1
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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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Huang Y, Du B, Yu M, Cao Y, Liang K, Zhang L. Picea wilsonii NAC31 and DREB2A Cooperatively Activate ERD1 to Modulate Drought Resistance in Transgenic Arabidopsis. Int J Mol Sci 2024; 25:2037. [PMID: 38396714 PMCID: PMC10888420 DOI: 10.3390/ijms25042037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The NAC family of transcription factors (TFs) regulate plant development and abiotic stress. However, the specific function and response mechanism of NAC TFs that increase drought resistance in Picea wilsonii remain largely unknown. In this study, we functionally characterized a member of the PwNAC family known as PwNAC31. PwNAC31 is a nuclear-localized protein with transcriptional activation activity and contains an NAC domain that shows extensive homology with ANAC072 in Arabidopsis. The expression level of PwNAC31 is significantly upregulated under drought and ABA treatments. The heterologous expression of PwNAC31 in atnac072 Arabidopsis mutants enhances the seed vigor and germination rates and restores the hypersensitive phenotype of atnac072 under drought stress, accompanied by the up-regulated expression of drought-responsive genes such as DREB2A (DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN 2A) and ERD1 (EARLY RESPONSIVE TO DEHYDRATION STRESS 1). Yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that PwNAC31 interacts with DREB2A and ABF3 (ABSCISIC ACID-RESPONSIVE ELEMENT-BINDING FACTOR 3). Yeast one-hybrid and dual-luciferase assays showed that PwNAC31, together with its interaction protein DREB2A, directly regulated the expression of ERD1 by binding to the DRE element of the ERD1 promoter. Collectively, our study provides evidence that PwNAC31 activates ERD1 by interacting with DREB2A to enhance drought tolerance in transgenic Arabidopsis.
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Affiliation(s)
- Yiming Huang
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Bingshuai Du
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Mingxin Yu
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Yibo Cao
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Kehao Liang
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Lingyun Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Feng M, Zhang A, Nguyen V, Bisht A, Almqvist C, De Veylder L, Carlsbecker A, Melnyk CW. A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing. Nat Plants 2024; 10:53-65. [PMID: 38168607 PMCID: PMC10808061 DOI: 10.1038/s41477-023-01568-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/23/2023] [Indexed: 01/05/2024]
Abstract
The widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.
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Affiliation(s)
- Ming Feng
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ai Zhang
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Van Nguyen
- Department of Organismal Biology, Physiological Botany, Evolutionary Biology Centre and Linnean Centre for Plant Biology, Uppsala University, Uppsala, Sweden
| | - Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Curt Almqvist
- Skogforsk (The Forestry Research Institute of Sweden), Uppsala Science Park, Uppsala, Sweden
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Evolutionary Biology Centre and Linnean Centre for Plant Biology, Uppsala University, Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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7
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (Bethesda) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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8
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Graham BA, Szabo I, Cicero C, Strickland D, Woods J, Coneybeare H, Dohms KM, Burg TM. Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex. Heredity (Edinb) 2023; 131:361-373. [PMID: 37813941 PMCID: PMC10674025 DOI: 10.1038/s41437-023-00652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
Examining the frequency and distribution of hybrids across contact zones provide insights into the factors mediating hybridization. In this study, we examined the effect of habitat and climate on hybridization patterns for three phenotypically, genetically, and ecologically distinct groups of the Canada jay (Perisoreus canadensis) in a secondary contact zone in western North America. Additionally, we tested whether the frequency of hybridization involving the three groups (referred to as Boreal, Pacific and Rocky Mountain morphotypes) is similar across the hybrid zones or whether some pairs have hybridized more frequently than others. We reanalyzed microsatellite, mtDNA and plumage data, and new microsatellite and plumage data for 526 individuals to identify putative genetic and phenotypic hybrids. The genetically and phenotypically distinct groups are associated with different habitats and occupy distinct climate niches across the contact zone. Most putative genetic hybrids (86%) had Rocky Mountain ancestry. Hybrids were observed most commonly in intermediate climate niches and in habitats where Engelmann spruce (Picea engelmannii) overlaps broadly with boreal and subalpine tree species. Our finding that hybrids occupy intermediate climate niches relative to parental morphotypes matches patterns for other plant and animal species found in this region. This study demonstrates how habitat and climate influence hybridization patterns in areas of secondary contact and adds to the growing body of research on tri-species hybrid zones.
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Affiliation(s)
- B A Graham
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada.
| | - I Szabo
- Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - C Cicero
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA
| | - D Strickland
- 1063 Oxtongue Lake Road, Dwight, ON, P0A 1H0, Canada
| | - J Woods
- 1221 23rd Avenue SW, Salmon Arm, BC, V1E 0A9, Canada
| | - H Coneybeare
- 5210 Frederick Road, Armstrong, BC, V0E 1B4, Canada
| | - K M Dohms
- Canadian Wildlife Services, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - T M Burg
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
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9
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC Plant Biol 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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10
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Wang X, Ingvarsson PK. Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome. Mol Ecol 2023; 32:5288-5304. [PMID: 37622583 DOI: 10.1111/mec.17106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill-Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.
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Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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11
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Krokene P, Børja I, Carneros E, Eldhuset TD, Nagy NE, Volařík D, Gebauer R. Effects of combined drought and pathogen stress on growth, resistance and gene expression in young Norway spruce trees. Tree Physiol 2023; 43:1603-1618. [PMID: 37171580 DOI: 10.1093/treephys/tpad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Drought-induced mortality is a major direct effect of climate change on tree health, but drought can also affect trees indirectly by altering their susceptibility to pathogens. Here, we report how a combination of mild or severe drought and pathogen infection affected the growth, pathogen resistance and gene expression in potted 5-year-old Norway spruce trees [Picea abies (L.) Karst.]. After 5 weeks of drought, trees were inoculated with the fungal pathogen Endoconidiophora polonica. Combined drought-pathogen stress over the next 8 weeks led to significant reductions in the growth of drought-treated trees relative to well-watered trees and more so in trees subjected to severe drought. Belowground, growth of the smallest fine roots was most affected. Aboveground, shoot diameter change was most sensitive to the combined stress, followed by shoot length growth and twig biomass. Both drought-related and some resistance-related genes were upregulated in bark samples collected after 5 weeks of drought (but before pathogen infection), and gene expression levels scaled with the intensity of drought stress. Trees subjected to severe drought were much more susceptible to pathogen infection than well-watered trees or trees subjected to mild drought. Overall, our results show that mild drought stress may increase the tree resistance to pathogen infection by upregulating resistance-related genes. Severe drought stress, on the other hand, decreased tree resistance. Because drought episodes are expected to become more frequent with climate change, combined effects of drought and pathogen stress should be studied in more detail to understand how these stressors interactively influence tree susceptibility to pests and pathogens.
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Affiliation(s)
- P Krokene
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
| | - I Børja
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
| | - E Carneros
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
- Center for Biological Research Margarita Salas-Spanish National Research Council (CSIC), Madrid, Spain
| | - T D Eldhuset
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
- Sagveien 17, 1414, Trollåsen, Norway
| | - N E Nagy
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
| | - D Volařík
- Department of Forest Botany, Dendrology and Geobicoenology, Mendel University in Brno, Zemědělská 3, Brno, 61300, Czech Republic
| | - R Gebauer
- Department of Forest Botany, Dendrology and Geobicoenology, Mendel University in Brno, Zemědělská 3, Brno, 61300, Czech Republic
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12
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Whitehill JGA, Yuen MMS, Chiang A, Ritland CE, Bohlmann J. Transcriptome features of stone cell development in weevil-resistant and susceptible Sitka spruce. New Phytol 2023; 239:2138-2152. [PMID: 37403300 DOI: 10.1111/nph.19103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect-resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell-type-specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.
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Affiliation(s)
- Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Forest Improvement and Research Management Branch, British Columbia Ministry of Forests, Lands, and Natural Resource Operations and Rural Development, 7380 Puckle Road, Saanichton, BC, V8M 1W4, Canada
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Angela Chiang
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Carol E Ritland
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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13
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Gao F, Cao X, Qin C, Chen S, Cai J, Sun C, Kong L, Tao J. Effects of plant growth regulators and sucrose on proliferation and quality of embryogenic tissue in Picea pungens. Sci Rep 2023; 13:13194. [PMID: 37580328 PMCID: PMC10425346 DOI: 10.1038/s41598-023-39389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Embryogenic tissue (ET) is important for genetic modification and plant re-generation. The proliferation ability and vigor of ET are crucial for plant propagation via somatic embryogenesis. In this study, ET was induced from mature zygotic embryos in blue spruce (Picea pungens Engelm.). There were significant differences in ET induction between two provenances, i.e. 78.8 ± 12.5% and 62.50 ± 12.8% respectively. Effects of 2,4-Dichlorophenoxy acetic acid (2,4-D), 6-Benzyl amino-purine (6-BA) and/or sucrose on ET proliferation and somatic embryo (SE) maturation were further investigated with four cell lines. The highest ET proliferation rate reached 1473.7 ± 556.0% biweekly. Concentrations of 2,4-D or 6-BA applied at tissue proliferation stage impacted SE maturation among the cell lines, whereas sucrose showed less effects. The highest rate, 408 ± 230 mature SEs/g FW, was achieved in SE maturation cultures. This research demonstrated that the culture conditions, i.e. the specific concentrations of 2,4-D and BA, at ET proliferation stage affected not only ET growth, but also the quality of ET for SE maturation. This study revealed the necessity and benefit in developing both the general and the genotype-specific protocols for efficient production of mature SEs, or somatic plants in blue spruce.
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Affiliation(s)
- Fang Gao
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China
| | - Xi Cao
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China
- College of Horticulture of Jilin Agricultural University, 2888 Xincheng St., Changchun, 130118, Jilin, China
| | - Caiyun Qin
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China
| | - Shigang Chen
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China
| | - Jufeng Cai
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China
| | - Changbin Sun
- Changchun Academy of Forestry, 5840 Jingyue St., Changchun, 130117, Jilin, China
| | - Lisheng Kong
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Jing Tao
- Jilin Provincial Academy of Forestry Sciences, 3528 Linhe St., Changchun, 130033, Jilin, China.
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14
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Capblancq T, Lachmuth S, Fitzpatrick MC, Keller SR. From common gardens to candidate genes: exploring local adaptation to climate in red spruce. New Phytol 2023; 237:1590-1605. [PMID: 36068997 PMCID: PMC10092705 DOI: 10.1111/nph.18465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/09/2022] [Indexed: 05/12/2023]
Abstract
Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
| | - Susanne Lachmuth
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Matthew C. Fitzpatrick
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Stephen R. Keller
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
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15
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Wang K, Wen Z, Asiegbu FO. The dark septate endophyte Phialocephala sphaeroides suppresses conifer pathogen transcripts and promotes root growth of Norway spruce. Tree Physiol 2022; 42:2627-2639. [PMID: 35878416 PMCID: PMC9743008 DOI: 10.1093/treephys/tpac089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Plant-associated microbes including dark septate endophytes (DSEs) of forest trees play diverse functional roles in host fitness including growth promotion and increased defence. However, little is known about the impact on the fungal transcriptome and metabolites during tripartite interaction involving plant host, endophyte and pathogen. To understand the transcriptional regulation of endophyte and pathogen during co-infection, Norway spruce (Picea abies) seedlings were infected with DSE Phialocephala sphaeroides, or conifer root-rot pathogen Heterobasidion parviporum, or both. Phialocephala sphaeroides showed low but stable transcripts abundance (a decrease of 40%) during interaction with Norway spruce and conifer pathogen. By contrast, H. parviporum transcripts were significantly reduced (92%) during co-infection. With RNA sequencing analysis, P. sphaeroides experienced a shift from cell growth to anti-stress and antagonistic responses, while it repressed the ability of H. parviporum to access carbohydrate nutrients by suppressing its carbohydrate/polysaccharide-degrading enzyme machinery. The pathogen on the other hand secreted cysteine peptidase to restrict free growth of P. sphaeroides. The expression of both DSE P. sphaeroides and pathogen H. parviporum genes encoding plant growth promotion products were equally detected in both dual and tripartite interaction systems. This was further supported by the presence of tryptophan-dependent indolic compound in liquid culture of P. sphaeroides. Norway spruce and Arabidopsis seedlings treated with P. sphaeroides culture filtrate exhibited auxin-like phenotypes, such as enhanced root hairs, and primary root elongation at low concentration but shortened primary root at high concentration. The results suggested that the presence of the endophyte had strong repressive or suppressive effect on H. parviporum transcripts encoding genes involved in nutrient acquisition.
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Affiliation(s)
- Kai Wang
- Corresponding authors: K.Wang (; ) and F.Asiegbu ()
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, PO Box 27, Helsinki FIN-00014, Finland
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16
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Varis SA, Virta S, Montalbán IA, Aronen T. Reducing Pre- and Post-Treatments in Cryopreservation Protocol and Testing Storage at -80 °C for Norway Spruce Embryogenic Cultures. Int J Mol Sci 2022; 23:ijms232415516. [PMID: 36555157 PMCID: PMC9779070 DOI: 10.3390/ijms232415516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Somatic embryogenesis (SE) is considered the most effective method for vegetative propagation of Norway spruce (Picea abies L. Karst). For mass propagation, a storage method that is able to handle large quantities of embryogenic tissues (ETs) reliably and at a low cost is required. The aim of the present study was to compare freezing at -80 °C in a freezer to cryopreservation using liquid nitrogen (LN) as a method for storing Norway spruce ETs. The possibility of simplifying both the pre-treatment and thawing processes in cryopreservation was also studied. The addition of abscisic acid (ABA) to the pre-treatment media and using polyethylene glycol PEG4000 instead of PEG6000 in a cryoprotectant solution were tested. Both the pre-and post-treatments on semi-solid media could be simplified by reducing the number of media, without any loss of genotype or embryo production capacity of ETs. On the contrary, the storage of ETs in a freezer at -80 °C instead of using LN was not possible, and the addition of ABA to the pre-treatment media did not provide benefits but increased costs. The lower regeneration rate after using PEG4000 instead of PEG6000 in a cryoprotectant solution in cryovials was unexpected and unwanted. The simplified pre-and post-treatment protocol will remarkably reduce the workload and costs in the mass-cryopreservation of future forest regeneration materials and in thawing the samples for mass propagations, respectively.
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Affiliation(s)
- Saila A. Varis
- Natural Resources Institute Finland (Luke), Vipusenkuja 5, FI-57200 Savonlinna, Finland
- Correspondence: (S.A.V.); (T.A.)
| | - Susanna Virta
- Natural Resources Institute Finland (Luke), Vipusenkuja 5, FI-57200 Savonlinna, Finland
| | | | - Tuija Aronen
- Natural Resources Institute Finland (Luke), Vipusenkuja 5, FI-57200 Savonlinna, Finland
- Correspondence: (S.A.V.); (T.A.)
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17
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Klápště J, Jaquish B, Porth I. Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection. PLoS One 2022; 17:e0263488. [PMID: 36459506 PMCID: PMC9718410 DOI: 10.1371/journal.pone.0263488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that interspecific hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible parents generally showed fast-growing trees were the most affected by weevil attacks. Such results indicate that interspecific 'hybrids' with a higher P. glauca ancestry might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.
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Affiliation(s)
- Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Barry Jaquish
- BC Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Vernon, B.C., Canada
| | - Ilga Porth
- Department of Wood and Forest Sciences, Université Laval, Québec City, Québec, Canada
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec City, Québec, Canada
- Centre for Forest Research, Université Laval, Québec City, Québec, Canada
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18
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Akhter S, Westrin KJ, Zivi N, Nordal V, Kretzschmar WW, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström JF. Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway. New Phytol 2022; 236:1951-1963. [PMID: 36076311 PMCID: PMC9825996 DOI: 10.1111/nph.18449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.
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Affiliation(s)
- Shirin Akhter
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Karl Johan Westrin
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nathan Zivi
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
- Skogforsk, Uppsala Science ParkUppsalaSE‐751 83Sweden
| | - Veronika Nordal
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Warren W. Kretzschmar
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Jens F. Sundström
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
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19
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. Plant J 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- 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, Vancouver, BC, V5Z 4S6, Canada
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20
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Ranade SS, Seipel G, Gorzsás A, García-Gil MR. Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in Norway spruce. Plant Cell Environ 2022; 45:2671-2681. [PMID: 35775408 DOI: 10.1111/pce.14387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 05/12/2023]
Abstract
During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - George Seipel
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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21
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Ling J, Xia Y, Hu J, Zhu T, Wang J, Zhang H, Kong L. Integrated Lipidomic and Transcriptomic Analysis Reveals Phospholipid Changes in Somatic Embryos of Picea asperata in Response to Partial Desiccation. Int J Mol Sci 2022; 23:ijms23126494. [PMID: 35742942 PMCID: PMC9223630 DOI: 10.3390/ijms23126494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
Partial desiccation treatment (PDT) is an effective technology for promoting the germination and conversion of conifer somatic embryos (SEs). PDT, as a drought stress, induces intensive physiological responses in phospholipid metabolism, which are not well understood in the conifer SEs. Here, we integrated lipidomics, transcriptomics and proteomics analyses to reveal the molecular basis of lipid remodeling under PDT in Picea asperata SEs. Among the 82 lipid molecular species determined by mass spectrometry, phosphatidic acid (PA) had a significant effect after PDT and was the most critical lipid in the response to PDT. The transcriptomics results showed that multiple transcripts in the glycerolipid and glycerophospholipid metabolism pathways were differentially expressed, and these included five PLDα1 transcripts that catalyze the conversion of phosphatidylcholine (PC) to PA. Furthermore, the enzyme activity of this phospholipase D (PLD) was significantly enhanced in response to PDT, and PDT also significantly increased the protein level of PLDα1 (MA_10436582g0020). In addition, PA is a key factor in gibberellin, abscisic acid and ethylene signal transduction. One GDI1, one DELLA, three ABI1s, two SnRK2s, one CTR and 12 ERFs showed significantly differential expression between SEs before and after PDT in this study. Our data suggest that the observed increases in the PA contents might result from the activation of PLDα by PDT. PA not only affects the physical and chemical properties of the cell membrane but also participates in plant hormone signal transduction. Our work provides novel insight into the molecular mechanism through which PDT promotes the germination of SEs of coniferous tree species and fills the gap in the understanding of the mechanism of somatic embryo lipid remodeling in response to PDT.
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Affiliation(s)
- Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.L.); (Y.X.); (J.H.)
| | - Yan Xia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.L.); (Y.X.); (J.H.)
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Jiwen Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.L.); (Y.X.); (J.H.)
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.L.); (Y.X.); (J.H.)
- Correspondence: (T.Z.); (J.W.)
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (J.L.); (Y.X.); (J.H.)
- Correspondence: (T.Z.); (J.W.)
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China;
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8P 5C2, Canada;
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22
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Prakash A, DeYoung S, Lachmuth S, Adams JL, Johnsen K, Butnor JR, Nelson DM, Fitzpatrick MC, Keller SR. Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce ( Picea rubens Sarg.). Philos Trans R Soc Lond B Biol Sci 2022; 377:20210008. [PMID: 35184589 PMCID: PMC8859516 DOI: 10.1098/rstb.2021.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/10/2022] [Indexed: 01/18/2023] Open
Abstract
Shifting range limits are predicted for many species as the climate warms. However, the rapid pace of climate change will challenge the natural dispersal capacity of long-lived, sessile organisms such as forest trees. Adaptive responses of populations will, therefore, depend on levels of genetic variation and plasticity for climate-responsive traits, which likely vary across the range due to expansion history and current patterns of selection. Here, we study levels of genetic and plastic variation for phenology and growth traits in populations of red spruce (Picea rubens), from the range core to the highly fragmented trailing edge. We measured more than 5000 offspring sampled from three genetically distinct regions (core, margin and edge) grown in three common gardens replicated along a latitudinal gradient. Genetic variation in phenology and growth showed low to moderate heritability and differentiation among regions, suggesting some potential to respond to selection. Phenology traits were highly plastic, but this plasticity was generally neutral or maladaptive in the effect on growth, revealing a potential liability under warmer climates. These results suggest future climate adaptation will depend on the regional availability of genetic variation in red spruce and provide a resource for the design and management of assisted gene flow. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Anoob Prakash
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
| | - Sonia DeYoung
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
| | - Susanne Lachmuth
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Jacquelyne L. Adams
- Bent Creek Experimental Forest, USDA Forest Service, Asheville, NC 28806, USA
| | - Kurt Johnsen
- Bent Creek Experimental Forest, USDA Forest Service, Asheville, NC 28806, USA
| | - John R. Butnor
- USDA Forest Service, Southern Research Station, University of Vermont, Burlington, VT 05405, USA
| | - David M. Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
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23
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Liu M, Wang K, Ghimire RP, Haapanen M, Kivimäenpää M, Asiegbu FO. Molecular and Chemical Screening for Inherent Disease Resistance Factors of Norway Spruce ( Picea abies) Clones Against Conifer Stem Rot Pathogen Heterobasidion parviporum. Phytopathology 2022; 112:872-880. [PMID: 34698543 DOI: 10.1094/phyto-09-21-0379-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Root and stem rot of conifer trees caused by Heterobasidion annosum species complex leads to huge economic losses in Europe, yet not much is known about the molecular and chemical basis for host resistance. To identify inherent chemical or molecular markers in clones found to be either resistant or susceptible, we sampled needle tissues of all the clones before pathogen inoculation. We conducted a short-term resistance screening by using the pathogen H. parviporum to inoculate 70 Norway spruce clones. Based on lesion size, subsets of highly susceptible and resistant clones were further analyzed. Terpene detection and RNA sequencing were performed to explore inherent variations in genotypes differing in resistance to pathogenic challenge at chemical and transcriptional levels. A negative correlation emerged between resistance and growth. Terpene profiles of resistant clones showed higher content of monoterpenes and sesquiterpenes, with concomitant increased transcript abundance of genes involved in the terpenoid pathway. A set of upregulated genes relevant to flavonoid biosynthesis was observed in resistant genotypes, whereas higher transcripts of lignin biosynthetic genes were prevalent in susceptible clones. Genes involved in flavonoid and lignin biosynthesis as well as terpene content may have a role in facilitating resistance of Norway spruce against H. parviporum. Our results provide strong support on the feasibility of sampling needle tissues before pathogen inoculation, and the approach could be of value for large-scale screening of novel biomarkers for durable resistance. The additional insights could form a basis for further research on resistance screening in this pathosystem.
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Affiliation(s)
- Mengxia Liu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Kai Wang
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, FI-00014 Helsinki, Finland
| | - Rajendra P Ghimire
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Matti Haapanen
- Natural Resources Institute Finland (LUKE), FI-00790 Helsinki, Finland
| | - Minna Kivimäenpää
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, FI-00014 Helsinki, Finland
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24
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Perreca E, Eberl F, Santoro MV, Wright LP, Schmidt A, Gershenzon J. Effect of Drought and Methyl Jasmonate Treatment on Primary and Secondary Isoprenoid Metabolites Derived from the MEP Pathway in the White Spruce Picea glauca. Int J Mol Sci 2022; 23:ijms23073838. [PMID: 35409197 PMCID: PMC8998179 DOI: 10.3390/ijms23073838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
White spruce (Picea glauca) emits monoterpenes that function as defensive signals and weapons after herbivore attack. We assessed the effects of drought and methyl jasmonate (MeJA) treatment, used as a proxy for herbivory, on monoterpenes and other isoprenoids in P. glauca. The emission of monoterpenes was significantly increased after MeJA treatment compared to the control, but drought suppressed the MeJA-induced increase. The composition of the emitted blend was altered strongly by stress, with drought increasing the proportion of oxygenated compounds and MeJA increasing the proportion of induced compounds such as linalool and (E)-β-ocimene. In contrast, no treatment had any significant effect on the levels of stored monoterpenes and diterpenes. Among other MEP pathway-derived isoprenoids, MeJA treatment decreased chlorophyll levels by 40%, but had no effect on carotenoids, while drought stress had no impact on either of these pigment classes. Of the three described spruce genes encoding 1-deoxy-D-xylulose-5-phosphate synthase (DXS) catalyzing the first step of the MEP pathway, the expression of only one, DXS2B, was affected by our treatments, being increased by MeJA and decreased by drought. These findings show the sensitivity of monoterpene emission to biotic and abiotic stress regimes, and the mediation of the response by DXS genes.
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Affiliation(s)
- Erica Perreca
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (F.E.); (M.V.S.); (A.S.); (J.G.)
- Correspondence:
| | - Franziska Eberl
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (F.E.); (M.V.S.); (A.S.); (J.G.)
- Faculty of Biological Sciences, Friedrich Schiller University, 07745 Jena, Germany
| | - Maricel Valeria Santoro
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (F.E.); (M.V.S.); (A.S.); (J.G.)
| | | | - Axel Schmidt
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (F.E.); (M.V.S.); (A.S.); (J.G.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (F.E.); (M.V.S.); (A.S.); (J.G.)
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Vergara A, Haas JC, Aro T, Stachula P, Street NR, Hurry V. Norway spruce deploys tissue-specific responses during acclimation to cold. Plant Cell Environ 2022; 45:427-445. [PMID: 34873720 DOI: 10.1111/pce.14241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.
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Affiliation(s)
- Alexander Vergara
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Julia C Haas
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Tuuli Aro
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Paulina Stachula
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Vaughan Hurry
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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27
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Gao Y, Cui Y, Zhao R, Chen X, Zhang J, Zhao J, Kong L. Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA-miRNA-mRNA Network in White Spruce. Int J Mol Sci 2022; 23:ijms23031111. [PMID: 35163033 PMCID: PMC8834816 DOI: 10.3390/ijms23031111] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
In conifers, somatic embryogenesis is uniquely initiated from immature embryos in a narrow time window, which is considerably hindered by the difficulty to induce embryogenic tissue (ET) from other tissues, including mature somatic embryos. In this study, the embryogenic ability of newly induced ET and DNA methylation levels was detected, and whole-transcriptome sequencing analyses were carried out. The results showed that ultra-low temperature treatment significantly enhanced ET induction from mature somatic embryos, with the induction rate from 0.4% to 15.5%, but the underlying mechanisms remain unclear. The newly induced ET showed higher capability in generating mature embryos than the original ET. DNA methylation levels fluctuated during the ET induction process. Here, WGCNA analysis revealed that OPT4, TIP1-1, Chi I, GASA5, GST, LAX3, WRKY7, MYBS3, LRR-RLK, PBL7, and WIN1 genes are involved in stress response and auxin signal transduction. Through co-expression analysis, lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might bind to pre-novel_miR_339 to promote the expression of WRKY7 genes for stress response; LAX3 could be protected by lncRNAs MSTRG.1070680.1 and MSTRG.33602.1 via serving as sponges for novel_miR_495 to initiate auxin signal transduction; lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might serve as sponges for novel_miR_527 to enhance the expression of Chi I for early somatic embryo development. This study provides new insight into the area of stress-enhanced early somatic embryogenesis in conifers, which is also attributable to practical applications.
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Affiliation(s)
- Ying Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Ying Cui
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Ruirui Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Xiaoyi Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Jinfeng Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
| | - Jian Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
- Correspondence: (J.Z.); (L.K.)
| | - Lisheng Kong
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.G.); (Y.C.); (R.Z.); (X.C.); (J.Z.)
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
- Correspondence: (J.Z.); (L.K.)
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Zacharias M, Pampuch T, Heer K, Avanzi C, Würth DG, Trouillier M, Bog M, Wilmking M, Schnittler M. Population structure and the influence of microenvironment and genetic similarity on individual growth at Alaskan white spruce treelines. Sci Total Environ 2021; 798:149267. [PMID: 34332391 DOI: 10.1016/j.scitotenv.2021.149267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Knowledge on the adaptation of trees to rapid environmental changes is essential to preserve forests and their ecosystem services under climate change. Treeline populations are particularly suitable for studying adaptation processes in trees, as environmental stress together with reduced gene flow can enhance local adaptation. We investigated white spruce (Picea glauca) populations in Alaska on one moisture-limited and two cold-limited treeline sites with a paired plot design of one forest and one treeline population each, resulting in six plots. Additionally, one forest plot in the middle of the distribution range complements the study design. We combined spatial, climatic and dendrochronological data with neutral genetic marker of 2203 trees to investigate population genetic structure and drivers of tree growth. We used several individual-based approaches including random slope mixed-effects models to test the influence of genetic similarity and microenvironment on growth performance. A high degree of genetic diversity was found within each of the seven plots associated with high rates of gene flow. We discovered a low genetic differentiation between the three sites which was better explained by geographic distances than by environmental differences, indicating genetic drift as the main driver of population differentiation. Our findings indicated that microenvironmental features had an overall larger influence on growth performances than genetic similarity among individuals. The effects of climate on growth differed between sites but were smaller than the effect of tree size. Overall, our results suggest that the high genetic diversity of white spruce may result in a wider range of phenotypes which enhances the efficiency of selection when the species is facing rapid climatic changes. In addition, the large intra-individual variability in growth responses may indicate the high phenotypic plasticity of white spruce which can buffer short-term environmental changes and, thus, allow enduring the present changing climate conditions.
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Affiliation(s)
- Melanie Zacharias
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Timo Pampuch
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Katrin Heer
- Conservation Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy.
| | - David G Würth
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Mario Trouillier
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Manuela Bog
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Wilmking
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Schnittler
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
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29
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Bag P, Lihavainen J, Delhomme N, Riquelme T, Robinson KM, Jansson S. An atlas of the Norway spruce needle seasonal transcriptome. Plant J 2021; 108:1815-1829. [PMID: 34624161 DOI: 10.1111/tpj.15530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February), and spring (March-April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.
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Affiliation(s)
- Pushan Bag
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jenna Lihavainen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Swedish University of Agricultural, Sciences (SLU) and Umeå University, Umeå, Sweden
| | - Thomas Riquelme
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Kathryn M Robinson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Stefan Jansson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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30
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Haas JC, Vergara A, Serrano AR, Mishra S, Hurry V, Street NR. Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. Tree Physiol 2021; 41:1230-1246. [PMID: 33416078 PMCID: PMC8271197 DOI: 10.1093/treephys/tpaa178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/27/2020] [Indexed: 05/12/2023]
Abstract
Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.
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Affiliation(s)
- Julia C Haas
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Alexander Vergara
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Alonso R Serrano
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Sanatkumar Mishra
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Vaughan Hurry
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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31
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Chen ZQ, Zan Y, Milesi P, Zhou L, Chen J, Li L, Cui B, Niu S, Westin J, Karlsson B, García-Gil MR, Lascoux M, Wu HX. Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Genome Biol 2021; 22:179. [PMID: 34120648 PMCID: PMC8201819 DOI: 10.1186/s13059-021-02392-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees. RESULTS We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery. CONCLUSION Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.
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Affiliation(s)
- Zhi-Qiang Chen
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Yanjun Zan
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Linghua Zhou
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
- College of Life Sciences, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - BinBin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, 071000, Hebei, China
| | - Shihui Niu
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Johan Westin
- Skogforsk, Box 3, SE-91821, Sävar, Sweden
- Unit for Field-Based Forest Research, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Bo Karlsson
- Skogforsk, Ekebo, 2250, SE-26890, Svalöv, Sweden
| | - Maria Rosario García-Gil
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
- CSIRO National Collection Research Australia, Black Mountain Laboratory, Canberra, ACT, 2601, Australia.
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32
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Liu M, Jaber E, Zeng Z, Kovalchuk A, Asiegbu FO. Physiochemical and molecular features of the necrotic lesion in the Heterobasidion-Norway spruce pathosystem. Tree Physiol 2021; 41:791-800. [PMID: 33105481 DOI: 10.1093/treephys/tpaa141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/03/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
In the forest of Northern Hemisphere, the fungi Heterobasidion annosum (Fr.) Bref. s.l. causes severe root and stem rot diseases, dramatically reducing the wood quality of conifer trees. The hallmark of the host response during the infection process is the formation of necrotic lesions and reaction zones. To characterize physiochemical and molecular features of the necrotic lesion, we conducted artificial inoculations on Norway spruce plants at different developmental stages: seedlings, young and mature trees. The results were further compared against data available on the formation of reaction zones. Strong necrosis browning or enlarged necrotic lesions were observed in infected tissues. This was accompanied by elevated pH. However, the increased pH, around 6.0 in necrotic lesions, was not as high as that documented in reaction zones, above 7.0 as marked by the intensity of the blue colour in response to 2,6-dichlorophenol indophenol dye. Peroxidase activity increased in infected plants and RNA-seq analysis of necrotic lesions showed marked upregulation of defence-related genes. Our findings highlight similarities and differences between the reaction zone and necrotic lesion formation in response of conifer trees to biotic stress.
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Affiliation(s)
- Mengxia Liu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, FIN-00014, Helsinki, Finland
| | - Emad Jaber
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, FIN-00014, Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, FIN-00014, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, FIN-00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, FIN-00014, Helsinki, Finland
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Kartashov AV, Zlobin IE, Pashkovskiy PP, Pojidaeva ES, Ivanov YV, Mamaeva AS, Fesenko IA, Kuznetsov VV. Quantitative analysis of differential dehydrin regulation in pine and spruce seedlings under water deficit. Plant Physiol Biochem 2021; 162:237-246. [PMID: 33706184 DOI: 10.1016/j.plaphy.2021.02.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Dehydrins are well-known components of plant responses to different stresses that cause dehydration, including drought, freezing, salinity, etc. In conifers, the dehydrin gene family is very large, implying that the members of this family have important physiological functions in conifer stress tolerance. However, dehydrin gene expression displays a wide range of responses to stress, from thousand-fold increased expression to decreased expression, and it is generally unknown how regulatory systems are connected at the mRNA and protein levels. Therefore, we studied these aspects of dehydrin regulation in Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst) seedlings under polyethylene glycol 6000-induced osmotic stress ranging from relatively low (culture medium water potential of -0.15 MPa) to very high (-1.0 MPa) intensities. In pine, the major dehydrin protein was Dhn1 in both the roots and needles, and in spruce, two isoforms of the Dhn4 protein were the major dehydrins; both of these proteins are AESK-type dehydrins. The genes encoding these major proteins were highly expressed even under control conditions; surprisingly, we also observed several highly expressed dehydrin genes that were not abundantly translated. Under osmotic stress, the most prominent expression changes were observed for the dehydrin genes with low basal expression levels, whereas highly expressed genes generally demonstrated rather modest changes in expression. We report proposed constitutive physiological functions of the AESK-type dehydrins in Pinaceae plants.
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Affiliation(s)
- Alexander V Kartashov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia.
| | - Ilya E Zlobin
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Pavel P Pashkovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Elena S Pojidaeva
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Yury V Ivanov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Anna S Mamaeva
- Laboratory of Functional Genomics and Plant Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Igor A Fesenko
- Laboratory of Functional Genomics and Plant Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Vladimir V Kuznetsov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
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34
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Zoia L, Salanti A, Giorgione C, Gentili R, Citterio S, Gandolfi I, Franzetti A, Orlandi M. Integrated biological and chemical characterisation of a pair of leonardesque canal lock gates. PLoS One 2021; 16:e0247478. [PMID: 33690726 PMCID: PMC7946225 DOI: 10.1371/journal.pone.0247478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Abstract
The Museo Nazionale della Scienza e della Tecnologia “Leonardo da Vinci” in Milan is exposing two pairs of canal lock gates, used to control the water flow in Milan canal system, whose design appears in the Leonardo’s Codex Atlanticus. The wood present in the gates has been deeply characterised by mean of a multidisciplinary investigation involving i) DNA barcoding of wood fragments; ii) microbial community characterisation, and iii) chemical analyses. DNA barcoding revealed that two fragments of the gates belonged to wood species widely used in the middle age: Fagus sylvatica and Picea abies. The chemical characterisations were based on the use of ionic liquid as dissolving medium in order to analyse the entire cell wall material by means of Gel Permeation Chromatography (GPC) and 2D-NMR-HSQC techniques. This multidisciplinary analytical approach was able to highlight the complex nature of the degradation occurred during the gate operation (XVI-XVIII centuries): an intricate interplay between microbial populations (i.e. Shewanella), inorganic factors (i.e. iron from nails), physical factors and the lignocellulosic material.
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Affiliation(s)
- Luca Zoia
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
- * E-mail:
| | - Anika Salanti
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Claudio Giorgione
- Museo Nazionale della Scienza e della Tecnologia “Leonardo da Vinci”, Milano, Italy
| | - Rodolfo Gentili
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Sandra Citterio
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Marco Orlandi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
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35
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Galeano E, Thomas BR. Effect of elevated gibberellic acid application on growth and gene expression patterns in white spruce families from a tree improvement program in Alberta, Canada. Tree Physiol 2021; 41:472-490. [PMID: 33080619 DOI: 10.1093/treephys/tpaa133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/02/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Nine open-pollinated families of Picea glauca (Moench) Voss from the Region D1 Controlled Parentage Program (Alberta, Canada) were systematically chosen from fast, medium and slow-growth rankings based on breeding values for height from field progeny tests at age 30 years. Seeds from these families were sown and grown to age 3 years to analyze the performance and correlations of growth, physiological traits and expression of gibberellin-related genes, with and without elevated gibberellic acid 3 (GA3) application, under greenhouse conditions. We observed a significant interaction effect between families and growth groups subjected to 50 μg μl-1 of GA3 treatment, causing a decrease in apical internode length, diameter, volume and absolute transcript level for fast-growing families but an increase for families in the slow-growth group for the same traits. We also observed that in the apical internode, the gene PgGA20ox1 had significantly more relative expression under the elevated GA3 treatment than the control trees. In the stem, PgGA3ox1 showed a significantly higher relative expression under elevated GA3 treatment compared with control trees. Also, the slow-growth group showed more relative expression of PgGA20ox1 (in the apical internode) and PgGA3ox1 (in the stem) than the fast-growth group. The apical internode length and diameter significantly increased by 24% and 16%, respectively, with the hormone treatment in the slow growing group. In general, the PgGID1 and PgDELLA1 genes were upregulated and downregulated respectively, in spruce shoots under the GA3 treatment, meaning a positive feedback regulation by those genes were influencing PgGA20ox1 and PgGA3ox1 expression in that tissue type. Moreover, there was a significant correlation between absolute transcript levels of PgGA20ox1 in the apical internode and apical internode length, and absolute transcript levels of PgGA3ox1 in the stem and the diameter, in the fast-growth group families. This study shows that expression of GA genes is a limiting factor for growth in certain white spruce families with a complex feedback mechanism. Finally, absolute transcript levels of endogenous GA relative to growth parameters in juvenile seedlings could potentially be used to accelerate the early selection of families with inherently rapid apical and radial growth expansion.
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Affiliation(s)
- Esteban Galeano
- Department of Renewable Resources, 442 Earth Sciences Building, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Barb R Thomas
- Department of Renewable Resources, 442 Earth Sciences Building, University of Alberta, Edmonton, AB T6G 2E3, Canada
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Depardieu C, Gérardi S, Nadeau S, Parent GJ, Mackay J, Lenz P, Lamothe M, Girardin MP, Bousquet J, Isabel N. Connecting tree-ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer. Mol Ecol 2021; 30:3898-3917. [PMID: 33586257 PMCID: PMC8451828 DOI: 10.1111/mec.15846] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/15/2021] [Accepted: 01/27/2021] [Indexed: 01/02/2023]
Abstract
As boreal forests face significant threats from climate change, understanding evolutionary trajectories of coniferous species has become fundamental to adapting management and conservation to a drying climate. We examined the genomic architecture underlying adaptive variation related to drought tolerance in 43 populations of a widespread boreal conifer, white spruce (Piceaglauca [Moench] Voss), by combining genotype–environment associations, genotype–phenotype associations, and transcriptomics. Adaptive genetic variation was identified by correlating allele frequencies for 6,153 single nucleotide polymorphisms from 2,606 candidate genes with temperature, precipitation and aridity gradients, and testing for significant associations between genotypes and 11 dendrometric and drought‐related traits (i.e., anatomical, growth response and climate‐sensitivity traits) using a polygenic model. We identified a set of 285 genes significantly associated with a climatic factor or a phenotypic trait, including 110 that were differentially expressed in response to drought under greenhouse‐controlled conditions. The interlinked phenotype–genotype–environment network revealed eight high‐confidence genes involved in white spruce adaptation to drought, of which four were drought‐responsive in the expression analysis. Our findings represent a significant step toward the characterization of the genomic basis of drought tolerance and adaptation to climate in conifers, which is essential to enable the establishment of resilient forests in view of new climate conditions. see also the Perspective by Lars Opgenoorth and Christian Rellstab
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Affiliation(s)
- Claire Depardieu
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Sébastien Gérardi
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Geneviève J. Parent
- Laboratory of GenomicsMaurice‐Lamontagne Institute, Fisheries and Oceans CanadaMont‐JoliQCCanada
| | - John Mackay
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Patrick Lenz
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Manuel Lamothe
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Martin P. Girardin
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
- Centre for Forest ResearchUniversité du Québec à MontréalMontréalQCCanada
| | - Jean Bousquet
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Nathalie Isabel
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
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Wang L, Liu J, Shen Y, Pu R, Hou M, Wei Q, Zhang X, Li G, Ren H, Wu G. Brassinosteroids synthesised by CYP85A/A1 but not CYP85A2 function via a BRI1-like receptor but not via BRI1 in Picea abies. J Exp Bot 2021; 72:1748-1763. [PMID: 33247718 DOI: 10.1093/jxb/eraa557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Brassinosteroids (BRs) are essential plant hormones. In angiosperms, brassinolide and castasterone, the first and second most active BRs, respectively, are synthesised by CYP85A2 and CYP85A/A1, respectively. BRs in angiosperms function through an essential receptor, BR Insensitive 1 (BRI1). In addition, some angiosperms also have non-essential BRI1-like 1/3 (BRL1/3). In conifers, BRs promote seed germination under drought stress; however, how BRs function in gymnosperms is unknown. In this study, we performed functional complementation of BR biosynthesis and receptor genes from Picea abies with respective Arabidopsis mutants. We found that P. abies possessed functional PaCYP85A and PaBRL1 but not PaCYP85A2 or PaBRI1, and this results in weak BR signaling, and both PaCYP85A and PaBRL1 were abundantly expressed. However, neither BR treatment of P. abies seedlings nor expression of PaBRL1 in the Arabidopsis Atbri1 mutant promoted plant height, despite the fact that BR-responsive genes were activated. Importantly, chimeric AtBRI1 replaced with the BR-binding domain of PaBRL1 complemented the Atbri1 phenotypes. Furthermore, PaBRL1 had less kinase activity than BRI1 in vitro. Overall, P. abies had weak but still active BR signaling, explaining aspects of its slow growth and high stress tolerance. Our study sheds light on the functional and evolutionary significance of distinct BR signaling that is independent of BRI1 and brassinolide.
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Affiliation(s)
- Li Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Jing Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Yitong Shen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Ruolan Pu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Meiying Hou
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Qiang Wei
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Xinzhen Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Guishuang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Hongyan Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
| | - Guang Wu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi Province, P.R. China
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Abstract
MAIN CONCLUSION Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Plant Physiology, Umeå Plant Science Centre, University of Umeå, 901 87 Umeå, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
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Baison J, Zhou L, Forsberg N, Mörling T, Grahn T, Olsson L, Karlsson B, Wu HX, Mellerowicz EJ, Lundqvist SO, García-Gil MR. Genetic control of tracheid properties in Norway spruce wood. Sci Rep 2020; 10:18089. [PMID: 33093525 PMCID: PMC7581746 DOI: 10.1038/s41598-020-72586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 09/03/2020] [Indexed: 01/20/2023] Open
Abstract
Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.
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Affiliation(s)
- J Baison
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Linghua Zhou
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Tommy Mörling
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Thomas Grahn
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Lars Olsson
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
| | - Bo Karlsson
- Skogforsk, Ekebo 2250, 268 90, Svalov, Sweden
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden
| | - Sven-Olof Lundqvist
- RISE Bioeconomy, Box 5604, 114 86, Stockholm, Sweden
- IIC, Rosenlundsgatan 48B, 11863, Stockholm, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Umeå, Sweden.
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Nakamura M, Batista RA, Köhler C, Hennig L. Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce. J Exp Bot 2020; 71:6366-6378. [PMID: 32894759 PMCID: PMC7586741 DOI: 10.1093/jxb/eraa365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/29/2020] [Indexed: 05/28/2023]
Abstract
Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species.
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Affiliation(s)
- Miyuki Nakamura
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
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Elfstrand M, Baison J, Lundén K, Zhou L, Vos I, Capador HD, Åslund MS, Chen Z, Chaudhary R, Olson Å, Wu HX, Karlsson B, Stenlid J, García-Gil MR. Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance. Plant Cell Environ 2020; 43:1779-1791. [PMID: 32276288 DOI: 10.1111/pce.13768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot. In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.
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Affiliation(s)
- Malin Elfstrand
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - John Baison
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Karl Lundén
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linghua Zhou
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Hernan Dario Capador
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matilda Stein Åslund
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Rajiv Chaudhary
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Olson
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Jan Stenlid
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - María Rosario García-Gil
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Avanzi C, Heer K, Büntgen U, Labriola M, Leonardi S, Opgenoorth L, Piermattei A, Urbinati C, Vendramin GG, Piotti A. Individual reproductive success in Norway spruce natural populations depends on growth rate, age and sensitivity to temperature. Heredity (Edinb) 2020; 124:685-698. [PMID: 32203247 PMCID: PMC7239854 DOI: 10.1038/s41437-020-0305-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 11/09/2022] Open
Abstract
Quantifying the individual reproductive success and understanding its determinants is a central issue in evolutionary research for the major consequences that the transmission of genetic variation from parents to offspring has on the adaptive potential of populations. Here, we propose to distil the myriad of information embedded in tree-ring time series into a set of tree-ring-based phenotypic traits to be investigated as potential drivers of reproductive success in forest trees. By using a cross-disciplinary approach that combines parentage analysis and a thorough dendrophenotypic characterisation of putative parents, we assessed sex-specific relationships between such dendrophenotypic traits (i.e., age, growth rate and parameters describing sensitivity to climate and to extreme climatic events) and reproductive success in Norway spruce. We applied a full probability method for reconstructing parent-offspring relationships between 604 seedlings and 518 adult trees sampled within five populations from southern and central Europe. We found that individual female and male reproductive success was positively associated with tree growth rate and age. Female reproductive success was also positively influenced by the correlation between growth and the mean temperature of the previous vegetative season. Overall, our results showed that Norway spruce individuals with the highest fitness are those who are able to keep high-growth rates despite potential growth limitations caused by reproductive costs and climatic limiting conditions. Identifying such functional links between the individual ecophysiological behaviour and its evolutionary gain would increase our understanding on how natural selection shapes the genetic composition of forest tree populations over time.
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Affiliation(s)
- Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Madonna del Piano 10, 50019, Sesto Fiorentino (Firenze), Italy.
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.
| | - Katrin Heer
- Conservation Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Ulf Büntgen
- Department of Geography, University of Cambridge, Downing Place, CB2 3EN, Cambridge, UK
- Swiss Federal Research Institute, WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
- Czech Globe, Global Change Research Institute CAS and Masaryk University, Kotlárská 2, 61137, Brno, Czech Republic
| | - Mariaceleste Labriola
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Madonna del Piano 10, 50019, Sesto Fiorentino (Firenze), Italy
| | - Stefano Leonardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Lars Opgenoorth
- Swiss Federal Research Institute, WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
- Department of Ecology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Alma Piermattei
- Department of Geography, University of Cambridge, Downing Place, CB2 3EN, Cambridge, UK
| | - Carlo Urbinati
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Madonna del Piano 10, 50019, Sesto Fiorentino (Firenze), Italy
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Madonna del Piano 10, 50019, Sesto Fiorentino (Firenze), Italy
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Zlobin IE, Vankova R, Pashkovskiy PP, Dobrev P, Kartashov AV, Ivanov YV, Kuznetsov VV. Profiles of endogenous phytohormones and expression of some hormone-related genes in Scots pine and Norway spruce seedlings under water deficit. Plant Physiol Biochem 2020; 151:457-468. [PMID: 32289639 DOI: 10.1016/j.plaphy.2020.03.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/13/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Different plant hormones are involved in plant adaptation to water deficit. In comparison to angiosperms, little is known about the impact of drought on the pool of phytohormones in gymnosperms. Therefore, we studied the effect of polyethylene glycol-induced water deficit on the changes in content of different phytohormones in Scots pine and Norway spruce seedlings, which are known for their different strategies of adaptation to water deficit. The following hormone classes were analysed: cytokinins, auxins, jasmonates, salicylic and benzoic acids, and 1-aminocyclopropane-1-carboxylic acid (an ethylene precursor). No consistent reaction to water stress was observed for the content of well-known stress-related hormones - salicylic acid and jasmonates. In contrast, drought induced a dose-dependent accumulation of cytokinins in pine needles, with less profound changes in spruce needles. The most prominent changes were observed for 1-aminocyclopropane-1-carboxylic acid content, which increased several-fold in spruce roots and pine needles under water deficit. Water-deficit-induced changes in the contents of cytokinins and 1-aminocyclopropane-1-carboxylic acid were accompanied by the differential regulation of genes involved in the metabolism of these hormones. Possible links between changes in hormone pools and the adaptation of seedlings to water deficit are discussed.
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Affiliation(s)
- Ilya E Zlobin
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia.
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, The Czech Academy of Sciences, Prague 6, Lysolaje, Czech Republic
| | - Pavel P Pashkovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Petre Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, The Czech Academy of Sciences, Prague 6, Lysolaje, Czech Republic
| | - Alexander V Kartashov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Yury V Ivanov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Vladimir V Kuznetsov
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
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Trujillo-Moya C, Ganthaler A, Stöggl W, Kranner I, Schüler S, Ertl R, Schlosser S, George JP, Mayr S. RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection. BMC Genomics 2020; 21:336. [PMID: 32357832 PMCID: PMC7195740 DOI: 10.1186/s12864-020-6587-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/18/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Norway spruce trees in subalpine forests frequently face infections by the needle rust fungus Chrysomyxa rhododendri, which causes significant growth decline and increased mortality of young trees. Yet, it is unknown whether trees actively respond to fungal attack by activating molecular defence responses and/or respective gene expression. RESULTS Here, we report results from an infection experiment, in which the transcriptomes (via RNA-Seq analysis) and phenolic profiles (via UHPLC-MS) of control and infected trees were compared over a period of 39 days. Gene expression between infected and uninfected ramets significantly differed after 21 days of infection and revealed already known, but also novel candidate genes involved in spruce molecular defence against pathogens. CONCLUSIONS Combined RNA-Seq and biochemical data suggest that Norway spruce response to infection by C. rhododendri is restricted locally and primarily activated between 9 and 21 days after infestation, involving a potential isolation of the fungus by a hypersensitive response (HR) associated with an activation of phenolic pathways. Identified key regulatory genes represent a solid basis for further specific analyses in spruce varieties with varying susceptibility, to better characterise resistant clones and to elucidate the resistance mechanism.
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Affiliation(s)
- Carlos Trujillo-Moya
- Federal Research and Training Centre for Forests, Landscape and Natural Hazards (BFW)-Department of Forest Genetics, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Andrea Ganthaler
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Stöggl
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Ilse Kranner
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Silvio Schüler
- Federal Research and Training Centre for Forests, Landscape and Natural Hazards (BFW)- Department of Forest Growth & Silviculture, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Sarah Schlosser
- VetCore Facility for Research, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Jan-Peter George
- Federal Research and Training Centre for Forests, Landscape and Natural Hazards (BFW)-Department of Forest Genetics, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Stefan Mayr
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
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Yang Q, Blanco NE, Hermida-Carrera C, Lehotai N, Hurry V, Strand Å. Two dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring. Nat Commun 2020; 11:128. [PMID: 31913273 PMCID: PMC6949249 DOI: 10.1038/s41467-019-13954-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/05/2019] [Indexed: 01/25/2023] Open
Abstract
Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO2 assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO2 assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.
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Affiliation(s)
- Qi Yang
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE 901 87, Umeå, Sweden
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Nicolás E Blanco
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE 901 87, Umeå, Sweden.
- Centre of Photosynthetic and Biochemical Studies (CEFOBI-CONICET), Faculty of Biochemical Science and Pharmacy, Rosario National University, S2002LRK, Rosario, Argentina.
| | - Carmen Hermida-Carrera
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE 901 87, Umeå, Sweden
| | - Nóra Lehotai
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE 901 87, Umeå, Sweden
| | - Vaughan Hurry
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83, Umeå, Sweden.
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE 901 87, Umeå, Sweden.
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Abstract
Somatic embryogenesis in Norway spruce combined with reverse genetics can be used as a model to study the regulation of embryo development in conifers. The somatic embryo system includes a sequence of developmental stages, which are similar in morphology to their zygotic counterparts. The system can be sufficiently synchronized to enable the collection and study of a large number of somatic embryos at each developmental stage.Here we describe a protocol for establishing transgenic cell lines in which genes of interest are upregulated or downregulated. Furthermore, we present methods for comparing embryo morphology and development in transgenic and control cell lines, including phenotyping the embryos, histological analysis, and tracking embryo development. The expression pattern of different genes is determined by GUS reporter assays.
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Affiliation(s)
- Sara von Arnold
- Department of Plant Biology and Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Emma Larsson
- Department of Plant Biology and Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Center for Plant Biology, Uppsala University, Uppsala, Sweden
| | - David Clapham
- Department of Plant Biology and Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Elfstrand M, Zhou L, Baison J, Olson Å, Lundén K, Karlsson B, Wu HX, Stenlid J, García‐Gil MR. Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds. Mol Ecol 2020; 29:199-213. [PMID: 31755612 PMCID: PMC7003977 DOI: 10.1111/mec.15314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 10/31/2019] [Accepted: 11/20/2019] [Indexed: 12/19/2022]
Abstract
The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
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Affiliation(s)
- Malin Elfstrand
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Linghua Zhou
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - John Baison
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - Åke Olson
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Karl Lundén
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Harry X. Wu
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
| | - Jan Stenlid
- Uppsala BiocentreDepartment of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - M. Rosario García‐Gil
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
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Blokhina O, Laitinen T, Hatakeyama Y, Delhomme N, Paasela T, Zhao L, Street NR, Wada H, Kärkönen A, Fagerstedt K. Ray Parenchymal Cells Contribute to Lignification of Tracheids in Developing Xylem of Norway Spruce. Plant Physiol 2019; 181:1552-1572. [PMID: 31558578 PMCID: PMC6878020 DOI: 10.1104/pp.19.00743] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/05/2019] [Indexed: 05/08/2023]
Abstract
A comparative transcriptomic study and a single-cell metabolome analysis were combined to determine whether parenchymal ray cells contribute to the biosynthesis of monolignols in the lignifying xylem of Norway spruce (Picea abies). Ray parenchymal cells may function in the lignification of upright tracheids by supplying monolignols. To test this hypothesis, parenchymal ray cells and upright tracheids were dissected with laser-capture microdissection from tangential cryosections of developing xylem of spruce trees. The transcriptome analysis revealed that among the genes involved in processes typical for vascular tissues, genes encoding cell wall biogenesis-related enzymes were highly expressed in both developing tracheids and ray cells. Interestingly, most of the shikimate and monolignol biosynthesis pathway-related genes were equally expressed in both cell types. Nonetheless, 1,073 differentially expressed genes were detected between developing ray cells and tracheids, among which a set of genes expressed only in ray cells was identified. In situ single cell metabolomics of semi-intact plants by picoliter pressure probe-electrospray ionization-mass spectrometry detected monolignols and their glycoconjugates in both cell types, indicating that the biosynthetic route for monolignols is active in both upright tracheids and parenchymal ray cells. The data strongly support the hypothesis that in developing xylem, ray cells produce monolignols that contribute to lignification of tracheid cell walls.
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Affiliation(s)
- Olga Blokhina
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Helsinki University, Fi-00014 Helsinki, Finland
| | - Teresa Laitinen
- Viikki Plant Science Centre, Department of Agricultural Sciences, Helsinki University, Fi-00014 Helsinki, Finland
| | - Yuto Hatakeyama
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, 833-0041 Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden
| | - Tanja Paasela
- Viikki Plant Science Centre, Department of Agricultural Sciences, Helsinki University, Fi-00014 Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Plant Genetics, 00790 Helsinki, Finland
| | - Lei Zhao
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Helsinki University, Fi-00014 Helsinki, Finland
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umea, Sweden
| | - Hiroshi Wada
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, 833-0041 Fukuoka, Japan
| | - Anna Kärkönen
- Viikki Plant Science Centre, Department of Agricultural Sciences, Helsinki University, Fi-00014 Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Plant Genetics, 00790 Helsinki, Finland
| | - Kurt Fagerstedt
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Helsinki University, Fi-00014 Helsinki, Finland
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Budeanu M, Apostol EN, Popescu F, Postolache D, Ioniţă L. Testing of the narrow crowned Norway spruce ideotype (Picea abies f. pendula) and the hybrids with normal crown form (pyramidalis) in multisite comparative trials. Sci Total Environ 2019; 689:980-990. [PMID: 31280179 DOI: 10.1016/j.scitotenv.2019.06.518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/29/2019] [Accepted: 06/29/2019] [Indexed: 06/09/2023]
Abstract
The study aims to analyse the stability of the narrow crowned Norway spruce (pendula form) compared to the normal spruce form (pyramidalis form) and the hybrids of the two forms, in 5 field trials (Comandău, Lepşa 1&2, Ilva Mică and Voineasa) located in the Romanian Carpathians. Trees height (Th), breast height diameter (Dbh), height growth of the last year, crown diameter (Cd), number of branches per whorl (Nbw) and dominant branch diameter (Dbd) traits were measured and survival rate (Sr) was determined, at 20 years old. Also, branches finesse (Bf), trees volume (Tv) and trees slenderness (Ts) were calculated. In order to compare the wood density (Cwd) there were collected cores. In all trials ANOVA revealed significant (p < 0.05) differences between the two forms of spruce and the hybrids (mainly between those that have a different crown form mother), especially for the stability and quality traits. Factorial ANOVA revealed a high influence (p < 0.001) of the locality and also a significant influence (p < 0.05) of the locality × spruce form interaction. The factor "form" was significant for some traits involved in Norway spruce stability (Ts, Cd, Nbw). The pendula trees present higher values for Sr, Dbh and Tv, and lower values for Ts, Cd, Nbw, Dbd and Bf, compared to pyramidalis spruce form, which showed a higher stability. Heritability was in generally low (h2 < 0.4), with exceptions of Ts which presents a medium rate of heritage. For the same trait, different heritability was registered in different environmental conditions. The Cwd was higher only with 2% for the pendula form in Lepşa trial, while in Comandău trial the pyramidalis registered a higher value (7%). In the new breeding programme, the selection strategy may be pursued with the pendula trees selection based on Ts and branches traits.
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Affiliation(s)
- Marius Budeanu
- National Institute for Research and Development in Forestry "Marin Drăcea", Voluntari, 128 Eroilor Boulevard, 077190, Ilfov County, Romania
| | - Ecaterina Nicoleta Apostol
- National Institute for Research and Development in Forestry "Marin Drăcea", Voluntari, 128 Eroilor Boulevard, 077190, Ilfov County, Romania.
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Voluntari, 128 Eroilor Boulevard, 077190, Ilfov County, Romania.
| | - Dragoş Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Voluntari, 128 Eroilor Boulevard, 077190, Ilfov County, Romania
| | - Lucia Ioniţă
- National Institute for Research and Development in Forestry "Marin Drăcea", Voluntari, 128 Eroilor Boulevard, 077190, Ilfov County, Romania
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50
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Blagojevic D, Lee Y, Brede DA, Lind OC, Yakovlev I, Solhaug KA, Fossdal CG, Salbu B, Olsen JE. Comparative sensitivity to gamma radiation at the organismal, cell and DNA level in young plants of Norway spruce, Scots pine and Arabidopsis thaliana. Planta 2019; 250:1567-1590. [PMID: 31372744 DOI: 10.1007/s00425-019-03250-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Persistent DNA damage in gamma-exposed Norway spruce, Scots pine and Arabidopsis thaliana, but persistent adverse effects at the organismal and cellular level in the conifers only. Gamma radiation emitted from natural and anthropogenic sources may have strong negative impact on plants, especially at high dose rates. Although previous studies implied different sensitivity among species, information from comparative studies under standardized conditions is scarce. In this study, sensitivity to gamma radiation was compared in young seedlings of the conifers Scots pine and Norway spruce and the herbaceous Arabidopsis thaliana by exposure to 60Co gamma dose rates of 1-540 mGy h-1 for 144 h, as well as 360 h for A. thaliana. Consistent with slightly less prominent shoot apical meristem, in the conifers growth was significantly inhibited with increasing dose rate ≥ 40 mGy h-1. Post-irradiation, the conifers showed dose-rate-dependent inhibition of needle and root development consistent with increasingly disorganized apical meristems with increasing dose rate, visible damage and mortality after exposure to ≥ 40 mGy h-1. Regardless of gamma duration, A. thaliana showed no visible or histological damage or mortality, only delayed lateral root development after ≥ 100 mGy h-1 and slightly, but transiently delayed post-irradiation reproductive development after ≥ 400 mGy h-1. In all species dose-rate-dependent DNA damage occurred following ≥ 1-10 mGy h-1 and was still at a similar level at day 44 post-irradiation. In conclusion, the persistent DNA damage (possible genomic instability) following gamma exposure in all species may suggest that DNA repair is not necessarily mobilized more extensively in A. thaliana than in Norway spruce and Scots pine, and the far higher sensitivity at the organismal and cellular level in the conifers indicates lower tolerance to DNA damage than in A. thaliana.
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Affiliation(s)
- Dajana Blagojevic
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - YeonKyeong Lee
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Dag A Brede
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Ole Christian Lind
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Igor Yakovlev
- Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway
| | - Knut Asbjørn Solhaug
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | | | - Brit Salbu
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Jorunn E Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
- Centre of Environmental Radioactivity (CERAD), Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
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