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Zhao Y, Sun T, Liu J, Zhang R, Yu Y, Zhou G, Liu J, Gao B. The Key Role of Plant Hormone Signaling Transduction and Flavonoid Biosynthesis Pathways in the Response of Chinese Pine ( Pinus tabuliformis) to Feeding Stimulation by Pine Caterpillar ( Dendrolimus tabulaeformis). Int J Mol Sci 2024; 25:6354. [PMID: 38928063 PMCID: PMC11203464 DOI: 10.3390/ijms25126354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In nature, plants have developed a series of resistance mechanisms to face various external stresses. As understanding of the molecular mechanisms underlying plant resistance continues to deepen, exploring endogenous resistance in plants has become a hot topic in this field. Despite the multitude of studies on plant-induced resistance, how plants respond to stress under natural conditions remains relatively unclear. To address this gap, we investigated Chinese pine (Pinus tabuliformis) using pine caterpillar (Dendrolimus tabulaeformis) under natural conditions. Healthy Chinese pine trees, approximately 10 years old, were selected for studying induced resistance in Huangtuliangzi Forestry, Pingquan City, Chengde City, Hebei Province, China. Pine needles were collected at 2 h and 8 h after feeding stimulation (FS) via 10 pine caterpillars and leaf clipping control (LCC), to simulate mechanical damage caused by insect chewing for the quantification of plant hormones and transcriptome and metabolome assays. The results show that the different modes of treatments significantly influence the contents of JA and SA in time following treatment. Three types of differentially accumulated metabolites (DAMs) were found to be involved in the initial response, namely phenolic acids, lipids, and flavonoids. Weighted gene co-expression network analysis indicated that 722 differentially expressed genes (DEGs) are positively related to feeding stimulation and the specific enriched pathways are plant hormone signal transduction and flavonoid biosynthesis, among others. Two TIFY transcription factors (PtTIFY54 and PtTIFY22) and a MYB transcription factor (PtMYB26) were found to be involved in the interaction between plant hormones, mainly in the context of JA signal transduction and flavonoid biosynthesis. The results of this study provide an insight into how JA activates, serving as a reference for understanding the molecular mechanisms of resistance formation in conifers responding to mandibulate insects.
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Affiliation(s)
- Yanan Zhao
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Tianhua Sun
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Jie Liu
- College of Agronomy, Hebei Agricultural University, Baoding 071000, China;
| | - Ruibo Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Yongjie Yu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Guona Zhou
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Junxia Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
| | - Baojia Gao
- College of Forestry, Hebei Agricultural University, Baoding 071000, China; (Y.Z.); (T.S.); (R.Z.); (Y.Y.); (G.Z.); (J.L.)
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Li Z, Zhou Z, Hou Q, Shen L, Zhao H, Wen X. Physiological, Proteomic, and Resin Yield-Related Genes Expression Analysis Provides Insights into the Mechanisms Regulating Resin Yield in Masson Pine. Int J Mol Sci 2023; 24:13813. [PMID: 37762116 PMCID: PMC10531451 DOI: 10.3390/ijms241813813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Masson pine (Pinus massoniana Lamb.) is an important resin-producing conifer species in China. Resin yield is a highly heritable trait and varies greatly among different genotypes. However, the mechanisms regulating the resin yield of masson pine remain largely unknown. In this study, physiological, proteomic, and gene expression analysis was performed on xylem tissues of masson pine with high and low resin yield. Physiological investigation showed that the activity of terpene synthase, as well as the contents of soluble sugar, jasmonic acid (JA), methyl jasmonate (MeJA), gibberellins (GA1, GA4, GA9, GA19, and GA20), indole-3-acetic acid (IAA), and abscisic acid (ABA) were significantly increased in the high yielder, whereas sucrose and salicylic acid (SA) were significantly decreased compared with the low one. A total of 2984 differentially expressed proteins (DEPs) were identified in four groups, which were mainly enriched in the biosynthesis of secondary metabolites, protein processing in the endoplasmic reticulum, carbohydrate metabolism, phytohormone biosynthesis, glutathione metabolism, and plant-pathogen interaction. Integrated physiological and proteomic analysis revealed that carbohydrate metabolism, terpenoid biosynthesis, resistance to stress, as well as JA and GA biosynthesis and signaling, play key roles in regulating resin yield. A series of proteins associated with resin yield, e.g., terpene synthase proteins (TPSs), ATP-binding cassette transporters (ABCs), glutathione S-transferase proteins (GSTs), and heat shock proteins (HSPs), were identified. Resin yield-related gene expression was also associated with resin yield. Our study unveils the implicated molecular mechanisms regulating resin yield and is of pivotal significance to breeding strategies of high resin-yielding masson pine cultivars.
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Affiliation(s)
- Zhengchun Li
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Zijing Zhou
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Luonan Shen
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Hong Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xiaopeng Wen
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
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Nantongo JS, Potts BM, Frickey T, Telfer E, Dungey H, Fitzgerald H, O'Reilly-Wapstra JM. Analysis of the transcriptome of the needles and bark of Pinus radiata induced by bark stripping and methyl jasmonate. BMC Genomics 2022; 23:52. [PMID: 35026979 PMCID: PMC8759178 DOI: 10.1186/s12864-021-08231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plants are attacked by diverse insect and mammalian herbivores and respond with different physical and chemical defences. Transcriptional changes underlie these phenotypic changes. Simulated herbivory has been used to study the transcriptional and other early regulation events of these plant responses. In this study, constitutive and induced transcriptional responses to artificial bark stripping are compared in the needles and the bark of Pinus radiata to the responses from application of the plant stressor, methyl jasmonate. The time progression of the responses was assessed over a 4-week period. RESULTS Of the 6312 unique transcripts studied, 86.6% were differentially expressed between the needles and the bark prior to treatment. The most abundant constitutive transcripts were related to defence and photosynthesis and their expression did not differ between the needles and the bark. While no differential expression of transcripts were detected in the needles following bark stripping, in the bark this treatment caused an up-regulation and down-regulation of genes associated with primary and secondary metabolism. Methyl jasmonate treatment caused differential expression of transcripts in both the bark and the needles, with individual genes related to primary metabolism more responsive than those associated with secondary metabolism. The up-regulation of genes related to sugar break-down and the repression of genes related with photosynthesis, following both treatments was consistent with the strong down-regulation of sugars that has been observed in the same population. Relative to the control, the treatments caused a differential expression of genes involved in signalling, photosynthesis, carbohydrate and lipid metabolism as well as defence and water stress. However, non-overlapping transcripts were detected between the needles and the bark, between treatments and at different times of assessment. Methyl jasmonate induced more transcriptional responses in the bark than bark stripping, although the peak of expression following both treatments was detected 7 days post treatment application. The effects of bark stripping were localised, and no systemic changes were detected in the needles. CONCLUSION There are constitutive and induced differences in the needle and bark transcriptome of Pinus radiata. Some expression responses to bark stripping may differ from other biotic and abiotic stresses, which contributes to the understanding of plant molecular responses to diverse stresses. Whether the gene expression changes are heritable and how they differ between resistant and susceptible families identified in earlier studies needs further investigation.
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Affiliation(s)
- J S Nantongo
- School of Natural Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania, 7001, Australia.
- National Forestry Resources Research Institute, Mukono, Uganda.
| | - B M Potts
- School of Natural Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania, 7001, Australia
- ARC Training Centre for Forest Value, Hobart, Tasmania, Australia
| | | | | | | | - H Fitzgerald
- School of Natural Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania, 7001, Australia
| | - J M O'Reilly-Wapstra
- School of Natural Sciences, University of Tasmania, Private Bag 5, Hobart, Tasmania, 7001, Australia
- ARC Training Centre for Forest Value, Hobart, Tasmania, Australia
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Constitutive Defense Strategy of Coffee Under Field Conditions: A Comparative Assessment of Resistant and Susceptible Cultivars to Rust. Mol Biotechnol 2021; 64:263-277. [PMID: 34595725 DOI: 10.1007/s12033-021-00405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Coffea arabica is the most economically important coffee species worldwide. However, its production is severely limited by diseases such as rust. The mechanisms underlying constitutive defense responses in coffee are still poorly understood, compared with induced defense mechanisms. We aimed to characterize constitutive defense responses of thirteen cultivars of C. arabica. Cultivars were classified under field conditions according to the level of resistance to rust: resistant (R), moderately resistant (MR), and susceptible (S). Based on this classification, the stability of eight reference genes (RGs) was evaluated. The most stable RGs were EF1α, APT1, and 24S. We also evaluated the expression of CaWRKY1, CaPAL1, CaCAD1, and CaPOX1, and activities of PAL, CAD, and POX, which are involved in lignin biosynthesis, and leaf content of total phenolic compounds and lignin. Gene expression and enzymatic activity were not correlated with defense metabolites in the R cultivar group but showed a negative correlation with phenolic compounds in MR cultivars. Cultivar S showed positive correlations of gene expression and enzyme activity with phenolic compounds. These results may assist coffee breeding programs regarding selection of genotypes and in optimization of rust resistance.
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Šķipars V, Ruņģis D. Transcript Dynamics in Wounded and Inoculated Scots Pine. Int J Mol Sci 2021; 22:ijms22041505. [PMID: 33546141 PMCID: PMC7913219 DOI: 10.3390/ijms22041505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 11/16/2022] Open
Abstract
Comparative transcriptome analysis provides a useful tool for the exploration of plant-pathogen interaction by allowing in-depth comparison of gene expression between unaffected, inoculated and wounded organisms. Here we present the results of comparative transcriptome analysis in genetically identical one-year-old Scots pine ramets after wounding and inoculation with Heterobasidion annosum. We identified 230 genes that were more than 2-fold upregulated in inoculated samples (compared to controls) and 116 downregulated genes. Comparison of inoculated samp les with wounded samples identified 32 differentially expressed genes (30 were upregulated after inoculation). Several of the genes upregulated after inoculation are involved in protection from oxidative stress, while genes involved in photosynthesis, water transport and drought stress tolerance were downregulated. An NRT3 family protein was the most upregulated transcript in response to both inoculation and wounding, while a U-box domain-containing protein gene was the most upregulated gene comparing inoculation to wounding. The observed transcriptome dynamics suggest involvement of auxin, ethylene, jasmonate, gibberellin and reactive oxygen species pathways and cell wall modification regulation in response to H. annosum infection. The results are compared to methyl jasmonate induced transcriptome dynamics.
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Whitehill JG, Bohlmann J. A molecular and genomic reference system for conifer defence against insects. PLANT, CELL & ENVIRONMENT 2019; 42:2844-2859. [PMID: 31042808 PMCID: PMC6852437 DOI: 10.1111/pce.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 05/29/2023]
Abstract
Insect pests are part of natural forest ecosystems contributing to forest rejuvenation but can also cause ecological disturbance and economic losses that are expected to increase with climate change. The white pine or spruce weevil (Pissodes strobi) is a pest of conifer forests in North America. Weevil-host interactions with various spruce (Picea) species have been explored as a genomic and molecular reference system for conifer defence against insects. Interactions occur in two major phases of the insect life cycle. In the exophase, adult weevils are free-moving and display behaviour of host selection for oviposition that is affected by host traits. In the endophase, insects live within the host where mobility and development from eggs to young adults are affected by a complex system of host defences. Genetic resistance exists in several spruce species and involves synergism of constitutive and induced chemical and physical defences that comprise the conifer defence syndrome. Here, we review conifer defences that disrupt the weevil life cycle and mechanisms by which trees resist weevil attack. We highlight molecular and genomic aspects and a possible role for the weevil microbiome. Knowledge of this conifer defence system is supporting forest health strategies and tree breeding for insect resistance.
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Affiliation(s)
| | - Jörg Bohlmann
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of BotanyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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Ruiz Daniels R, Taylor RS, Serra-Varela MJ, Vendramin GG, González-Martínez SC, Grivet D. Inferring selection in instances of long-range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin. Mol Ecol 2018; 27:3331-3345. [PMID: 29972881 DOI: 10.1111/mec.14786] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 01/03/2023]
Abstract
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions ("allele surfing") can be a confounding factor. To address this potential issue, we first assess the long-range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2), focusing on bioclimatic variables important for the species' adaptation (i.e., temperature, precipitation and water availability); and (b) FST -related methods (pcadapt). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species' past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long-range colonizations.
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Affiliation(s)
- Rose Ruiz Daniels
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
| | | | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Department of Plant Production and Forest Resources, University of Valladolid, Palencia, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
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Porth I, White R, Jaquish B, Ritland K. Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce. THE NEW PHYTOLOGIST 2018; 218:1349-1359. [PMID: 29504642 DOI: 10.1111/nph.15075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.
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Affiliation(s)
- Ilga Porth
- Département des Sciences du Bois et de la Forêt, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Richard White
- Department of Statistics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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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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Nemesio-Gorriz M, Hammerbacher A, Ihrmark K, Källman T, Olson Å, Lascoux M, Stenlid J, Gershenzon J, Elfstrand M. Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies. PLANT PHYSIOLOGY 2016; 171:2671-81. [PMID: 27317690 PMCID: PMC4972290 DOI: 10.1104/pp.16.00685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/11/2016] [Indexed: 05/18/2023]
Abstract
Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.
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Affiliation(s)
- Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Almuth Hammerbacher
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Thomas Källman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Martin Lascoux
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jonathan Gershenzon
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
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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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Kavembe GD, Franchini P, Irisarri I, Machado-Schiaffino G, Meyer A. Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa. J Mol Evol 2015; 81:90-109. [DOI: 10.1007/s00239-015-9696-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
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Raherison ESM, Giguère I, Caron S, Lamara M, MacKay JJ. Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures. THE NEW PHYTOLOGIST 2015; 207:172-187. [PMID: 25728802 PMCID: PMC5024012 DOI: 10.1111/nph.13343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 01/18/2015] [Indexed: 05/13/2023]
Abstract
Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation. We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue-based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation. Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure.
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Affiliation(s)
- Elie S M Raherison
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Isabelle Giguère
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Sébastien Caron
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Mebarek Lamara
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - John J MacKay
- Department of Plant Sciences, University of Oxford, OX1 3RB, Oxford, UK
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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Kersten B, Ghirardo A, Schnitzler JP, Kanawati B, Schmitt-Kopplin P, Fladung M, Schroeder H. Integrated transcriptomics and metabolomics decipher differences in the resistance of pedunculate oak to the herbivore Tortrix viridana L. BMC Genomics 2013; 14:737. [PMID: 24160444 PMCID: PMC4007517 DOI: 10.1186/1471-2164-14-737] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The interaction between insect pests and their host plants is a never-ending race of evolutionary adaption. Plants have developed an armament against insect herbivore attacks, and attackers continuously learn how to address it. Using a combined transcriptomic and metabolomic approach, we investigated the molecular and biochemical differences between Quercus robur L. trees that resisted (defined as resistant oak type) or were susceptible (defined as susceptible oak type) to infestation by the major oak pest, Tortrix viridana L. RESULTS Next generation RNA sequencing revealed hundreds of genes that exhibited constitutive and/or inducible differential expression in the resistant oak compared to the susceptible oak. Distinct differences were found in the transcript levels and the metabolic content with regard to tannins, flavonoids, and terpenoids, which are compounds involved in the defence against insect pests. The results of our transcriptomic and metabolomic analyses are in agreement with those of a previous study in which we showed that female moths prefer susceptible oaks due to their specific profile of herbivore-induced volatiles. These data therefore define two oak genotypes that clearly differ on the transcriptomic and metabolomic levels, as reflected by their specific defensive compound profiles. CONCLUSIONS We conclude that the resistant oak type seem to prefer a strategy of constitutive defence responses in contrast to more induced defence responses of the susceptible oaks triggered by feeding. These results pave the way for the development of biomarkers for an early determination of potentially green oak leaf roller-resistant genotypes in natural pedunculate oak populations in Europe.
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Affiliation(s)
| | | | | | | | | | | | - Hilke Schroeder
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927, Grosshansdorf, Germany.
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Buschiazzo E, Ritland C, Bohlmann J, Ritland K. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol 2012; 12:8. [PMID: 22264329 PMCID: PMC3328258 DOI: 10.1186/1471-2148-12-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 01/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. RESULTS Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10(-9) synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. CONCLUSIONS Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
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Affiliation(s)
- Emmanuel Buschiazzo
- Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
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