3,911 gene CNVs including de novo structural variations using comparative genome hybridization on arrays (aCGH) in a large progeny set. We inferred the heterozygosity at CNV loci within parents by comparing haploid and diploid tissues and genetically mapped 82 gene CNVs. Our analysis showed that CNVs were distributed over 10 linkage groups and identified four CNV hotspots that we predict to occur in other species of the Pinaceae. Significant relationships were found between 29 of the gene CNVs and adaptive traits based on regression analyses with timings of bud set and bud flush, and height growth, suggesting a role for CNVs in climate adaptation. The importance of CNVs in adaptive evolution of white spruce was also indicated by functional gene annotations and the clustering of 31% of the mapped adaptive gene CNVs in CNV hotspots. Taken together, these results illustrate the feasibility of studying CNVs in undomesticated species and represent a major step towards a better understanding of the roles of CNVs in adaptive evolution.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada
| | - Sébastien Caron
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Quebec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Sylvie Blais
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Jean Bousquet
- Institute for System and Integrative Biology (IBIS), Université Laval, Québec, QC, Canada.,Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - Nathalie Isabel
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Quebec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada
| | - John MacKay
- Centre for Forest Research, Université Laval, Québec, QC, Canada.,Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC, Canada.,Department of Plant Sciences, University of Oxford, Oxford, UK
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28
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Fuentealba A, Pureswaran D, Bauce É, Despland E. How does synchrony with host plant affect the performance of an outbreaking insect defoliator? Oecologia 2017; 184:847-857. [DOI: 10.1007/s00442-017-3914-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/05/2017] [Indexed: 11/28/2022]
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29
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Mageroy MH, Lachance D, Jancsik S, Parent G, Séguin A, Mackay J, Bohlmann J. In vivo function of Pgβglu-1 in the release of acetophenones in white spruce. PeerJ 2017; 5:e3535. [PMID: 28698822 PMCID: PMC5502087 DOI: 10.7717/peerj.3535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/13/2017] [Indexed: 12/03/2022] Open
Abstract
Eastern spruce budworm (Choristoneura fumiferiana Clemens) (ESBW) is a major forest pest which feeds on young shoots of white spruce (Picea glauca) and can cause landscape level economic and ecological losses. Release of acetophenone metabolites, piceol and pungenol, from their corresponding glycosides, picein and pungenin, can confer natural resistance of spruce to ESBW. A beta-glucosidase gene, Pgβglu-1, was recently discovered and the encoded enzyme was characterized in vitro to function in the release of the defensive acetophenone aglycons. Here we describe overexpression of Pgβglu-1 in a white spruce genotype whose metabolome contains the glucosylated acetophenones, but no detectable amounts of the aglycons. Transgenic overexpression of Pgβglu-1 resulted in release of the acetophenone aglycons in planta. This work provides in vivo evidence for the function of Pgβglu-1.
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Affiliation(s)
- Melissa H Mageroy
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Norwegian Institute of Bioeconomy Research, Aas, Norway
| | - Denis Lachance
- Laurentian Forestry Centre, Natural Resources Canada, Quebec, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Geneviève Parent
- Department of Wood and Forest Sciences, Laval University, Quebec, Canada.,Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Quebec, Canada
| | - John Mackay
- Department of Wood and Forest Sciences, Laval University, Quebec, Canada.,Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Complex Sexual Deception in an Orchid Is Achieved by Co-opting Two Independent Biosynthetic Pathways for Pollinator Attraction. Curr Biol 2017. [DOI: 10.1016/j.cub.2017.05.065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Parent GJ, Giguère I, Germanos G, Lamara M, Bauce É, MacKay JJ. Insect herbivory (Choristoneura fumiferana, Tortricidea) underlies tree population structure (Picea glauca, Pinaceae). Sci Rep 2017; 7:42273. [PMID: 28205578 PMCID: PMC5311968 DOI: 10.1038/srep42273] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/09/2017] [Indexed: 12/04/2022] Open
Abstract
Variation in insect herbivory can lead to population structure in plant hosts as indicated by defence traits. In annual herbaceous, defence traits may vary between geographic areas but evidence of such patterns is lacking for long-lived species. This may result from the variety of selection pressures from herbivores, long distance gene flow, genome properties, and lack of research. We investigated the antagonistic interaction between white spruce (Picea glauca) and spruce budworm (SBW, Choristoneura fumiferana) the most devastating forest insect of eastern North America in common garden experiments. White spruces that are able to resist SBW attack were reported to accumulate the acetophenones piceol and pungenol constitutively in their foliage. We show that levels of these acetophenones and transcripts of the gene responsible for their release is highly heritable and that their accumulation is synchronized with the most devastating stage of SBW. Piceol and pungenol concentrations negatively correlate with rate of development in female SBW and follow a non-random geographic variation pattern that is partially explained by historical damage from SBW and temperature. Our results show that accumulation of acetophenones is an efficient resistance mechanism against SBW in white spruce and that insects can affect population structure of a long-lived plant.
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Affiliation(s)
- Geneviève J Parent
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes, Université Laval, Québec, Qc, G1V 0A6, Canada.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Isabelle Giguère
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes, Université Laval, Québec, Qc, G1V 0A6, Canada
| | - Gaby Germanos
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes, Université Laval, Québec, Qc, G1V 0A6, Canada
| | - Mebarek Lamara
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes, Université Laval, Québec, Qc, G1V 0A6, Canada
| | - Éric Bauce
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada
| | - John J MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, Qc, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes, Université Laval, Québec, Qc, G1V 0A6, Canada.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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32
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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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Nemesio-Gorriz M, Hammerbacher A, Ihrmark K, Källman T, Olson Å, Lascoux M, Stenlid J, Gershenzon J, Elfstrand M. Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies. PLANT PHYSIOLOGY 2016; 171:2671-81. [PMID: 27317690 PMCID: PMC4972290 DOI: 10.1104/pp.16.00685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/11/2016] [Indexed: 05/18/2023]
Abstract
Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.
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Affiliation(s)
- Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Almuth Hammerbacher
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Thomas Källman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Martin Lascoux
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jonathan Gershenzon
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
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Sainsbury F, Jutras PV, Vorster J, Goulet MC, Michaud D. A Chimeric Affinity Tag for Efficient Expression and Chromatographic Purification of Heterologous Proteins from Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:141. [PMID: 26913045 PMCID: PMC4753422 DOI: 10.3389/fpls.2016.00141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/27/2016] [Indexed: 05/23/2023]
Abstract
The use of plants as expression hosts for recombinant proteins is an increasingly attractive option for the production of complex and challenging biopharmaceuticals. Tools are needed at present to marry recent developments in high-yielding gene vectors for heterologous expression with routine protein purification techniques. In this study, we designed the Cysta-tag, a new purification tag for immobilized metal affinity chromatography (IMAC) of plant-made proteins based on the protein-stabilizing fusion partner SlCYS8. We show that the Cysta-tag may be used to readily purify proteins under native conditions, and then be removed enzymatically to isolate the protein of interest. We also show that commonly used protease recognition sites for linking purification tags are differentially stable in leaves of the commonly used expression host Nicotiana benthamiana, with those linkers susceptible to cysteine proteases being less stable then serine protease-cleavable linkers. As an example, we describe a Cysta-tag experimental scheme for the one-step purification of a clinically useful protein, human α1-antitrypsin, transiently expressed in N. benthamiana. With potential applicability to the variety of chromatography formats commercially available for IMAC-based protein purification, the Cysta-tag provides a convenient means for the efficient and cost-effective purification of recombinant proteins from plant tissues.
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Affiliation(s)
- Frank Sainsbury
- Département de Phytologie–Centre de Recherche et d’Innovation sur les Végétaux, Université Laval, QuébecQC, Canada
- Centre for Biomolecular Engineering, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, BrisbaneQLD, Australia
| | - Philippe V. Jutras
- Département de Phytologie–Centre de Recherche et d’Innovation sur les Végétaux, Université Laval, QuébecQC, Canada
- Centre for Biomolecular Engineering, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, BrisbaneQLD, Australia
| | - Juan Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Marie-Claire Goulet
- Département de Phytologie–Centre de Recherche et d’Innovation sur les Végétaux, Université Laval, QuébecQC, Canada
| | - Dominique Michaud
- Département de Phytologie–Centre de Recherche et d’Innovation sur les Végétaux, Université Laval, QuébecQC, Canada
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35
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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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36
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LeClair G, Williams M, Silk P, Eveleigh E, Mayo P, Brophy M, Francis B. Spruce Budworm (Lepidoptera: Tortricidae) Oral Secretions II: Chemistry. ENVIRONMENTAL ENTOMOLOGY 2015; 44:1531-1543. [PMID: 26454474 DOI: 10.1093/ee/nvv149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
As sessile organisms, plants have evolved different methods to defend against attacks and have adapted their defense measures to discriminate between mechanical damage and herbivory by insects. One of the ways that plant defenses are triggered is via elicitors from insect oral secretions (OS). In this study, we investigated the ability of second-instar (L2) spruce budworm [SBW; Choristoneura fumiferana (Clemens)] to alter the volatile organic compounds (VOCs) of four conifer species [Abies balsamea (L.) Mill., Picea mariana (Miller) B.S.P., Picea glauca (Moench) Voss, Picea rubens (Sargent)] and found that the emission profiles from all host trees were drastically changed after herbivory. We then investigated whether some of the main elicitors (fatty acid conjugates [FACs], β-glucosidase, and glucose oxidase) studied were present in SBW OS. FACs (glutamine and glutamic acid) based on linolenic, linoleic, oleic, and stearic acids were all observed in varying relative quantities. Hydroxylated FACs, such as volicitin, were not observed. Enzyme activity for β-glucosidase was also measured and found present in SBW OS, whereas glucose oxidase activity was not found in the SBW labial glands. These results demonstrate that SBW L2 larvae have the ability to induce VOC emissions upon herbivory and that SBW OS contain potential elicitors to induce these defensive responses. These data will be useful to further evaluate whether these elicitors can separately induce the production of specific VOCs and to investigate whether and how these emissions benefit the plant.
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37
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Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJM, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:189-212. [PMID: 26017574 DOI: 10.1111/tpj.12886] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/15/2015] [Indexed: 05/21/2023]
Abstract
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Affiliation(s)
- René L Warren
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anthony Raymond
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Greg A Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Benjamin P Vandervalk
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Hamid Mohamadi
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Daniel Paulino
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Gordon Robertson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Margarete Hoffmann
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Alvin Yanchuk
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Jean Bousquet
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - John MacKay
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Quezada-Garcia R, Fuentealba A, Nguyen N, Bauce É. Do Offspring of Insects Feeding on Defoliation-Resistant Trees Have Better Biological Performance When Exposed to Nutritionally-Imbalanced Food? INSECTS 2015; 6:112-121. [PMID: 26463069 PMCID: PMC4553532 DOI: 10.3390/insects6010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/07/2015] [Indexed: 06/05/2023]
Abstract
White spruce (Picea glauca (Moench) Voss) trees that are resistant or susceptible to spruce budworm (Choristoneura fumiferana (Clem.)) attack were identified in a southern Quebec plantation. Due to high mortality-induced selective pressures imposed by resistant trees on spruce budworm larvae, insects that survive on resistant trees exhibited greater biological performance than those on susceptible trees. We tested the hypothesis that this better biological performance is maintained across generations when progeny were subjected to nutritional stress. We collected pupae from resistant and susceptible trees (phenotype). Adults were reared under controlled laboratory conditions. Progeny were subsequently reared on two types of artificial diet (high vs. low quality). Low quality diet simulated food quality deterioration during outbreak conditions. Results confirmed that surviving insects collected from resistant trees have better performance than those from susceptible trees. Offspring performance (pupal mass, developmental time) was affected only by diet quality. These results suggest that adaptive advantages that would be acquired from parents fed on resistant trees are lost when progeny are exposed to nutritionally-imbalanced food, but the effects persist when larvae are fed a balanced diet. Offspring mortality, fecundity and fertility were positively influenced by parental origin (tree phenotype).
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Affiliation(s)
- Roberto Quezada-Garcia
- Faculté de foresterie, de géographie et de Géomatique Université Laval, Québec, QC G1V 0A6, Canada.
| | - Alvaro Fuentealba
- Faculté de foresterie, de géographie et de Géomatique Université Laval, Québec, QC G1V 0A6, Canada.
- Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, QC H4B 1R6, Canada.
| | - Ngoc Nguyen
- Direction de l'aménagement et de l'environnement forestiers Ministère des Forêts, de la Faune et des Parcs, 5700, 4e Av. Ouest, Québec, QC G1V 0A6, Canada.
| | - Éric Bauce
- Faculté de foresterie, de géographie et de Géomatique Université Laval, Québec, QC G1V 0A6, Canada.
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De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJM, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J. Insights into conifer giga-genomes. PLANT PHYSIOLOGY 2014; 166:1724-32. [PMID: 25349325 PMCID: PMC4256843 DOI: 10.1104/pp.114.248708] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Inanc Birol
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Jean Bousquet
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Stefan Jansson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Steven J M Jones
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Christopher I Keeling
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - John MacKay
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Ove Nilsson
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Kermit Ritland
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Nathaniel Street
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Alvin Yanchuk
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Philipp Zerbe
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
| | - Jörg Bohlmann
- Department of Ecology and Environmental Sciences (A.R.D.L.T., P.K.I.) and Umeå Plant Science Center, Department of Plant Physiology (P.K.I., S.J., O.N., N.S.), Umeå University, SE-901 87 Umea, Sweden;Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6 (I.B., S.J.M.J.);Canada Research Chair in Forest and Environmental Genomics (J.Bou.) and Center for Forest Research and Institute for Systems and Integrative Biology (J.Bou., J.M.), Université Laval, Quebec, Quebec, Canada G1V 0A6;Michael Smith Laboratories (C.I.K., P.Z., J.Boh.) and Department of Forest and Conservation Sciences (K.R., J.Boh.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andBritish Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, British Columbia, Canada V8W 9C2 (A.Y.)
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