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Guo Y, Xu H, Chen B, Grünhofer P, Schreiber L, Lin J, Zhao Y. Genome-wide analysis of long non-coding RNAs in shoot apical meristem and vascular cambium in Populus tomentosa. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153759. [PMID: 35820347 DOI: 10.1016/j.jplph.2022.153759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Shoot apical and lateral meristems play essential roles in the formation and development of primary and secondary growth in plants. A delicate regulatory mechanism is needed to maintain homeostatic balance between the primary and secondary growth, as well as the self-renewal of meristems with the rate of cell division and differentiation of new meristems. However, little is known about the roles of long non-coding RNAs (lncRNAs) in the regulation of maintenance and differentiation of primary and secondary growth in Populus, especially in the cambium division and differentiation into secondary xylem. Here, 1298 lncRNAs were identified both in the apical meristem and vascular cambium, with 80 lncRNAs being expressed only in shoot apical meristem and 45 only in vascular cambium. There are 410 differentially expressed lncRNAs in shoot apical meristem and vascular cambium, among which 271 lncRNAs were up-regulated and 139 were down-regulated in cambium. The GO enrichment analysis revealed that differentially expressed lncRNAs mainly influenced the expression of lncRNAs related to the ribosome pathway, plant hormone signal pathway and photosynthesis pathway. The differentially expressed lncRNAs mainly target mRNA through cis-regulation in the vascular cambium. In addition, six key lncRNAs and also their significantly upregulated target genes were identified. Theses target genes are involved in plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. In addition, six key lncRNAs were identified, their significantly upregulated target genes are related to plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. Investigating lncRNA-mRNA interactions, we further found some genes that may be related to the development of vascular cambium, such as domain-containing transcription factors, cellulose synthesis genes, calcium dependent protein kinase 2, cytokinin receptor 1, glycosyl transferase and polyphenol oxidase. Our findings provide new insights into the lncRNA-mRNA networks in the development of vascular cambium of secondary growth in Populus.
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Affiliation(s)
- Yayu Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Bo Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Paul Grünhofer
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Yuanyuan Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
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Guo Y, Xu H, Wu H, Shen W, Lin J, Zhao Y. Seasonal changes in cambium activity from active to dormant stage affect the formation of secondary xylem in Pinus tabulaeformis Carr. TREE PHYSIOLOGY 2022; 42:585-599. [PMID: 34505153 DOI: 10.1093/treephys/tpab115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Understanding the changing patterns of vascular cambium during seasonal cycles is crucial to reveal the mechanisms that control cambium activity and wood formation, but this area has been underexplored, especially in conifers. Here, we quantified the changing cellular morphology patterns of cambial zones during the active, transition and dormant stages. With the help of toluidine blue and periodic acid-Schiff staining to visualize cell walls and identify their constituents, we observed decreasing cambial cell layers, thickening of newly formed xylem cell walls and increased polysaccharide granules in phloem from June to the following March over the course of our collecting period. Pectin immunofluorescence showed that dormant-stage cambium can produce highly abundant de-esterified homogalacturonan and (1-4)-β-d-galactan epitopes, whereas active cambium can strong accumulate high methylesterified homogalacturonan. Calcofluor white staining and confocal Raman spectroscopy analysis revealed regular changes in the chemical composition of cell walls, such as relative lower cellulose deposition in transition stage in vascular cambium, and higher lignin accumulation was found in dormant stage in secondary xylem. Moreover, real-time quantitative polymerase chain reaction analysis suggested that various IAA (Aux/IAA protein), CesA, CslA and HDZ genes, as well as NAC, PME3 and PME4, may be involved in cambium activities and secondary xylem formation. Taken together, these findings provide new information about cambium activity and cell differentiation in the formation, structure and chemistry in conifers during the active-dormant transition.
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Affiliation(s)
- Yayu Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Hongyang Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Weiwei Shen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Yuanyuan Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing 100083, China
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Cytokinin Perception in Ancient Plants beyond Angiospermae. Int J Mol Sci 2021; 22:ijms222313077. [PMID: 34884882 PMCID: PMC8657898 DOI: 10.3390/ijms222313077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Cytokinins (CKs) control many plant developmental processes and responses to environmental cues. Although the CK signaling is well understood, we are only beginning to decipher its evolution. Here, we investigated the CK perception apparatus in early-divergent plant species such as bryophyte Physcomitrium patens, lycophyte Selaginella moellendorffii, and gymnosperm Picea abies. Of the eight CHASE-domain containing histidine kinases (CHKs) examined, two CHKs, PpCHK3 and PpCHK4, did not bind CKs. All other CHK receptors showed high-affinity CK binding (KD of nM range), with a strong preference for isopentenyladenine over other CK nucleobases in the moss and for trans-zeatin over cis-zeatin in the gymnosperm. The pH dependences of CK binding for these six CHKs showed a wide range, which may indicate different subcellular localization of these receptors at either the plasma- or endoplasmic reticulum membrane. Thus, the properties of the whole CK perception apparatuses in early-divergent lineages were demonstrated. Data show that during land plant evolution there was a diversification of the ligand specificity of various CHKs, in particular, the rise in preference for trans-zeatin over cis-zeatin, which indicates a steadily increasing specialization of receptors to various CKs. Finally, this distinct preference of individual receptors to different CK versions culminated in vascular plants, especially angiosperms.
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Li H, Chen G, Pang H, Wang Q, Dai X. Investigation Into Different Wood Formation Mechanisms Between Angiosperm and Gymnosperm Tree Species at the Transcriptional and Post-transcriptional Level. FRONTIERS IN PLANT SCIENCE 2021; 12:698602. [PMID: 34276747 PMCID: PMC8283789 DOI: 10.3389/fpls.2021.698602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/01/2021] [Indexed: 05/19/2023]
Abstract
Enormous distinctions of the stem structure and cell types between gymnosperms and angiosperms tree species are expected to cause quite different wood physical and mechanical attributes, however, the molecular mechanisms underlying the differing wood morphology are still unclear. In this study, we compared the transcriptomes obtained by RNA-Seq between Populus alba × P. glandulosa clone 84K, and Larix kaempferi (Lamb.) Carr trees. Available genome resource served as reference for P. alba × P. glandulosa and the Iso-Seq results of a three-tissues mixture (xylem, phloem, and leaf) were used as the reference for L. kaempferi to compare the xylem-specifically expressed genes and their alternative splicing model. Through screening, we obtained 13,907 xylem-specifically expressed genes (5,954 up-regulated, 7,953 down-regulated) in the xylem of P. alba × P. glandulosa, and 2,596 xylem-specifically expressed genes (1,648 up-regulated, 948 down-regulated) in the xylem of L. kaempferi. From the GO and KEGG analyses, some genes associated with two wood formation-related pathways, namely those for phenylpropanoid biosynthesis, and starch and sucrose metabolism, were successfully screened. Then the distributions and gene expression models between P. alba × P. glandulosa and L. kaempferi in those pathways were compared, which suggested differential wood formation processes between the angiosperm and gymnosperm trees. Furthermore, a Weight Gene Co-expression Network Analysis (WGCNA) for total xylem-specifically expressed genes in two species was conducted, from which wood formation-related modules were selected to build a co-expression network for the two tree species. The genes within this co-expression network showed different co-expression relationships between the angiosperm and gymnosperm woody species. Comparing the alternative splicing events for wood formation-related genes suggests a different post-transcriptional regulation process exists between the angiosperm and gymnosperm trees. Our research thus provides the foundation for the in-depth investigation of different wood formation mechanisms of angiosperm and gymnosperm species.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Guanghui Chen
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Hongying Pang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
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Lopes ST, Sobral D, Costa B, Perdiguero P, Chaves I, Costa A, Miguel CM. Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak. TREE PHYSIOLOGY 2020; 40:129-141. [PMID: 31860724 DOI: 10.1093/treephys/tpz118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023]
Abstract
Cork cambium (or phellogen) is a secondary meristem responsible for the formation of phelloderm and phellem/cork, which together compose the periderm. In Quercus suber L., the phellogen is active throughout the entire life of the tree, producing a continuous and renewable outer bark of cork. To identify specific candidate genes associated with cork cambium activity and phellem differentiation, we performed a comparative transcriptomic study of Q. suber secondary growth tissues (xylem and phellogen/phellem) using RNA-seq. The present work provides a high-resolution map of all the transcripts identified in the phellogen/phellem tissues. A total of 6013 differentially expressed genes were identified, with 2875 of the transcripts being specifically enriched during the cork formation process versus secondary xylem formation. Furthermore, cork samples originating from the original phellogen (`virgin' cork) and from a traumatic phellogen (`amadia' cork) were also compared. Our results point to a shortlist of potentially relevant candidate genes regulating phellogen activity and phellem differentiation, including novel genes involved in the suberization process, as well as genes associated to ethylene and jasmonate signaling and to meristem function. The future functional characterization of some of the identified candidate genes will help to elucidate the molecular mechanisms underlying cork cambium activity and phellem differentiation.
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Affiliation(s)
- Susana T Lopes
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Daniel Sobral
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156 Oeiras, Portugal
| | - Bruno Costa
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Pedro Perdiguero
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária, Avenida da República, Quinta do Marquês 2780-157 Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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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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Drought Sensitivity of Norway Spruce at the Species' Warmest Fringe: Quantitative and Molecular Analysis Reveals High Genetic Variation Among and Within Provenances. G3-GENES GENOMES GENETICS 2018; 8:1225-1245. [PMID: 29440346 PMCID: PMC5873913 DOI: 10.1534/g3.117.300524] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Norway spruce (Picea abies) is by far the most important timber species in Europe, but its outstanding role in future forests is jeopardized by its high sensitivity to drought. We analyzed drought response of Norway spruce at the warmest fringe of its natural range. Based on a 35-year old provenance experiment we tested for genetic variation among and within seed provenances across consecutively occurring strong drought events using dendroclimatic time series. Moreover, we tested for associations between ≈1,700 variable SNPs and traits related to drought response, wood characteristics and climate-growth relationships. We found significant adaptive genetic variation among provenances originating from the species’ Alpine, Central and Southeastern European range. Genetic variation between individuals varied significantly among provenances explaining up to 44% of the phenotypic variation in drought response. Varying phenotypic correlations between drought response and wood traits confirmed differences in selection intensity among seed provenances. Significant associations were found between 29 SNPs and traits related to drought, climate-growth relationships and wood properties which explained between 11 and 43% of trait variation, though 12 of them were due to single individuals having extreme phenotypes of the respective trait. The majority of these SNPs are located within exons of genes and the most important ones are preferentially expressed in cambium and xylem expansion layers. Phenotype-genotype associations were stronger if only provenances with significant quantitative genetic variation in drought response were considered. The present study confirms the high adaptive variation of Norway spruce in Central and Southeastern Europe and demonstrates how quantitative genetic, dendroclimatic and genomic data can be linked to understand the genetic basis of adaptation to climate extremes in trees.
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Bartholomé J, Bink MCAM, van Heerwaarden J, Chancerel E, Boury C, Lesur I, Isik F, Bouffier L, Plomion C. Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness. PLoS One 2016; 11:e0165323. [PMID: 27806077 PMCID: PMC5091878 DOI: 10.1371/journal.pone.0165323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/10/2016] [Indexed: 01/26/2023] Open
Abstract
Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.
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Affiliation(s)
| | - Marco CAM Bink
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | - Joost van Heerwaarden
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | | | | | - Isabelle Lesur
- BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France
- HelixVenture, Mérignac, France
| | - Fikret Isik
- North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC, United States of America
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Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. Mol Biol Rep 2016; 43:1129-46. [DOI: 10.1007/s11033-016-4046-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022]
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10
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Ouyang K, Li J, Zhao X, Que Q, Li P, Huang H, Deng X, Singh SK, Wu AM, Chen X. Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq. PLoS One 2016; 11:e0159407. [PMID: 27438485 PMCID: PMC4954708 DOI: 10.1371/journal.pone.0159407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/02/2016] [Indexed: 12/13/2022] Open
Abstract
Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees.
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Affiliation(s)
- Kunxi Ouyang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Juncheng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xianhai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Qingmin Que
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Pei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hao Huang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, P.R. China
| | - Xiaomei Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Sunil Kumar Singh
- Department of Botany, Faculty of Science, The MS University of Baroda, Vadodara, Gujarat, India
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- * E-mail: (AW); (XC)
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- * E-mail: (AW); (XC)
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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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12
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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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13
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Uddenberg D, Akhter S, Ramachandran P, Sundström JF, Carlsbecker A. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. FRONTIERS IN PLANT SCIENCE 2015; 6:970. [PMID: 26579190 PMCID: PMC4630563 DOI: 10.3389/fpls.2015.00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 05/20/2023]
Abstract
Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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Affiliation(s)
- Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Shirin Akhter
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Jens F. Sundström
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
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Sengupta S, Majumder AL. Physiological and genomic basis of mechanical-functional trade-off in plant vasculature. FRONTIERS IN PLANT SCIENCE 2014; 5:224. [PMID: 24904619 PMCID: PMC4035604 DOI: 10.3389/fpls.2014.00224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/05/2014] [Indexed: 05/13/2023]
Abstract
Some areas in plant abiotic stress research are not frequently addressed by genomic and molecular tools. One such area is the cross reaction of gravitational force with upward capillary pull of water and the mechanical-functional trade-off in plant vasculature. Although frost, drought and flooding stress greatly impact these physiological processes and consequently plant performance, the genomic and molecular basis of such trade-off is only sporadically addressed and so is its adaptive value. Embolism resistance is an important multiple stress- opposition trait and do offer scopes for critical insight to unravel and modify the input of living cells in the process and their biotechnological intervention may be of great importance. Vascular plants employ different physiological strategies to cope with embolism and variation is observed across the kingdom. The genomic resources in this area have started to emerge and open up possibilities of synthesis, validation and utilization of the new knowledge-base. This review article assesses the research till date on this issue and discusses new possibilities for bridging physiology and genomics of a plant, and foresees its implementation in crop science.
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Affiliation(s)
- Sonali Sengupta
- Division of Plant Biology, Acharya J C Bose Biotechnology Innovation Centre, Bose InstituteKolkata, India
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