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Cruz-Nicolás J, Jaramillo-Correa JP, Gernandt DS. Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus). Mol Phylogenet Evol 2024; 192:108011. [PMID: 38195010 DOI: 10.1016/j.ympev.2024.108011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/08/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
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2
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Wang P, Zhou J, Sun W, Li H, Li D, Zhuge Q. Characteristics and function of the pathogenesis-related protein 1 gene family in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111857. [PMID: 37673220 DOI: 10.1016/j.plantsci.2023.111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
The pathogen-associated protein 1 (PR1) plays an important role in plant response to biotic and abiotic stresses. In this study, 17 PtPR1 genes were identified in Populus trichocarpa genome. The 17 PtPR1 genes were distributed on 7 chromosomes, and divided into A, B subfamilies by evolutionary tree analysis. RTqPCR analysis showed that the PtPR1 gene family showed different degrees of response to drought stress. PtPR1 genes showed changes in expression in response to fungal pathogen Septotinia populiperda or insect attacks (Nausinoe geometralis, Hyphantria cunea). Also, we found that subfamily B of PtPR1 may play an important role in response to biotic stress. We identified a new resistance gene PtPR1A. Overexpression of PtPR1A in Arabidopsis thaliana significantly enhanced the resistance to Pseudomonas syringae, while overexpression of PtPR1A in poplar significantly enhanced the resistance to S. populiperda. The present study investigates the expression pattern of the PtPR1 genes under biotic and abiotic stresses, and it found that the characteristics of the PtPR1 genes diverged, which provided a theoretical basis for the further study of the PtPR1 genes in the plant defense response.
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Affiliation(s)
- Pu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jie Zhou
- Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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3
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Visser EA, Kampmann TP, Wegrzyn JL, Naidoo S. Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms. PLANT, CELL & ENVIRONMENT 2023; 46:1705-1725. [PMID: 36541367 DOI: 10.1111/pce.14522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3- and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible). Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.
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Affiliation(s)
- Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tamanique P Kampmann
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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4
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Hussain A, Farooq M, Naqvi RZ, Aslam MQ, Siddiqui HA, Amin I, Liu C, Liu X, Scheffler J, Asif M, Mansoor S. Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. Mol Biotechnol 2023; 65:34-51. [PMID: 35778659 DOI: 10.1007/s12033-022-00527-8] [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: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Cotton is an important crop that produces fiber and cottonseed oil for the textile and oil industry. However, cotton leaf curl virus disease (CLCuD) stress is limiting its yield in several Asian countries. In this study, we have sequenced Mac7 accession, a Gossypium hirsutum resistance source against several biotic stresses. By aligning with the Gossypium hirsutum (AD1) 'TM-1' genome, a total of 4.7 and 1.2 million SNPs and InDels were identified in the Mac7 genome. The gene ontology and metabolic pathway enrichment indicated SNPs and InDels role in nucleotide bindings, secondary metabolite synthesis, and plant-pathogen interaction pathways. Furthermore, the RNA-seq data in different tissues and qPCR expression profiling under CLCuD provided individual gene roles in resistant and susceptible accessions. Interestingly, the differential NLR genes demonstrated higher expression in resistant plants rather than in susceptible plants expression. The current resequencing results may provide primary data to identify DNA resistance markers which will be helpful in marker-assisted breeding for development of Mac7-derived resistance lines.
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Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.,Bioinformatics Group, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | | | - Xin Liu
- Beijing Genomics Institute (BGI), Shenzhen, China
| | - Jodi Scheffler
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture-Agricultural Research Service, USDA-ARS), 141 Experimental Station Road, Stoneville, MS, USA
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.
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Zhou R, Dong Y, Liu X, Feng S, Wang C, Ma X, Liu J, Liang Q, Bao Y, Xu S, Lang X, Gai S, Yang KQ, Fang H. JrWRKY21 interacts with JrPTI5L to activate the expression of JrPR5L for resistance to Colletotrichum gloeosporioides in walnut. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1152-1166. [PMID: 35765867 DOI: 10.1111/tpj.15883] [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: 12/20/2021] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Walnut (Juglans regia L.) anthracnose, induced by Colletotrichum gloeosporioides, is a catastrophic disease impacting the walnut industry in China. Although WRKY transcription factors play a key role in plant immunity, the function of the WRKY gene family in walnut resistance to C. gloeosporioides is not clear. Here, through transcriptome sequencing and quantitative real-time polymerase chain reaction (qRT-PCR), we identified a differentially expressed gene, JrWRKY21, that was significantly upregulated upon C. gloeosporioides infection in walnut. JrWRKY21 positively regulated walnut resistance to C. gloeosporioides, as demonstrated by virus-induced gene silencing and transient gene overexpression. Additionally, JrWRKY21 directly interacted with the transcriptional activator of the pathogenesis-related (PR) gene JrPTI5L in vitro and in vivo, and could bind to the W-box in the JrPTI5L promoter for transcriptional activation. Moreover, JrPTI5L could induce the expression of the PR gene JrPR5L through binding to the GCCGAC motif in the promoter. Our data support that JrWRKY21 can indirectly activate the expression of the JrPR5L gene via the WRKY21-PTI5L protein complex to promote resistance against C. gloeosporioides in walnut. The results will enhance our understanding of the mechanism behind walnut disease resistance and facilitate the genetic improvement of walnut by molecular breeding for anthracnose-resistant varieties.
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Affiliation(s)
- Rui Zhou
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xia Liu
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Shan Feng
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Jianning Liu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Yan Bao
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Shengyi Xu
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Xinya Lang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian, Shandong Province, China
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Full-Length Transcriptome Sequencing-Based Analysis of Pinus sylvestris var. mongolica in Response to Sirex noctilio Venom. INSECTS 2022; 13:insects13040338. [PMID: 35447780 PMCID: PMC9029201 DOI: 10.3390/insects13040338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Sirex noctilio, as a devastating international forestry quarantine pest whose venom can cause a series of physiological changes in the host plants, such as needle wilting, yellowing, decreased transpiration rate and increased respiration rate, etc. In this study, a full-length reference transcript of Pinus sylvestris var. mongolica was constructed by combining second- and third-generation transcriptome sequencing technologies. We also identified the specific expression genes and transcription factors of P. sylvestris var. mongolica under S. noctilio venom and wounding stress. S. noctilio venom mainly induced the expression of genes related to ROS, GAPDH and GPX, and mechanical damage mainly induced the photosynthesis−related genes. The results provide a better understanding of the molecular regulation of pine trees in response to S. noctilio venom. Abstract Sirex noctilio is a major international quarantine pest that recently emerged in northeast China to specifically invade conifers. During female oviposition, venom is injected into the host together with its symbiotic fungus to alter the normal Pinus physiology and weaken or even kill the tree. In China, the Mongolian pine (Pinus sylvestris var. mongolica), an important wind-proof and sand-fixing species, is the unique host of S. noctilio. To explore the interplay between S. noctilio venom and Mongolian pine, we performed a transcriptome comparative analysis of a 10-year-old Mongolian pine after wounding and inoculation with S. noctilio venom. The analysis was performed at 12 h, 24 h and 72 h. PacBio ISO-seq was used and integrated with RNA-seq to construct an accurate full-length transcriptomic database. We obtained 52,963 high-precision unigenes, consisting of 48,654 (91.86%) unigenes that were BLASTed to known sequences in the public database and 4309 unigenes without any annotation information, which were presumed to be new genes. The number of differentially expressed genes (DEGs) increased with the treatment time, and the DEGs were most abundant at 72 h. A total of 706 inoculation-specific DEGs (475 upregulated and 231 downregulated) and 387 wounding-specific DEGs (183 upregulated and 204 downregulated) were identified compared with the control. Under venom stress, we identified 6 DEGs associated with reactive oxygen species (ROS) and 20 resistance genes in Mongolian pine. Overall, 52 transcription factors (TFs) were found under venom stress, 45 of which belonged to the AP2/ERF TF family and were upregulated. A total of 13 genes related to the photosystem, 3 genes related photo-regulation, and 9 TFs were identified under wounding stress. In conclusion, several novel putative genes were found in Mongolian pine by PacBio ISO seq. Meanwhile, we also identified various genes that were resistant to S. noctilio venom, such as GAPDH, GPX, CAT, FL2, CERK1, and HSP83A, etc.
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Zamora-Ballesteros C, Martín-García J, Suárez-Vega A, Diez JJ. Genome-wide identification and characterization of Fusarium circinatum-responsive lncRNAs in Pinus radiata. BMC Genomics 2022; 23:194. [PMID: 35264109 PMCID: PMC8908662 DOI: 10.1186/s12864-022-08408-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Background One of the most promising strategies of Pine Pitch Canker (PPC) management is the use of reproductive plant material resistant to the disease. Understanding the complexity of plant transcriptome that underlies the defence to the causal agent Fusarium circinatum, would greatly facilitate the development of an accurate breeding program. Long non-coding RNAs (lncRNAs) are emerging as important transcriptional regulators under biotic stresses in plants. However, to date, characterization of lncRNAs in conifer trees has not been reported. In this study, transcriptomic identification of lncRNAs was carried out using strand-specific paired-end RNA sequencing, from Pinus radiata samples inoculated with F. circinatum at an early stage of infection. Results Overall, 13,312 lncRNAs were predicted through a bioinformatics approach, including long intergenic non-coding RNAs (92.3%), antisense lncRNAs (3.3%) and intronic lncRNAs (2.9%). Compared with protein-coding RNAs, pine lncRNAs are shorter, have lower expression, lower GC content and harbour fewer and shorter exons. A total of 164 differentially expressed (DE) lncRNAs were identified in response to F. circinatum infection in the inoculated versus mock-inoculated P. radiata seedlings. The predicted cis-regulated target genes of these pathogen-responsive lncRNAs were related to defence mechanisms such as kinase activity, phytohormone regulation, and cell wall reinforcement. Co-expression network analysis of DE lncRNAs, DE protein-coding RNAs and lncRNA target genes also indicated a potential network regulating pectinesterase activity and cell wall remodelling. Conclusions This study presents the first comprehensive genome-wide analysis of P. radiata lncRNAs and provides the basis for future functional characterizations of lncRNAs in relation to pine defence responses against F. circinatum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08408-9.
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Affiliation(s)
- Cristina Zamora-Ballesteros
- Department of Vegetal Production and Forest Resources, University of Valladolid, Av Madrid 44, 34004 Palencia, Spain. .,Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain.
| | - Jorge Martín-García
- Department of Vegetal Production and Forest Resources, University of Valladolid, Av Madrid 44, 34004 Palencia, Spain.,Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, University of León, Campus de Vegazana s/n, 24071 León, Spain
| | - Julio Javier Diez
- Department of Vegetal Production and Forest Resources, University of Valladolid, Av Madrid 44, 34004 Palencia, Spain.,Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
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Amaral J, Valledor L, Alves A, Martín-García J, Pinto G. Studying tree response to biotic stress using a multi-disciplinary approach: The pine pitch canker case study. FRONTIERS IN PLANT SCIENCE 2022; 13:916138. [PMID: 36160962 PMCID: PMC9501998 DOI: 10.3389/fpls.2022.916138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/18/2022] [Indexed: 05/09/2023]
Abstract
In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused on the pathogen itself or on determining the levels of susceptibility of different hosts to F. circinatum infection. However, over the last years, plenty of information on the mechanisms that may explain the susceptibility or resistance to PPC has been published. This data are useful to better understand tree response to biotic stress and, most importantly, to aid the development of innovative and scientific-based disease control measures. This review gathers and discusses the main advances on PPC knowledge, especially focusing on multi-disciplinary studies investigating the response of pines with different levels of susceptibility to PPC upon infection. After an overview of the general knowledge of the disease, the importance of integrating information from physiological and Omics studies to unveil the mechanisms behind PPC susceptibility/resistance and to develop control strategies is explored. An extensive review of the main host responses to PPC was performed, including changes in water relations, signalling (ROS and hormones), primary metabolism, and defence (resin, phenolics, and PR proteins). A general picture of pine response to PPC is suggested according to the host susceptibility level and the next steps and gaps on PPC research are pointed out.
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Affiliation(s)
- Joana Amaral
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
- *Correspondence: Joana Amaral,
| | - Luis Valledor
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
- University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Artur Alves
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Jorge Martín-García
- Department of Vegetal Production and Forest Resources, University of Valladolid, Palencia, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, Spain
| | - Glória Pinto
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
- Glória Pinto,
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9
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Reboledo G, Agorio AD, Vignale L, Batista-García RA, Ponce De León I. Transcriptional profiling reveals conserved and species-specific plant defense responses during the interaction of Physcomitrium patens with Botrytis cinerea. PLANT MOLECULAR BIOLOGY 2021; 107:365-385. [PMID: 33521880 DOI: 10.1007/s11103-021-01116-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Evolutionary conserved defense mechanisms present in extant bryophytes and angiosperms, as well as moss-specific defenses are part of the immune response of Physcomitrium patens. Bryophytes and tracheophytes are descendants of early land plants that evolved adaptation mechanisms to cope with different kinds of terrestrial stresses, including drought, variations in temperature and UV radiation, as well as defense mechanisms against microorganisms present in the air and soil. Although great advances have been made on pathogen perception and subsequent defense activation in angiosperms, limited information is available in bryophytes. In this study, a transcriptomic approach uncovered the molecular mechanisms underlying the defense response of the bryophyte Physcomitrium patens (previously Physcomitrella patens) against the important plant pathogen Botrytis cinerea. A total of 3.072 differentially expressed genes were significantly affected during B. cinerea infection, including genes encoding proteins with known functions in angiosperm immunity and involved in pathogen perception, signaling, transcription, hormonal signaling, metabolic pathways such as shikimate and phenylpropanoid, and proteins with diverse role in defense against biotic stress. Similarly as in other plants, B. cinerea infection leads to downregulation of genes involved in photosynthesis and cell cycle progression. These results highlight the existence of evolutionary conserved defense responses to pathogens throughout the green plant lineage, suggesting that they were probably present in the common ancestors of land plants. Moreover, several genes acquired by horizontal transfer from prokaryotes and fungi, and a high number of P. patens-specific orphan genes were differentially expressed during B. cinerea infection, suggesting that they are important players in the moss immune response.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astri D Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Lucía Vignale
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | | | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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Zamora-Ballesteros C, Pinto G, Amaral J, Valledor L, Alves A, Diez JJ, Martín-García J. Dual RNA-Sequencing Analysis of Resistant ( Pinus pinea) and Susceptible ( Pinus radiata) Hosts during Fusarium circinatum Challenge. Int J Mol Sci 2021; 22:5231. [PMID: 34063405 PMCID: PMC8156185 DOI: 10.3390/ijms22105231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.
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Affiliation(s)
- Cristina Zamora-Ballesteros
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
| | - Gloria Pinto
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Joana Amaral
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Luis Valledor
- Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain;
| | - Artur Alves
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Julio J. Diez
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
| | - Jorge Martín-García
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
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11
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Pérez-Torres CA, Ibarra-Laclette E, Hernández-Domínguez EE, Rodríguez-Haas B, Pérez-Lira AJ, Villafán E, Alonso-Sánchez A, García-Ávila CDJ, Ramírez-Pool JA, Sánchez-Rangel D. Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PeerJ 2021; 9:e11215. [PMID: 33954045 PMCID: PMC8052963 DOI: 10.7717/peerj.11215] [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: 10/05/2020] [Accepted: 03/15/2021] [Indexed: 01/13/2023] Open
Abstract
Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly, the alcohol metabolic process biological category had the highest number of upregulated genes, and the enzyme group in this category may play an important role in the mechanisms of secondary metabolite detoxification. Hydrolytic enzymes, such as endoglucanases and a pectate lyase, were also identified, as well as some proteases. In conclusion, our research was conducted mainly to explain how the vascular tissue of a recognized host of the ambrosia complex responds during F. kuroshium infection since Fusarium dieback is an ambrosia beetle-vectored disease and many variables facilitate its establishment.
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Affiliation(s)
- Claudia-Anahí Pérez-Torres
- Catedrático CONACyT en la Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | | | | | | | - Alan-Josué Pérez-Lira
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | | | - Clemente de Jesús García-Ávila
- Centro Nacional de Referencia Fitosanitaria, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac, Estado de México, México
| | - José-Abrahán Ramírez-Pool
- Centro Nacional de Referencia Fitosanitaria, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac, Estado de México, México.,Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Diana Sánchez-Rangel
- Catedrático CONACyT en la Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
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12
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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13
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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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14
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Joshi V, Joshi N, Vyas A, Jadhav S. Pathogenesis-related proteins: Role in plant defense. BIOCONTROL AGENTS AND SECONDARY METABOLITES 2021:573-590. [PMID: 0 DOI: 10.1016/b978-0-12-822919-4.00025-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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15
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Irigoyen ML, Garceau DC, Bohorquez-Chaux A, Lopez-Lavalle LAB, Perez-Fons L, Fraser PD, Walling LL. Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid. BMC Genomics 2020; 21:93. [PMID: 31996126 PMCID: PMC6990599 DOI: 10.1186/s12864-019-6443-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/29/2019] [Indexed: 11/16/2022] Open
Abstract
Background Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. Results The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. Conclusions This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.
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Affiliation(s)
- Maria L Irigoyen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Danielle C Garceau
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | | | - Laura Perez-Fons
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Linda L Walling
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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16
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Hernandez-Escribano L, Visser EA, Iturritxa E, Raposo R, Naidoo S. The transcriptome of Pinus pinaster under Fusarium circinatum challenge. BMC Genomics 2020; 21:28. [PMID: 31914917 PMCID: PMC6950806 DOI: 10.1186/s12864-019-6444-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/30/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circinatum, the molecular mechanisms of defense in this host are still unknown. Phytohormones produced by the plant and by the pathogen are known to play a crucial role in determining the outcome of plant-pathogen interactions. Therefore, the aim of this study was to determine the role of phytohormones in F. circinatum virulence, that compromise host resistance. RESULTS A high quality P. pinaster de novo transcriptome assembly was generated, represented by 24,375 sequences from which 17,593 were full length genes, and utilized to determine the expression profiles of both organisms during the infection process at 3, 5 and 10 days post-inoculation using a dual RNA-sequencing approach. The moderate resistance shown by Pinus pinaster at the early time points may be explained by the expression profiles pertaining to early recognition of the pathogen, the induction of pathogenesis-related proteins and the activation of complex phytohormone signaling pathways that involves crosstalk between salicylic acid, jasmonic acid, ethylene and possibly auxins. Moreover, the expression of F. circinatum genes related to hormone biosynthesis suggests manipulation of the host phytohormone balance to its own benefit. CONCLUSIONS We hypothesize three key steps of host manipulation: perturbing ethylene homeostasis by fungal expression of genes related to ethylene biosynthesis, blocking jasmonic acid signaling by coronatine insensitive 1 (COI1) suppression, and preventing salicylic acid biosynthesis from the chorismate pathway by the synthesis of isochorismatase family hydrolase (ICSH) genes. These results warrant further testing in F. circinatum mutants to confirm the mechanism behind perturbing host phytohormone homeostasis.
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Affiliation(s)
- Laura Hernandez-Escribano
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Investigación Forestal (INIA-CIFOR), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Eugenia Iturritxa
- NEIKER, Granja Modelo de Arkaute, Apdo 46, 01080, Vitoria-Gasteiz, Spain
| | - Rosa Raposo
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Investigación Forestal (INIA-CIFOR), Madrid, Spain
- Instituto de Gestión Forestal Sostenible (iuFOR), Universidad de Valladolid/INIA, Valladolid, Spain
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa.
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17
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Teshome DT, Zharare GE, Naidoo S. The Threat of the Combined Effect of Biotic and Abiotic Stress Factors in Forestry Under a Changing Climate. FRONTIERS IN PLANT SCIENCE 2020; 11:601009. [PMID: 33329666 PMCID: PMC7733969 DOI: 10.3389/fpls.2020.601009] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/05/2020] [Indexed: 05/11/2023]
Abstract
Plants encounter several biotic and abiotic stresses, usually in combination. This results in major economic losses in agriculture and forestry every year. Climate change aggravates the adverse effects of combined stresses and increases such losses. Trees suffer even more from the recurrence of biotic and abiotic stress combinations owing to their long lifecycle. Despite the effort to study the damage from individual stress factors, less attention has been given to the effect of the complex interactions between multiple biotic and abiotic stresses. In this review, we assess the importance, impact, and mitigation strategies of climate change driven interactions between biotic and abiotic stresses in forestry. The ecological and economic importance of biotic and abiotic stresses under different combinations is highlighted by their contribution to the decline of the global forest area through their direct and indirect roles in forest loss and to the decline of biodiversity resulting from local extinction of endangered species of trees, emission of biogenic volatile organic compounds, and reduction in the productivity and quality of forest products and services. The abiotic stress factors such as high temperature and drought increase forest disease and insect pest outbreaks, decrease the growth of trees, and cause tree mortality. Reports of massive tree mortality events caused by "hotter droughts" are increasing all over the world, affecting several genera of trees including some of the most important genera in plantation forests, such as Pine, Poplar, and Eucalyptus. While the biotic stress factors such as insect pests, pathogens, and parasitic plants have been reported to be associated with many of these mortality events, a considerable number of the reports have not taken into account the contribution of such biotic factors. The available mitigation strategies also tend to undermine the interactive effect under combined stresses. Thus, this discussion centers on mitigation strategies based on research and innovation, which build on models previously used to curb individual stresses.
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Affiliation(s)
- Demissew Tesfaye Teshome
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- *Correspondence: Sanushka Naidoo,
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19
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Thole V, Bassard JE, Ramírez-González R, Trick M, Ghasemi Afshar B, Breitel D, Hill L, Foito A, Shepherd L, Freitag S, Nunes dos Santos C, Menezes R, Bañados P, Naesby M, Wang L, Sorokin A, Tikhonova O, Shelenga T, Stewart D, Vain P, Martin C. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 2019; 20:995. [PMID: 31856735 PMCID: PMC6924045 DOI: 10.1186/s12864-019-6183-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. RESULTS To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige. CONCLUSIONS We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.
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Affiliation(s)
- Vera Thole
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
- Present address: Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 Rue General Zimmer, 67084 Strasbourg, France
| | | | - Martin Trick
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bijan Ghasemi Afshar
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Dario Breitel
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present address: Tropic Biosciences UK LTD, Norwich Research Park, Norwich, NR4 7UG UK
| | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | | | - Sabine Freitag
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
| | - Cláudia Nunes dos Santos
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Rua Câmara Pestana 6, 1150-082 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pilar Bañados
- Facultad De Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna Ote, 4860 Macul, Chile
| | | | - Liangsheng Wang
- Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Artem Sorokin
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Olga Tikhonova
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Tatiana Shelenga
- Fruit Crops Genetic Resources Department, N. I. Vavilov Research Institute of Plant Industry, B. Morskaya Street 42-44, St. Petersburg, 190000 Russia
| | - Derek Stewart
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA UK
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Philippe Vain
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019; 9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
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Visser EA, Wegrzyn JL, Steenkamp ET, Myburg AA, Naidoo S. Dual RNA-Seq Analysis of the Pine- Fusarium circinatum Interaction in Resistant ( Pinus tecunumanii) and Susceptible ( Pinus patula) Hosts. Microorganisms 2019; 7:E315. [PMID: 31487786 PMCID: PMC6780516 DOI: 10.3390/microorganisms7090315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022] Open
Abstract
Fusarium circinatum poses a serious threat to many pine species in both commercial and natural pine forests. Knowledge regarding the molecular basis of pine-F. circinatum host-pathogen interactions could assist efforts to produce more resistant planting stock. This study aimed to identify molecular responses underlying resistance against F. circinatum. A dual RNA-seq approach was used to investigate host and pathogen expression in F. circinatum challenged Pinus tecunumanii (resistant) and Pinus patula (susceptible), at three- and seven-days post inoculation. RNA-seq reads were mapped to combined host-pathogen references for both pine species to identify differentially expressed genes (DEGs). F. circinatum genes expressed during infection showed decreased ergosterol biosynthesis in P. tecunumanii relative to P. patula. For P. tecunumanii, enriched gene ontologies and DEGs indicated roles for auxin-, ethylene-, jasmonate- and salicylate-mediated phytohormone signalling. Correspondingly, key phytohormone signaling components were down-regulated in P. patula. Key F. circinatum ergosterol biosynthesis genes were expressed at lower levels during infection of the resistant relative to the susceptible host. This study further suggests that coordination of phytohormone signaling is required for F. circinatum resistance in P. tecunumanii, while a comparatively delayed response and impaired phytohormone signaling contributes to susceptibility in P. patula.
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Affiliation(s)
- Erik A Visser
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Centre for Bioinformatics and Computational Biology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
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Carella P, Gogleva A, Hoey DJ, Bridgen AJ, Stolze SC, Nakagami H, Schornack S. Conserved Biochemical Defenses Underpin Host Responses to Oomycete Infection in an Early-Divergent Land Plant Lineage. Curr Biol 2019; 29:2282-2294.e5. [PMID: 31303485 DOI: 10.1016/j.cub.2019.05.078] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/28/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
Abstract
The expansion of plants onto land necessitated the evolution of robust defense strategies to protect against a wide array of microbial invaders. Whereas host responses to microbial colonization are extensively explored in evolutionarily young land plant lineages such as angiosperms, we know relatively little about plant-pathogen interactions in early-diverging land plants thought to better represent the ancestral state. Here, we define the transcriptional and proteomic response of the early-divergent liverwort Marchantia polymorpha to infection with the oomycete pathogen Phytophthora palmivora. We uncover a robust molecular response to oomycete colonization in Marchantia that consists of conserved land plant gene families. Direct macroevolutionary comparisons of host infection responses in Marchantia and the model angiosperm Nicotiana benthamiana further reveal a shared set of orthologous microbe-responsive genes that include members of the phenylpropanoid metabolic pathway. In addition, we identify a role for the Marchantia R2R3-MYB transcription factor MpMyb14 in activating phenylpropanoid (flavonoid) biosynthesis during oomycete infection. Mpmyb14 mutants infected with P. palmivora fail to activate phenylpropanoid biosynthesis gene expression and display enhanced disease susceptibility compared to wild-type plants. Conversely, the ectopic induction of MpMyb14 led to the accumulation of anthocyanin-like pigments and dramatically enhanced liverwort resistance to P. palmivora infection. Collectively, our results demonstrate that the Marchantia response to oomycete infection displays evolutionarily conserved features indicative of an ancestral pathogen deterrence strategy centered on phenylpropanoid-mediated biochemical defenses.
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Affiliation(s)
- Philip Carella
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Anna Gogleva
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - David John Hoey
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Anthony John Bridgen
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg, Cologne 50829, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg, Cologne 50829, Germany
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 EA3, UK.
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Naidoo S, Slippers B, Plett JM, Coles D, Oates CN. The Road to Resistance in Forest Trees. FRONTIERS IN PLANT SCIENCE 2019; 10:273. [PMID: 31001287 PMCID: PMC6455082 DOI: 10.3389/fpls.2019.00273] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/19/2019] [Indexed: 05/09/2023]
Abstract
In recent years, forests have been exposed to an unprecedented rise in pests and pathogens. This, coupled with the added challenge of climate change, renders forest plantation stock vulnerable to attack and severely limits productivity. Genotypes resistant to such biotic challenges are desired in plantation forestry to reduce losses. Conventional breeding has been a main avenue to obtain resistant genotypes. More recently, genetic engineering has become a viable approach to develop resistance against pests and pathogens in forest trees. Tree genomic resources have contributed to advancements in both these approaches. Genome-wide association studies and genomic selection in tree populations have accelerated breeding tools while integration of various levels of omics information facilitates the selection of candidate genes for genetic engineering. Furthermore, tree associations with non-pathogenic endophytic and subterranean microbes play a critical role in plant health and may be engineered in forest trees to improve resistance in the future. We look at recent studies in forest trees describing defense mechanisms using such approaches and propose the way forward to developing superior genotypes with enhanced resistance against biotic stress.
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Affiliation(s)
- Sanushka Naidoo
- Division of Genetics, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Bernard Slippers
- Division of Genetics, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jonathan M. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Donovin Coles
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Caryn N. Oates
- Division of Genetics, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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