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Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers. FORESTS 2022. [DOI: 10.3390/f13040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The global change scenarios highlight the urgency of clarifying the mechanisms driving the determination of wood traits in forest trees. Coniferous xylem is characterized by the alternation between earlywood (EW) and latewood (LW), on which proportions the wood density depend, one of the most important mechanical xylem qualities. However, the molecular mechanisms triggering the transition between the production of cells with the typical features of EW to the LW are still far from being completely elucidated. The increasing availability of omics resources for conifers, e.g., genomes and transcriptomes, would lay the basis for the comprehension of wood formation dynamics, boosting both breeding and gene-editing approaches. This review is intended to introduce the importance of wood formation dynamics and xylem traits of conifers in a changing environment. Then, an up-to-date overview of the omics resources available for conifers was reported, focusing on both genomes and transcriptomes. Later, an analysis of wood formation studies using omics approaches was conducted, with the aim of elucidating the main metabolic pathways involved in EW and LW determination. Finally, the future perspectives and the urgent needs on this research topic were highlighted.
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Transcriptome and Co-Expression Network Analyses Identify the Molecular Signatures Underlying Drought Resistance in Yellowhorn. FORESTS 2020. [DOI: 10.3390/f11080840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Drought is a key factor that limits plant growth and yield. Yellowhorn is an important and vigorously promoted oil tree in China. It can survive under certain drought conditions, but a lack of water severely restricts its growth and results in yield losses in arid and semi-arid areas. Therefore, it is important to identify the key pathways and genes to understand the mechanisms of its drought resistance. In this study, we evaluated drought resistance in four types of yellowhorn, and obtained 2669 and 2451 differentially expressed genes (DEGs) via the transcriptome analysis of the comparison of water-saving/water-consuming and fast-growing/slow-growing yellowhorn, respectively, under long-term drought conditions. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs showed the key biological processes and metabolic pathways involved in drought resistance, which demonstrated that there are both the same and different biological processes involved in regulating water use efficiency (WUE) and growth in response to drought stress. Furthermore, the network analysis indicated hub genes (especially seven protein kinases) and potential co-expressed gene clusters in a greenyellow module associated with WUE and a blue module associated with growth. These identified hub genes and key biological processes can significantly enhance our knowledge about the molecular mechanisms of drought resistance in yellowhorn.
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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce. Sci Rep 2020; 10:12711. [PMID: 32728135 PMCID: PMC7391732 DOI: 10.1038/s41598-020-69386-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/07/2020] [Indexed: 11/08/2022] Open
Abstract
The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
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Liu L, Wang Z, Su Y, Wang T. Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng. Int J Mol Sci 2020; 21:ijms21124305. [PMID: 32560294 PMCID: PMC7352595 DOI: 10.3390/ijms21124305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023] Open
Abstract
Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.
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Affiliation(s)
- Li Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
- Correspondence: (Y.S.); (T.W.); Tel.: +86-020-84111939 (Y.S.); +86-020-85280185 (T.W.)
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.S.); (T.W.); Tel.: +86-020-84111939 (Y.S.); +86-020-85280185 (T.W.)
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Roberts WR, Roalson EH. Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae). PeerJ 2020; 8:e8778. [PMID: 32201652 PMCID: PMC7071821 DOI: 10.7717/peerj.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/21/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex traits that are orchestrated by multiple genes and pathways, the gene regulatory networks have not been explored. Gene co-expression networks provide a systems level approach to identify important contributors to floral diversification. METHODS RNA-sequencing was used to assay gene expression across two stages of flower development (an early bud and an intermediate stage) in 10 species of Achimenes (Gesneriaceae). Two stage-specific co-expression networks were created from 9,503 orthologs and analyzed to identify module hubs and the network periphery. Module association with bee, butterfly, and hummingbird pollination syndromes was tested using phylogenetic mixed models. The relationship between network connectivity and evolutionary rates (d N/d S) was tested using linear models. RESULTS Networks contained 65 and 62 modules that were largely preserved between developmental stages and contained few stage-specific modules. Over a third of the modules in both networks were associated with flower color, shape, and pollination syndrome. Within these modules, several hub nodes were identified that related to the production of anthocyanin and carotenoid pigments and the development of flower shape. Evolutionary rates were decreased in highly connected genes and elevated in peripheral genes. DISCUSSION This study aids in the understanding of the genetic architecture and network properties underlying the development of floral form and provides valuable candidate modules and genes for future studies.
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Affiliation(s)
- Wade R. Roberts
- School of Biological Sciences, Washington State University, Pullman, WA, USA
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Eric H. Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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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 PHYSIOLOGY 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] [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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Van Ghelder C, Parent GJ, Rigault P, Prunier J, Giguère I, Caron S, Stival Sena J, Deslauriers A, Bousquet J, Esmenjaud D, MacKay J. The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs. Sci Rep 2019; 9:11614. [PMID: 31406137 PMCID: PMC6691002 DOI: 10.1038/s41598-019-47950-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of the RNL subfamily and a lack of data in Gymnosperms. We developed, searched and annotated transcriptomes assemblies of seven conifers and identified a resource of 3816 expressed NLR sequences. Our analyses encompassed sequences data spanning the major groups of land plants and determinations of NLR transcripts levels in response to drought in white spruce. We showed that conifers have among the most diverse and numerous RNLs in tested land plants. We report an evolutionary swap in the formation of RNLs, which emerged from the fusion of an RPW8 domain to a NB-ARC domain of CNL. We uncovered a quantitative relationship between RNLs and TNLs across all land plants investigated, with an average ratio of 1:10. The conifer RNL repertoire harbours four distinct groups, with two that differ from Angiosperms, one of which contained several upregulated sequences in response to drought while the majority of responsive NLRs are downregulated.
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Affiliation(s)
- Cyril Van Ghelder
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France. .,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Geneviève J Parent
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.,Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Philippe Rigault
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec, QC, G1S 1E7, Canada.,Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Julien Prunier
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Sébastien Caron
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec, QC, G1S 1E7, Canada
| | - Juliana Stival Sena
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V 4C7, Canada
| | - Annie Deslauriers
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada.,Canada Research Chair in Forest Genomics, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Daniel Esmenjaud
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - John MacKay
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.,Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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Lamara M, Parent GJ, Giguère I, Beaulieu J, Bousquet J, MacKay JJ. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC PLANT BIOLOGY 2018; 18:231. [PMID: 30309315 PMCID: PMC6182838 DOI: 10.1186/s12870-018-1434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Outbreaks of spruce budworm (SBW, Choristoneura fumiferana Clem.) cause major recurrent damage in boreal conifers such as white spruce (Picea glauca [Moench] Voss) and large losses of forest biomass in North America. Although defensive phenolic compounds have recently been linked to chemical resistance against SBW, their genetic basis remains poorly understood in forest trees, especially in conifers. Here, we used diverse association genetics approaches to discover genes and their variants that may control the accumulation of acetophenones, and dissect the genetic architecture of these defence compounds against SBW in white spruce mature trees. RESULTS Out of 4747 single nucleotide polymorphisms (SNPs) from 2312 genes genotyped in a population of 211 unrelated individuals, genetic association analyses identified 35 SNPs in 33 different genes that were significantly associated with the defence traits by using single-locus, multi-locus and multi-trait approaches. The multi-locus approach was particularly effective at detecting SNP-trait associations that explained a large fraction of the phenotypic variance (from 20 to 43%). Significant genes were regulatory including the NAC transcription factor, or they were involved in carbohydrate metabolism, falling into the binding, catalytic or transporter activity functional classes. Most of them were highly expressed in foliage. Weak positive phenotypic correlations were observed between defence and growth traits, indicating little or no evidence of defence-growth trade-offs. CONCLUSIONS This study provides new insights on the genetic architecture of tree defence traits, contributing to our understanding of the physiology of resistance mechanisms to biotic factors and providing a basis for the genetic improvement of the constitutive defence of white spruce against SBW.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | | | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Beaulieu
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - John J. MacKay
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
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Stival Sena J, Giguère I, Rigault P, Bousquet J, Mackay J. Expansion of the dehydrin gene family in the Pinaceae is associated with considerable structural diversity and drought-responsive expression. TREE PHYSIOLOGY 2018; 38:442-456. [PMID: 29040752 DOI: 10.1093/treephys/tpx125] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
Temperatures are expected to increase over the next century in all terrestrial biomes and particularly in boreal forests, where drought-induced mortality has been predicted to rise. Genomics research is helping to develop hypotheses regarding the molecular basis of drought tolerance and recent work proposed that the osmo-protecting dehydrin proteins have undergone a clade-specific expansion in the Pinaceae, a major group of conifer trees. The objectives of this study were to identify all of the putative members of the gene family, trace their evolutionary origin, examine their structural diversity and test for drought-responsive expression. We identified 41 complete dehydrin coding sequences in Picea glauca, which is four times more than most angiosperms studied to date, and more than in pines. Phylogenetic reconstructions indicated that the family has undergone an expansion in conifers, with parallel evolution implicating the sporadic resurgence of certain amino acid sequence motifs, and a major duplication giving rise to a clade specific to the Pinaceae. A variety of plant dehydrin structures were identified with variable numbers of the A-, E-, S- and K-segments and an N-terminal (N1) amino acid motif including assemblages specific to conifers. The expression of several of the spruce dehydrins was tissue preferential under non-stressful conditions or responded to water stress after 7-18 days without watering, reflecting changes in osmotic potential. We found that dehydrins with N1 K2 and N1 AESK2 sequences were the most responsive to the lack of water. Together, the family expansion, drought-responsive expression and structural diversification involving loss and gain of amino acid motifs suggests that subfunctionalization has driven the diversification seen among dehydrin gene duplicates. Our findings clearly indicate that dehydrins represent a large family of candidate genes for drought tolerance in spruces and in other Pinaceae that may underpin adaptability in spatially and temporally variable environments.
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Affiliation(s)
- Juliana Stival Sena
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - Isabelle Giguère
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - Philippe Rigault
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec QC G1S 1E7, Canada
| | - Jean Bousquet
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
| | - John Mackay
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, 1030 rue de la Médecine, Université Laval, Québec QC G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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García CF, Pedrini N, Sánchez-Paz A, Reyna-Blanco CS, Lavarias S, Muhlia-Almazán A, Fernández-Giménez A, Laino A, de-la-Re-Vega E, Lukaszewicz G, López-Zavala AA, Brieba LG, Criscitello MF, Carrasco-Miranda JS, García-Orozco KD, Ochoa-Leyva A, Rudiño-Piñera E, Sanchez-Flores A, Sotelo-Mundo RR. De novo assembly and transcriptome characterization of the freshwater prawn Palaemonetes argentinus: Implications for a detoxification response. Mar Genomics 2018; 37:74-81. [DOI: 10.1016/j.margen.2017.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/25/2017] [Accepted: 08/26/2017] [Indexed: 12/14/2022]
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12
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Jokipii‐Lukkari S, Sundell D, Nilsson O, Hvidsten TR, Street NR, Tuominen H. NorWood: a gene expression resource for evo-devo studies of conifer wood development. THE NEW PHYTOLOGIST 2017; 216:482-494. [PMID: 28186632 PMCID: PMC6079643 DOI: 10.1111/nph.14458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/22/2016] [Indexed: 05/04/2023]
Abstract
The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
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Affiliation(s)
- Soile Jokipii‐Lukkari
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - David Sundell
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - Torgeir R. Hvidsten
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Sciences1430ÅsNorway
| | - Nathaniel R. Street
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Hannele Tuominen
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
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13
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Mageroy MH, Jancsik S, Man Saint Yuen M, Fischer M, Withers SG, Paetz C, Schneider B, Mackay J, Bohlmann J. A Conifer UDP-Sugar Dependent Glycosyltransferase Contributes to Acetophenone Metabolism and Defense against Insects. PLANT PHYSIOLOGY 2017; 175:641-651. [PMID: 28794260 PMCID: PMC5619895 DOI: 10.1104/pp.17.00611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/01/2017] [Indexed: 05/15/2023]
Abstract
Acetophenones are phenolic compounds involved in the resistance of white spruce (Picea glauca) against spruce budworm (Choristoneura fumiferiana), a major forest pest in North America. The acetophenones pungenol and piceol commonly accumulate in spruce foliage in the form of the corresponding glycosides, pungenin and picein. These glycosides appear to be inactive against the insect but can be cleaved by a spruce β-glucosidase, PgβGLU-1, which releases the active aglycons. The reverse glycosylation reaction was hypothesized to involve a family 1 UDP-sugar dependent glycosyltransferase (UGT) to facilitate acetophenone accumulation in the plant. Metabolite and transcriptome profiling over a developmental time course of white spruce bud burst and shoot growth revealed two UGTs, PgUGT5 and PgUGT5b, that glycosylate pungenol. Recombinant PgUGT5b enzyme produced mostly pungenin, while PgUGT5 produced mostly isopungenin. Both UGTs also were active in vitro on select flavonoids. However, the context of transcript and metabolite accumulation did not support a biological role in flavonoid metabolism but correlated with the formation of pungenin in growing shoots. Transcript levels of PgUGT5b were higher than those of PgUGT5 in needles across different genotypes of white spruce. These results support a role of PgUGT5b in the biosynthesis of the glycosylated acetophenone pungenin in white spruce.
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Affiliation(s)
- Melissa H Mageroy
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Norwegian Institute for Bioeconomy Research, NO-1430 As, Norway
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Michael Fischer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T1Z1, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T1Z1, Canada
| | - Christian Paetz
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Bernd Schneider
- Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - John Mackay
- Department of Wood and Forest Sciences, Université Laval, Quebec City, Quebec G1V0A6, Canada
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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14
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Laitinen T, Morreel K, Delhomme N, Gauthier A, Schiffthaler B, Nickolov K, Brader G, Lim KJ, Teeri TH, Street NR, Boerjan W, Kärkönen A. A Key Role for Apoplastic H 2O 2 in Norway Spruce Phenolic Metabolism. PLANT PHYSIOLOGY 2017; 174:1449-1475. [PMID: 28522458 PMCID: PMC5490890 DOI: 10.1104/pp.17.00085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/16/2017] [Indexed: 05/18/2023]
Abstract
Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic hydrogen peroxide (H2O2) in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by potassium iodide repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time-course analyses coupled to candidate substrate-product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids, and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures and supported that monolignols are oxidatively coupled not only in the cell wall but also in the cytoplasm, where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting that cells are able to transport glycosylated dilignols to the apoplast. Transcriptomic analyses revealed that scavenging of apoplastic H2O2 resulted in remodulation of the transcriptome, with reduced carbon flux into the shikimate pathway propagating down to monolignol biosynthesis. Aggregated coexpression network analysis identified candidate enzymes and transcription factors for monolignol oxidation and apoplastic H2O2 production in addition to potential H2O2 receptors. The results presented indicate that the redox state of the apoplast has a profound influence on cellular metabolism.
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Affiliation(s)
- Teresa Laitinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Adrien Gauthier
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Bastian Schiffthaler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå, Sweden
| | - Kaloian Nickolov
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- Department of Biology, University of Oulu, 90014 Oulu, Finland
| | - Günter Brader
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kean-Jin Lim
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Teemu H Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187 Umeå, Sweden
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Kärkönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- Natural Resources Institute Finland (Luke), Green Technology, 00790 Helsinki, Finland
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15
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Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:189-203. [PMID: 28090692 DOI: 10.1111/tpj.13478] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 05/21/2023]
Abstract
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Betty Pelgas
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John Mackay
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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16
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Pascual MB, El-Azaz J, de la Torre FN, Cañas RA, Avila C, Cánovas FM. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers. FRONTIERS IN PLANT SCIENCE 2016; 7:1030. [PMID: 27468292 PMCID: PMC4942462 DOI: 10.3389/fpls.2016.01030] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.
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Affiliation(s)
| | | | | | | | | | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de MálagaMálaga, Spain
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17
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Verta JP, Landry CR, MacKay J. Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations. THE NEW PHYTOLOGIST 2016; 211:159-171. [PMID: 26891783 DOI: 10.1111/nph.13888] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Regulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long-lived such as in the case of conifer trees. We developed an RNA sequencing (RNA-seq)-based approach for both expression-quantitative trait locus (eQTL) mapping and the detection of cis-acting (allele-specific) vs trans-acting (non-allele-specific) eQTLs. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self-fertilized white spruce (Picea glauca) individual to dissect eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs linked to the expressed genes was particularly complex, consisting of cis-acting, trans-acting and, surprisingly, compensatory cis-trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTLs were under compensation, indicating that close linkage between compensatory cis-trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid-diploid eQTL analysis in spruce revealed that compensatory cis-trans eQTLs segregate within populations and evolve in close genetic linkage.
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Affiliation(s)
- Jukka-Pekka Verta
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Département de Biologie, Université Laval, Québec, QC, Canada G1V 0A6
| | - John MacKay
- Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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18
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Zhang Y, Han X, Sang J, He X, Liu M, Qiao G, Zhuo R, He G, Hu J. Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PeerJ 2016; 4:e2097. [PMID: 27330860 PMCID: PMC4906661 DOI: 10.7717/peerj.2097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.
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Affiliation(s)
- Yunxing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
- Institute of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo, Henan, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jian Sang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Xuelian He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Guiping He
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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19
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Lamara M, Raherison E, Lenz P, Beaulieu J, Bousquet J, MacKay J. Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. THE NEW PHYTOLOGIST 2016; 210:240-55. [PMID: 26619072 PMCID: PMC5063130 DOI: 10.1111/nph.13762] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/13/2015] [Indexed: 05/02/2023]
Abstract
Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects. Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
| | - Elie Raherison
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
| | - Patrick Lenz
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canadian Wood Fibre CentreCanadian Forest ServiceNatural Resources CanadaQuébecQCG1V 4C7Canada
| | - Jean Beaulieu
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canadian Wood Fibre CentreCanadian Forest ServiceNatural Resources CanadaQuébecQCG1V 4C7Canada
- Canada Research Chair in Forest and Environmental GenomicsUniversité LavalQuébecQCG1V 0A6Canada
| | - Jean Bousquet
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canada Research Chair in Forest and Environmental GenomicsUniversité LavalQuébecQCG1V 0A6Canada
| | - John MacKay
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Department of Plant SciencesUniversity of OxfordOxford0X1 3RBUK
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20
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Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F. Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1123-35. [PMID: 26628518 PMCID: PMC4753849 DOI: 10.1093/jxb/erv513] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, D-93053 Regensburg, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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Prunier J, Verta JP, MacKay JJ. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. THE NEW PHYTOLOGIST 2016; 209:44-62. [PMID: 26206592 DOI: 10.1111/nph.13565] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/14/2015] [Indexed: 05/21/2023]
Abstract
Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - John J MacKay
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
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