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Zhang C, Xie W, Fu H, Chen Y, Chen H, Cai T, Yang Q, Zhuang Y, Zhong X, Chen K, Gao M, Liu F, Wan Y, Pandey MK, Varshney RK, Zhuang W. Whole genome resequencing identifies candidate genes and allelic diagnostic markers for resistance to Ralstonia solanacearum infection in cultivated peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1048168. [PMID: 36684803 PMCID: PMC9845939 DOI: 10.3389/fpls.2022.1048168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Bacterial wilt disease (BWD), caused by Ralstonia solanacearum is a major challenge for peanut production in China and significantly affects global peanut field productivity. It is imperative to identify genetic loci and putative genes controlling resistance to R. solanacearum (RRS). Therefore, a sequencing-based trait mapping approach termed "QTL-seq" was applied to a recombination inbred line population of 581 individuals from the cross of Yueyou 92 (resistant) and Xinhuixiaoli (susceptible). A total of 381,642 homozygous single nucleotide polymorphisms (SNPs) and 98,918 InDels were identified through whole genome resequencing of resistant and susceptible parents for RRS. Using QTL-seq analysis, a candidate genomic region comprising of 7.2 Mb (1.8-9.0 Mb) was identified on chromosome 12 which was found to be significantly associated with RRS based on combined Euclidean Distance (ED) and SNP-index methods. This candidate genomic region had 180 nonsynonymous SNPs and 14 InDels that affected 75 and 11 putative candidate genes, respectively. Finally, eight nucleotide binding site leucine rich repeat (NBS-LRR) putative resistant genes were identified as the important candidate genes with high confidence. Two diagnostic SNP markers were validated and revealed high phenotypic variation in the different resistant and susceptible RIL lines. These findings advocate the expediency of the QTL-seq approach for precise and rapid identification of candidate genomic regions, and the development of diagnostic markers that are applicable in breeding disease-resistant peanut varieties.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Wenping Xie
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiwen Fu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuting Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhui Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Zhong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kun Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijia Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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Yang B, Zhao Y, Guo Z. Research Progress and Prospect of Alfalfa Resistance to Pathogens and Pests. PLANTS 2022; 11:plants11152008. [PMID: 35956485 PMCID: PMC9370300 DOI: 10.3390/plants11152008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/21/2022]
Abstract
Alfalfa is one of the most important legume forages in the world and contributes greatly to the improvement of ecosystems, nutrition, and food security. Diseases caused by pathogens and pests severely restrict the production of alfalfa. Breeding resistant varieties is the most economical and effective strategy for the control of alfalfa diseases and pests, and the key to breeding resistant varieties is to identify important resistance genes. Plant innate immunity is the theoretical basis for identifying resistant genes and breeding resistant varieties. In recent years, the framework of plant immunity theory has been gradually formed and improved, and considerable progress has been made in the identification of alfalfa resistance genes and the revelation of the related mechanisms. In this review, we summarize the basic theory of plant immunity and identify alfalfa resistance genes to different pathogens and insects and resistance mechanisms. The current situation, problems, and future prospects of alfalfa resistance research are also discussed. Breeding resistant cultivars with effective resistance genes, together with other novel plant protection technologies, will greatly improve alfalfa production.
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Affiliation(s)
- Bo Yang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Du H, Yang J, Chen B, Zhang X, Xu X, Wen C, Geng S. Dual RNA-seq Reveals the Global Transcriptome Dynamics of Ralstonia solanacearum and Pepper ( Capsicum annuum) Hypocotyls During Bacterial Wilt Pathogenesis. PHYTOPATHOLOGY 2022; 112:630-642. [PMID: 34346759 DOI: 10.1094/phyto-01-21-0032-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial wilt, caused by Ralstonia solanacearum, is a serious disease in pepper. However, the interaction between the pathogen and pepper remains largely unknown. This study aimed to gain insights into determinants of pepper susceptibility and R. solanacearum pathogenesis. We assembled the complete genome of R. solanacearum strain Rs-SY1 and identified 5,106 predicted genes, including 84 type III effectors (T3E). RNA-seq was used to identify differentially expressed genes (DEGs) in susceptible pepper CM334 at 1 and 5 days postinoculation (dpi) with R. solanacearum. Dual RNA-seq was used to simultaneously capture transcriptome changes in the host and pathogen at 3 and 7 dpi. A total of 1,400, 3,335, 2,878, and 4,484 DEGs of pepper (PDEGs) were identified in the CM334 hypocotyls at 1, 3, 5, and 7 dpi, respectively. Functional enrichment of the PDEGs suggests that inducing ethylene production, suppression of photosynthesis, downregulation of polysaccharide metabolism, and weakening of cell wall defenses may contribute to successful infection by R. solanacearum. When comparing in planta and nutrient agar growth of the R. solanacearum, 218 and 1,042 DEGs of R. solanacearum (RDEGs) were detected at 3 and 7 dpi, respectively. Additional analysis of the RDEGs suggested that enhanced starch and sucrose metabolism, and upregulation of virulence factors may promote R. solanacearum colonization. Strikingly, 26 R. solanacearum genes were found to have similar DEG patterns during a variety of host-R. solanacearum interactions. This study provides a foundation for a better understanding of the transcriptional changes during pepper-R. solanacearum interactions and will aid in the discovery of potential susceptibility and virulence factors.
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Affiliation(s)
- Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiulan Xu
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
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Shi JL, Zai WS, Xiong ZL, Wan HJ, Wu WR. NB-LRR genes: characteristics in three Solanum species and transcriptional response to Ralstonia solanacearum in tomato. PLANTA 2021; 254:96. [PMID: 34655339 DOI: 10.1007/s00425-021-03745-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
NB-LRR genes in the three Solanum species showed specific constitution characteristics and evolved multiple clusters and duplicates. Some genes could respond to biotic stresses such as tomato bacterial wilt. Nucleotide-binding and leucine-rich repeat (NB-LRR, NLR) is a largest resistance gene family in plants, which plays a key role in response to biotic stresses. In this study, NB-LRR genes in cultivated tomato Solanum lycopersicum (Sl) and its wild relatives S. pennellii (Spe) and S. pimpinellifolium (Spi) were analyzed using bioinformatics approaches. In total, 238, 202 and 217 NB-LRR genes of 8 different types were found in Sl, Spe and Spi, respectively. The three species showed similar genomic characteristics. The NB-LRR genes were mainly distributed on chromosomes 4, 5 and 11 and located at the distal zones, forming multiple clusters and tandem duplicates. A large number of homologs appeared through gene expansion, with most Ka/Ks values being less than 1, indicating that purifying selection had occurred in evolution. These genes were mainly expressed in root and could respond to different biotic stresses. RT-qPCR analysis revealed that SlNLR genes could respond to tomato bacterial wilt, with SlNLR1 probably involved in the resistance response, whereas others being the opposite. The transcription factors (TFs) and interaction proteins that regulate target genes were mainly Dof, NAC and MYB families and kinases. The results provide a basis for the isolation and application of related genes in plant disease resistance breeding.
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Affiliation(s)
- Jian Lei Shi
- Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Wen Shan Zai
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Zhi Li Xiong
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Hong Jian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wei Ren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
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Wei Y, Zhang Y, Meng J, Wang Y, Zhong C, Ma H. Transcriptome and metabolome profiling in naturally infested Casuarina equisetifolia clones by Ralstonia solanacearum. Genomics 2021; 113:1906-1918. [PMID: 33771635 DOI: 10.1016/j.ygeno.2021.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/06/2021] [Accepted: 03/21/2021] [Indexed: 12/01/2022]
Abstract
Casuarina equisetifolia is an important pioneer tree and suffers from bacterial wilt caused by Ralstonia solanacearum. We collected resistant (R) and susceptible (S) C. equisetifolia clones naturally infected by R. solanacearum and compared their transcriptome and metabolome with a clone (CK) from a non-infested forest, in order to study their response and resistance to bacterial wilt. We identified 18 flavonoids differentially accumulated among the three clonal groups as potential selection biomarkers against R. solanacearum. Flavonoid synthesis-related genes were up-regulated in the resistant clones, probably enhancing accumulation of flavonoids and boosting resistance against bacterial wilt. The down-regulation of auxin/indoleacetic acid-related genes and up-regulation of brassinosteroid, salicylic acid and jasmonic acid-related differentially expressed genes in the R vs CK and R vs S clonal groups may have triggered defense signals and increased expression of defense-related genes against R. solanacearum. Overall, this study provides an important insight into pathogen-response and resistance to bacterial wilt in C. equisetifolia.
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Affiliation(s)
- Yongcheng Wei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
| | - Yong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
| | - Jingxiang Meng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
| | - Yujiao Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
| | - Chonglu Zhong
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
| | - Haibin Ma
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China.
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Du H, Wen C, Zhang X, Xu X, Yang J, Chen B, Geng S. Identification of a Major QTL ( qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper ( Capsicum annuum) Using SLAF-BSA and QTL Mapping. Int J Mol Sci 2019; 20:ijms20235887. [PMID: 31771239 PMCID: PMC6928630 DOI: 10.3390/ijms20235887] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/04/2019] [Accepted: 11/21/2019] [Indexed: 11/24/2022] Open
Abstract
The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt (BW), a major disease of pepper (Capsicum annuum). The genetic basis of resistance to this disease in pepper is not well known. This study aimed to identify BW resistance markers in pepper. Analysis of the dynamics of bioluminescent R. solanacearum colonization in reciprocal grafts of a resistant (BVRC 1) line and a susceptible (BVRC 25) line revealed that the resistant rootstock effectively suppressed the spreading of bacteria into the scion. The two clear-cut phenotypic distributions of the disease severity index in 440 F2 plants derived from BVRC 25 × BVRC 1 indicated that a major genetic factor as well as a few minor factors that control BW resistance. By specific-locus amplified fragment sequencing combined with bulked segregant analysis, two adjacent resistance-associated regions on chromosome 10 were identified. Quantitative trait (QTL) mapping revealed that these two regions belong to a single QTL, qRRs-10.1. The marker ID10-194305124, which reached a maximum log-likelihood value at 9.79 and accounted for 19.01% of the phenotypic variation, was located the closest to the QTL peak. A cluster of five predicted R genes and three defense-related genes, which are located in close proximity to the significant markers ID10-194305124 or ID10-196208712, are important candidate genes that may confer BW resistance in pepper.
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Gentzbittel L, Ben C, Mazurier M, Shin MG, Lorenz T, Rickauer M, Marjoram P, Nuzhdin SV, Tatarinova TV. WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants. Genome Biol 2019; 20:106. [PMID: 31138283 PMCID: PMC6537182 DOI: 10.1186/s13059-019-1697-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) that overcomes some of the bottlenecks limiting the current methods. We demonstrated its performance by predicting quantitative disease resistance and quantitative functional traits in the wild model plant species, Medicago truncatula, using geographical locations as covariates for admixture analysis. The method's prediction reliability equals or outperforms all existing algorithms for quantitative phenotype prediction. WhoGEM analysis produces evidence that variation in genome admixture proportions explains most of the phenotypic variation for quantitative phenotypes.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab, Université de Toulouse, CNRS, Avenue de l’Agrobiopole BP 32607, Auzeville-Tolosane, F-31326 Castanet-Tolosan, France
| | - Cécile Ben
- EcoLab, Université de Toulouse, CNRS, Avenue de l’Agrobiopole BP 32607, Auzeville-Tolosane, F-31326 Castanet-Tolosan, France
| | - Mélanie Mazurier
- EcoLab, Université de Toulouse, CNRS, Avenue de l’Agrobiopole BP 32607, Auzeville-Tolosane, F-31326 Castanet-Tolosan, France
| | - Min-Gyoung Shin
- University of Southern California, 1050 Childs Way (USC), Los Angeles, CA 90089-0371 USA
| | - Todd Lorenz
- University of La Verne, 1950 3rd Street, La Verne, CA 91750 USA
| | - Martina Rickauer
- EcoLab, Université de Toulouse, CNRS, Avenue de l’Agrobiopole BP 32607, Auzeville-Tolosane, F-31326 Castanet-Tolosan, France
| | - Paul Marjoram
- University of Southern California, 1050 Childs Way (USC), Los Angeles, CA 90089-0371 USA
| | - Sergey V. Nuzhdin
- University of Southern California, 1050 Childs Way (USC), Los Angeles, CA 90089-0371 USA
| | - Tatiana V. Tatarinova
- University of La Verne, 1950 3rd Street, La Verne, CA 91750 USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074 Krasnoyarsk, Russia
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Noman A, Aqeel M, Lou Y. PRRs and NB-LRRs: From Signal Perception to Activation of Plant Innate Immunity. Int J Mol Sci 2019; 20:ijms20081882. [PMID: 30995767 PMCID: PMC6514886 DOI: 10.3390/ijms20081882] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
To ward off pathogens and pests, plants use a sophisticated immune system. They use pattern-recognition receptors (PRRs), as well as nucleotide-binding and leucine-rich repeat (NB-LRR) domains, for detecting nonindigenous molecular signatures from pathogens. Plant PRRs induce local and systemic immunity. Plasma-membrane-localized PRRs are the main components of multiprotein complexes having additional transmembrane and cytosolic kinases. Topical research involving proteins and their interactive partners, along with transcriptional and posttranscriptional regulation, has extended our understanding of R-gene-mediated plant immunity. The unique LRR domain conformation helps in the best utilization of a surface area and essentially mediates protein–protein interactions. Genome-wide analyses of inter- and intraspecies PRRs and NB-LRRs offer innovative information about their working and evolution. We reviewed plant immune responses with relevance to PRRs and NB-LRRs. This article focuses on the significant functional diversity, pathogen-recognition mechanisms, and subcellular compartmentalization of plant PRRs and NB-LRRs. We highlight the potential biotechnological application of PRRs and NB-LRRs to enhance broad-spectrum disease resistance in crops.
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Affiliation(s)
- Ali Noman
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310027, China.
- Department of Botany, Government College University, Faisalabad 38000, Pakistan.
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Science, Lanzhou University, Lanzhou 730000, China.
| | - Yonggen Lou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310027, China.
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Wang L, Zhou X, Ren X, Huang L, Luo H, Chen Y, Chen W, Liu N, Liao B, Lei Y, Yan L, Shen J, Jiang H. A Major and Stable QTL for Bacterial Wilt Resistance on Chromosome B02 Identified Using a High-Density SNP-Based Genetic Linkage Map in Cultivated Peanut Yuanza 9102 Derived Population. Front Genet 2018; 9:652. [PMID: 30619474 PMCID: PMC6305283 DOI: 10.3389/fgene.2018.00652] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
Bacterial wilt (BW) is one of the important diseases limiting the production of peanut (Arachis hypogaea L.) worldwide. The sufficient precise information on the quantitative trait loci (QTL) for BW resistance is essential for facilitating gene mining and applying in molecular breeding. Cultivar Yuanza 9102 is BW resistant, bred from wide cross between cultivated peanut Baisha 1016 and a wild diploid peanut species A. chacoense with BW resistance. In this study, we aim to map the major QTLs related to BW-resistance in Yuanza 9102. A high density SNP-based genetic linkage map was constructed through double-digest restriction-site-associated DNA sequencing (ddRADseq) technique based on Yuanza 9102 derived recombinant inbred lines (RILs) population. The map contained 2,187 SNP markers distributed on 20 linkage groups (LGs) spanning 1566.10 cM, and showed good synteny with AA genome from A. duranensis and BB genome from A. ipaensis. Phenotypic frequencies of BW resistance among RIL population showed two-peak distribution in four environments. Four QTLs explaining 5.49 to 23.22% phenotypic variance were identified to be all located on chromosome B02. The major QTL, qBWB02.1 (12.17–23.33% phenotypic variation explained), was detected in three environments showing consistent and stable expression. Furthermore, there was positive additive effect among these major and minor QTLs. The major QTL region was mapped to a region covering 2.3 Mb of the pseudomolecule B02 of A. ipaensis which resides in 21 nucleotide-binding site -leucine-rich repeat (NBS-LRR) encoding genes. The result of the major stable QTL (qBWB02.1) not only offers good foundation for discovery of BW resistant gene but also provide opportunity for deployment of the QTL in marker-assisted breeding in peanut.
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Affiliation(s)
- Lifang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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10
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Morel A, Guinard J, Lonjon F, Sujeeun L, Barberis P, Genin S, Vailleau F, Daunay M, Dintinger J, Poussier S, Peeters N, Wicker E. The eggplant AG91-25 recognizes the Type III-secreted effector RipAX2 to trigger resistance to bacterial wilt (Ralstonia solanacearum species complex). MOLECULAR PLANT PATHOLOGY 2018; 19:2459-2472. [PMID: 30073750 PMCID: PMC6638172 DOI: 10.1111/mpp.12724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 05/04/2023]
Abstract
To deploy durable plant resistance, we must understand its underlying molecular mechanisms. Type III effectors (T3Es) and their recognition play a central role in the interaction between bacterial pathogens and crops. We demonstrate that the Ralstonia solanacearum species complex (RSSC) T3E ripAX2 triggers specific resistance in eggplant AG91-25, which carries the major resistance locus EBWR9. The eggplant accession AG91-25 is resistant to the wild-type R. pseudosolanacearum strain GMI1000, whereas a ripAX2 defective mutant of this strain can cause wilt. Notably, the addition of ripAX2 from GMI1000 to PSS4 suppresses wilt development, demonstrating that RipAX2 is an elicitor of AG91-25 resistance. RipAX2 has been shown previously to induce effector-triggered immunity (ETI) in the wild relative eggplant Solanum torvum, and its putative zinc (Zn)-binding motif (HELIH) is critical for ETI. We show that, in our model, the HELIH motif is not necessary for ETI on AG91-25 eggplant. The ripAX2 gene was present in 68.1% of 91 screened RSSC strains, but in only 31.1% of a 74-genome collection comprising R. solanacearum and R. syzygii strains. Overall, it is preferentially associated with R. pseudosolanacearum phylotype I. RipAX2GMI1000 appears to be the dominant allele, prevalent in both R. pseudosolanacearum and R. solanacearum, suggesting that the deployment of AG91-25 resistance could control efficiently bacterial wilt in the Asian, African and American tropics. This study advances the understanding of the interaction between RipAX2 and the resistance genes at the EBWR9 locus, and paves the way for both functional genetics and evolutionary analyses.
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Affiliation(s)
- Arry Morel
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | - Jérémy Guinard
- Université de La RéunionUMR PVBMTF‐97410Saint‐Pierre, La RéunionFrance
- CIRADUMR PVBMTF‐97410Saint‐Pierre, La RéunionFrance
| | - Fabien Lonjon
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | | | - Patrick Barberis
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | - Stéphane Genin
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | - Fabienne Vailleau
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | | | | | - Stéphane Poussier
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | - Nemo Peeters
- LIPMUniversité de Toulouse, INRA, CNRS,F‐31326Castanet‐TolosanFrance
| | - Emmanuel Wicker
- CIRADUMR PVBMTF‐97410Saint‐Pierre, La RéunionFrance
- IPME, Université de Montpellier, CIRADIRDF‐34394MontpellierFrance
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11
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Rey T, Jacquet C. Symbiosis genes for immunity and vice versa. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:64-71. [PMID: 29550547 DOI: 10.1016/j.pbi.2018.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/13/2023]
Abstract
Basic molecular knowledge on plant-pathogen interactions has largely been gained from reverse and forward genetics in Arabidopsis thaliana. However, as this model plant is unable to establish endosymbiosis with mycorrhizal fungi or rhizobia, plant responses to mutualistic symbionts have been studied in parallel in other plant species, mainly legumes. The resulting analyses led to the identification of gene networks involved in various functions, from microbe recognition to signalling and plant responses, thereafter assigned to either mutualistic symbiosis or immunity, according to the nature of the initially inoculated microbe. The increasing development of new pathosystems and genetic resources in model legumes and the implementation of reverse genetics in plants such as rice and tomato that interact with both mycorrhizal fungi and pathogens, have highlighted the dual role of plant genes previously thought to be specific to mutualistic or pathogenic interactions. The next challenges will be to determine whether such genes have similar functions in both types of interaction and if not, whether the perception of microbial compounds or the involvement of specific plant signalling components is responsible for the appropriate plant responses to the encountered microorganisms.
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Affiliation(s)
- Thomas Rey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France.
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12
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Yamchi A, Ben C, Rossignol M, Zareie SR, Mirlohi A, Sayed-Tabatabaei BE, Pichereaux C, Sarrafi A, Rickauer M, Gentzbittel L. Proteomics analysis ofMedicago truncatularesponse to infection by the phytopathogenic bacteriumRalstonia solanacearumpoints to jasmonate and salicylate defence pathways. Cell Microbiol 2018; 20. [DOI: 10.1111/cmi.12796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Ahad Yamchi
- Department of Plant Breeding and Biotechnology; Gorgan University of Agricultural Sciences and Natural Resources; Gorgan Iran
| | - Cécile Ben
- EcoLab; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Michel Rossignol
- Universite de Toulouse, IFR40, Plateforme Protéomique du Génopole Toulouse Midi-Pyrénées; Institut de Pharmacologie et de Biologie Structurale; CNRS UMR 5089, 31077 Toulouse France
| | - Sayed Reza Zareie
- Department of Agricultural biotechnology, College of Agriculture; Isfahan University of Technology; 84156-83111 Isfahan Iran
| | - Aghafakhr Mirlohi
- Department of Agricultural biotechnology, College of Agriculture; Isfahan University of Technology; 84156-83111 Isfahan Iran
| | | | - Carole Pichereaux
- Universite de Toulouse, IFR40, Plateforme Protéomique du Génopole Toulouse Midi-Pyrénées; Institut de Pharmacologie et de Biologie Structurale; CNRS UMR 5089, 31077 Toulouse France
| | - Ahmad Sarrafi
- EcoLab; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Martina Rickauer
- EcoLab; Université de Toulouse, CNRS, INPT, UPS; Toulouse France
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13
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Garmier M, Gentzbittel L, Wen J, Mysore KS, Ratet P. Medicago truncatula: Genetic and Genomic Resources. ACTA ACUST UNITED AC 2017; 2:318-349. [PMID: 33383982 DOI: 10.1002/cppb.20058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Medicago truncatula was chosen by the legume community, along with Lotus japonicus, as a model plant to study legume biology. Since then, numerous resources and tools have been developed for M. truncatula. These include, for example, its genome sequence, core ecotype collections, transformation/regeneration methods, extensive mutant collections, and a gene expression atlas. This review aims to describe the different genetic and genomic tools and resources currently available for M. truncatula. We also describe how these resources were generated and provide all the information necessary to access these resources and use them from a practical point of view. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marie Garmier
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France.,Institute of Plant Sciences Paris-Saclay, Université Paris Diderot, Université Sorbonne Paris-Cité, Orsay, France
| | - Laurent Gentzbittel
- EcoLab, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National Polytechnique de Toulouse, Université Paul Sabatier, Castanet-Tolosan, France
| | | | | | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France.,Institute of Plant Sciences Paris-Saclay, Université Paris Diderot, Université Sorbonne Paris-Cité, Orsay, France
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14
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Bozsoki Z, Cheng J, Feng F, Gysel K, Vinther M, Andersen KR, Oldroyd G, Blaise M, Radutoiu S, Stougaard J. Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception. Proc Natl Acad Sci U S A 2017; 114:E8118-E8127. [PMID: 28874587 PMCID: PMC5617283 DOI: 10.1073/pnas.1706795114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The ability of root cells to distinguish mutualistic microbes from pathogens is crucial for plants that allow symbiotic microorganisms to infect and colonize their internal root tissues. Here we show that Lotus japonicus and Medicago truncatula possess very similar LysM pattern-recognition receptors, LjLYS6/MtLYK9 and MtLYR4, enabling root cells to separate the perception of chitin oligomeric microbe-associated molecular patterns from the perception of lipochitin oligosaccharide by the LjNFR1/MtLYK3 and LjNFR5/MtNFP receptors triggering symbiosis. Inactivation of chitin-receptor genes in Ljlys6, Mtlyk9, and Mtlyr4 mutants eliminates early reactive oxygen species responses and induction of defense-response genes in roots. Ljlys6, Mtlyk9, and Mtlyr4 mutants were also more susceptible to fungal and bacterial pathogens, while infection and colonization by rhizobia and arbuscular mycorrhizal fungi was maintained. Biochemical binding studies with purified LjLYS6 ectodomains further showed that at least six GlcNAc moieties (CO6) are required for optimal binding efficiency. The 2.3-Å crystal structure of the LjLYS6 ectodomain reveals three LysM βααβ motifs similar to other LysM proteins and a conserved chitin-binding site. These results show that distinct receptor sets in legume roots respond to chitin and lipochitin oligosaccharides found in the heterogeneous mixture of chitinaceous compounds originating from soil microbes. This establishes a foundation for genetic and biochemical dissection of the perception and the downstream responses separating defense from symbiosis in the roots of the 80-90% of land plants able to develop rhizobial and/or mycorrhizal endosymbiosis.
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Affiliation(s)
- Zoltan Bozsoki
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Jeryl Cheng
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Feng Feng
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Kira Gysel
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Maria Vinther
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Kasper R Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | | | - Mickael Blaise
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark;
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15
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Cai F, Watson BS, Meek D, Huhman DV, Wherritt DJ, Ben C, Gentzbittel L, Driscoll BT, Sumner LW, Bede JC. Medicago truncatula Oleanolic-Derived Saponins Are Correlated with Caterpillar Deterrence. J Chem Ecol 2017; 43:712-724. [PMID: 28744732 DOI: 10.1007/s10886-017-0863-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/06/2017] [Accepted: 06/21/2017] [Indexed: 11/24/2022]
Abstract
Plant resistance mechanisms to insect herbivory can potentially be bred into crops as an important strategy for integrated pest management. Medicago truncatula ecotypes inoculated with the rhizobium Ensifer medicae (Sinorhizobium medica) WSM419 were screened for resistance to herbivory by caterpillars of the beet armyworm, Spodoptera exigua, through leaf and whole plant choice studies; TN1.11 and F83005.5 are identified as the least and most deterrent ecotypes, respectively. In response to caterpillar herbivory, both ecotypes mount a robust burst of plant defensive jasmonate phytohormones. Restriction of caterpillars to either of these ecotypes does not adversely affect pest performance. This argues for an antixenosis (deterrence) resistance mechanism associated with the F83005.5 ecotype. Unbiased metabolomic profiling identified strong ecotype-specific differences in metabolite profile, particularly in the content of oleanolic-derived saponins that may act as antifeedants. Compared to the more susceptible ecotype, F83005.5 has higher levels of oleanolic-type zanhic acid- and medicagenic acid-derived compounds. Together, these data support saponin-mediated deterrence as a resistance mechanism of the F83005.5 ecotype and implicates these compounds as potential antifeedants that could be used in agricultural sustainable pest management strategies.
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Affiliation(s)
- Fanping Cai
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Bonnie S Watson
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - David Meek
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - David V Huhman
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Daniel J Wherritt
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Cecile Ben
- EcoLab, Université de Toulouse, Centre National de Recherche Scientifique, Institute National Polytechnique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Laurent Gentzbittel
- EcoLab, Université de Toulouse, Centre National de Recherche Scientifique, Institute National Polytechnique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Brian T Driscoll
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jacqueline C Bede
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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16
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Song H, Wang P, Li C, Han S, Zhao C, Xia H, Bi Y, Guo B, Zhang X, Wang X. Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis. PLoS One 2017; 12:e0171181. [PMID: 28158222 PMCID: PMC5291535 DOI: 10.1371/journal.pone.0171181] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/17/2017] [Indexed: 12/31/2022] Open
Abstract
Studies have demonstrated that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes respond to pathogen attack in plants. Characterization of NBS-LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS-LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in A. ipaënsis than in A. duranensis, possibly owing to tandem duplication events occurring more frequently in A. ipaënsis. The expression profile of NBS-LRR genes was different between A. duranensis and A. hypogaea after Aspergillus flavus infection. The up-regulated expression of NBS-LRR in A. duranensis was continuous, while these genes responded to the pathogen temporally in A. hypogaea.
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Affiliation(s)
- Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Suoyi Han
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, Georgia, United States of America
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
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17
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Zhang C, Chen H, Cai T, Deng Y, Zhuang R, Zhang N, Zeng Y, Zheng Y, Tang R, Pan R, Zhuang W. Overexpression of a novel peanut NBS-LRR gene AhRRS5 enhances disease resistance to Ralstonia solanacearum in tobacco. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:39-55. [PMID: 27311738 PMCID: PMC5253469 DOI: 10.1111/pbi.12589] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/16/2016] [Accepted: 06/10/2016] [Indexed: 05/20/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a ruinous soilborne disease affecting more than 450 plant species. Efficient control methods for this disease remain unavailable to date. This study characterized a novel nucleotide-binding site-leucine-rich repeat resistance gene AhRRS5 from peanut, which was up-regulated in both resistant and susceptible peanut cultivars in response to R. solanacearum. The product of AhRRS5 was localized in the nucleus. Furthermore, treatment with phytohormones such as salicylic acid (SA), abscisic acid (ABA), methyl jasmonate (MeJA) and ethephon (ET) increased the transcript level of AhRRS5 with diverse responses between resistant and susceptible peanuts. Abiotic stresses such as drought and cold conditions also changed AhRRS5 expression. Moreover, transient overexpression induced hypersensitive response in Nicotiana benthamiana. Overexpression of AhRRS5 significantly enhanced the resistance of heterogeneous tobacco to R. solanacearum, with diverse resistance levels in different transgenic lines. Several defence-responsive marker genes in hypersensitive response, including SA, JA and ET signals, were considerably up-regulated in the transgenic lines as compared with the wild type inoculated with R. solanacearum. Nonexpressor of pathogenesis-related gene 1 (NPR1) and non-race-specific disease resistance 1 were also up-regulated in response to the pathogen. These results indicate that AhRRS5 participates in the defence response to R. solanacearum through the crosstalk of multiple signalling pathways and the involvement of NPR1 and R gene signals for its resistance. This study may guide the resistance enhancement of peanut and other economic crops to bacterial wilt disease.
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Affiliation(s)
- Chong Zhang
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Hua Chen
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Tiecheng Cai
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ye Deng
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ruirong Zhuang
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ning Zhang
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Yuanhuan Zeng
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Yixiong Zheng
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of AgronomyZhongkai Agriculture and Engineering CollegeGuangzhouGuangdongChina
| | - Ronghua Tang
- Cash Crops Research InstituteGuangxi Academy of Agricultural SciencesNanningChina
| | - Ronglong Pan
- Department of Life Science and Institute of Bioinformatics and Structural BiologyCollege of Life ScienceNational Tsing Hua UniversityHsinchuTaiwan
| | - Weijian Zhuang
- College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Crop Molecular and Cell BiologyFujian Agriculture and Forestry UniversityFuzhouFujianChina
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18
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Meziadi C, Richard MMS, Derquennes A, Thareau V, Blanchet S, Gratias A, Pflieger S, Geffroy V. Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:351-357. [PMID: 26566851 DOI: 10.1016/j.plantsci.2015.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 05/03/2023]
Abstract
Common bean (Phaseolus vulgaris) is the most important grain legume for direct human consumption in the world, particularly in developing countries where it constitutes the main source of protein. Unfortunately, common bean yield stability is constrained by a number of pests and diseases. As use of resistant genotypes is the most economic and ecologically safe means for controlling plant diseases, efforts have been made to genetically characterize resistance genes (R genes) in common bean. Despite its agronomic importance, genomic resources available in common bean were limited until the recent sequencing of common bean genome (Andean genotype G19833). Besides allowing the annotation of Nucleotide Binding-Leucine Rich Repeat (NB-LRR) encoding gene family, which is the prevalent class of disease R genes in plants, access to the whole genome sequence of common bean can be of great help for intense selection to increase the overall efficiency of crop improvement programs using marker-assisted selection (MAS). This review presents the state of the art of common bean NB-LRR gene clusters, their peculiar location in subtelomeres and correlation with genetically characterized monogenic R genes, as well as how the availability of the whole genome sequence can boost the development of molecular markers for MAS.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Manon M S Richard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Amandine Derquennes
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France.
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Pensec F, Lebeau A, Daunay MC, Chiroleu F, Guidot A, Wicker E. Towards the Identification of Type III Effectors Associated with Ralstonia solanacearum Virulence on Tomato and Eggplant. PHYTOPATHOLOGY 2015; 105:1529-44. [PMID: 26368514 DOI: 10.1094/phyto-06-15-0140-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
For the development of pathogen-informed breeding strategies, identifying the microbial genes involved in interactions with the plant is a critical step. To identify type III effector (T3E) repertoires associated with virulence of the bacterial wilt pathogen Ralstonia solanacearum on Solanaceous crops, we used an original association genetics approach combining DNA microarray data and pathogenicity data on resistant eggplant, pepper, and tomato accessions. From this first screen, 25 T3Es were further full-length polymerase chain reaction-amplified within a 35-strain field collection, to assess their distribution and allelic diversity. Six T3E repertoire groups were identified, within which 11 representative strains were chosen to challenge the bacterial wilt-resistant egg plants 'Dingras multiple Purple' and 'AG91-25', and tomato Hawaii 7996. The virulence or avirulence phenotypes could not be explained by specific T3E repertoires, but rather by individual T3E genes. We identified seven highly avirulence-associated genes, among which ripP2, primarily referenced as conferring avirulence to Arabidopsis thaliana. Interestingly, no T3E was associated with avirulence to both egg-plants. Highly virulence-associated genes were also identified: ripA5_2, ripU, and ripV2. This study should be regarded as a first step toward investigating both avirulence and virulence function of the highlighted genes, but also their evolutionary dynamics in natural R. solanacearum populations.
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Affiliation(s)
- Flora Pensec
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
| | - Aurore Lebeau
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
| | - M C Daunay
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
| | - Frédéric Chiroleu
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
| | - Alice Guidot
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
| | - Emmanuel Wicker
- First, second, fourth, and sixth authors: CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint-Pierre, La Réunion, France; third author: INRA, Centre d'Avignon, Unité de Génétique et Amélioration des Fruits et Légumes, UR1052, Montfavet, France; and fifth author: INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes (LIPM), Castanet-Tolosan, France. Current address of first author: Institut National de la Recherche Agronomique, UMR A 1131 Santé de la Vigne et Qualité du Vin (SVQV), Colmar, France. Université de Strasbourg, Strasbourg, France
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20
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Bae C, Han SW, Song YR, Kim BY, Lee HJ, Lee JM, Yeam I, Heu S, Oh CS. Infection processes of xylem-colonizing pathogenic bacteria: possible explanations for the scarcity of qualitative disease resistance genes against them in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1219-29. [PMID: 25917599 DOI: 10.1007/s00122-015-2521-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/17/2015] [Indexed: 05/22/2023]
Abstract
Disease resistance against xylem-colonizing pathogenic bacteria in crops. Plant pathogenic bacteria cause destructive diseases in many commercially important crops. Among these bacteria, eight pathogens, Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, X. campestris pv. campestris, Erwinia amylovora, Pantoea stewartii subsp. stewartii, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. actinidiae, and Xylella fastidiosa, infect their host plants through different infection sites and paths and eventually colonize the xylem tissues of their host plants, resulting in wilting symptoms by blocking water flow or necrosis of xylem tissues. Noticeably, only a relatively small number of resistant cultivars in major crops against these vascular bacterial pathogens except X. oryzae pv. oryzae have been found or generated so far, although these pathogens threaten productivity of major crops. In this review, we summarize the lifestyles of major xylem-colonizing bacterial pathogens and then discuss the progress of current research on disease resistance controlled by qualitative disease resistance genes or quantitative trait loci against them. Finally, we propose infection processes of xylem-colonizing bacterial pathogens as one of possible reasons for why so few qualitative disease resistance genes against these pathogens have been developed or identified so far in crops.
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Affiliation(s)
- Chungyun Bae
- Department of Horticultural Biotechnology and Institute of Life Science and Resources, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
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21
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Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:269. [PMID: 25954294 PMCID: PMC4404971 DOI: 10.3389/fpls.2015.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/03/2015] [Indexed: 05/05/2023]
Abstract
Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Cécile Ben
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Martina Rickauer
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Nevin D. Young
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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22
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Zuluaga AP, Solé M, Lu H, Góngora-Castillo E, Vaillancourt B, Coll N, Buell CR, Valls M. Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii. BMC Genomics 2015; 16:246. [PMID: 25880642 PMCID: PMC4391584 DOI: 10.1186/s12864-015-1460-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 03/09/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. RESULTS In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. CONCLUSIONS Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied.
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Affiliation(s)
- A Paola Zuluaga
- Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain.
| | - Montserrat Solé
- Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain.
| | - Haibin Lu
- Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain.
| | - Elsa Góngora-Castillo
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Nuria Coll
- Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain.
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Marc Valls
- Genetics Department, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, 08193, Catalonia, Spain.
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23
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Exbrayat S, Bertoni G, Naghavie MR, Peyghambari A, Badri M, Debelle F. Genetic variability and identification of quantitative trait loci affecting plant growth and chlorophyll fluorescence parameters in the model legume Medicago truncatula under control and salt stress conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:983-1001. [PMID: 32481051 DOI: 10.1071/fp13370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/14/2014] [Indexed: 06/11/2023]
Abstract
Salinity is one of the major stresses that limits crop production worldwide and affects most physiological activities in plants. In order to study the genetic control of salt stress in the model legume Medicago truncatula Gaertn., an experiment was undertaken to determine the genetic variability and to identify quantitative trait loci (QTLs) controlling several traits related to plant growth and physiology in a population of recombinant inbred lines. Shoot and root DW, relative water content, leaf area, chlorophyll content, chlorophyll fluorescence parameters, and Na+ and K+ in shoots and roots were measured. The experiment was carried out with three replications. ANOVA showed a large genetic variation and transgressive segregation for the traits studied, suggesting putative complex tolerance mechanisms. A total of 21 QTLs were detected under control conditions and 19 QTLs were identified under 100mm salt stress conditions, with three QTLs being common to both situations. The percentage of total phenotypic variance explained by the QTLs ranged from 4.6% to 23.01%. Overlapping QTLs for different traits were also observed, which enables us to discriminate independent traits from linked ones. The results should be helpful information for further functional analysis of salt tolerance in M. truncatula.
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Affiliation(s)
- Sarah Exbrayat
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes (UMR441 and UMR 2594), 18 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Georges Bertoni
- Institut National Polytechnique (INP), Ecole Nationale Supérieure Agronomique de Toulouse (ENSAT), Unité Mixte Recherche DYNAFOR (Dynamiques et Écologie des Paysages Agriforestiers), Université de Toulouse, BP 32607, 31326 Castanet-Tolosan, France
| | - Mohamad Reza Naghavie
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Peyghambari
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran
| | - Mounavar Badri
- Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Frédéric Debelle
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes (UMR441 and UMR 2594), 18 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
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24
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Moreau S, Fromentin J, Vailleau F, Vernié T, Huguet S, Balzergue S, Frugier F, Gamas P, Jardinaud MF. The symbiotic transcription factor MtEFD and cytokinins are positively acting in the Medicago truncatula and Ralstonia solanacearum pathogenic interaction. THE NEW PHYTOLOGIST 2014; 201:1343-1357. [PMID: 24325235 DOI: 10.1111/nph.12636] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/03/2013] [Indexed: 05/03/2023]
Abstract
• A plant-microbe dual biological system was set up involving the model legume Medicago truncatula and two bacteria, the soil-borne root pathogen Ralstonia solanacearum and the beneficial symbiont Sinorhizobium meliloti. • Comparison of transcriptomes under symbiotic and pathogenic conditions highlighted the transcription factor MtEFD (Ethylene response Factor required for nodule Differentiation) as being upregulated in both interactions, together with a set of cytokinin-related transcripts involved in metabolism, signaling and response. MtRR4 (Response Regulator), a cytokinin primary response gene negatively regulating cytokinin signaling and known as a target of MtEFD in nodulation processes, was retrieved in this set of transcripts. • Refined studies of MtEFD and MtRR4 expression during M. truncatula and R. solanacearum interaction indicated differential kinetics of induction and requirement of central regulators of bacterial pathogenicity, HrpG and HrpB. Similar to MtRR4, MtEFD upregulation during the pathogenic interaction was dependent on cytokinin perception mediated by the MtCRE1 (Cytokinin REsponse 1) receptor. • The use of M. truncatula efd-1 and cre1-1 mutants evidenced MtEFD and cytokinin perception as positive factors for bacterial wilt development. These factors therefore play an important role in both root nodulation and root disease development.
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Affiliation(s)
- Sandra Moreau
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | - Justine Fromentin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | - Fabienne Vailleau
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, 18 chemin de Borde Rouge, F-31326, Castanet Tolosan, France
| | - Tatiana Vernié
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | - Stéphanie Huguet
- Unité de Recherche en Génomique Végétale (URGV), INRA, UMR 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, CP 5708, F-91057, Evry Cedex, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale (URGV), INRA, UMR 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, CP 5708, F-91057, Evry Cedex, France
| | - Florian Frugier
- Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 1 avenue de la terrasse, F-91198, Gif-sur-Yvette, France
| | - Pascal Gamas
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
| | - Marie-Françoise Jardinaud
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, 18 chemin de Borde Rouge, F-31326, Castanet Tolosan, France
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Huet G. Breeding for resistances to Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2014; 5:715. [PMID: 25566289 PMCID: PMC4264415 DOI: 10.3389/fpls.2014.00715] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/27/2014] [Indexed: 05/20/2023]
Abstract
Ralstonia solanacearum is one of the most devastating bacterial plant pathogens due to its large host range, worldwide geographic distribution and persistence in fields. This soilborne pathogen is the causal agent of bacterial wilt and it can infect major agricultural crops thereby reducing significantly their yield. To favor infection, the bacterium delivers, through the type three secretion system, effectors that manipulate plant immunity. In this review, the relative efficiency of control strategies and existing resistances to R. solanacearum will be presented. Then, the genetic and molecular insights gained from the study of bacterial wilt in model plants will be described. Finally, I will explore how the knowledge gathered from unraveling avirulence and virulence mechanisms of R. solanacearum effectors could help to develop more durable resistances in crop plants toward this destructive pathogen.
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Affiliation(s)
- Gaëlle Huet
- INRA, Laboratoire des Interactions Plantes-Microorganismes, UMR441, Castanet-TolosanFrance
- CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-TolosanFrance
- *Correspondence: Gaëlle Huet, Laboratoire des Interactions Plantes Microorganismes, 24 chemin de Borde Rouge - Auzeville, CS 52627, 31326 Castanet-Tolosan, France e-mail:
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26
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Peeters N, Guidot A, Vailleau F, Valls M. Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. MOLECULAR PLANT PATHOLOGY 2013; 14:651-62. [PMID: 23718203 PMCID: PMC6638647 DOI: 10.1111/mpp.12038] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease of banana and brown rot of potato. Since the last R. solanacearum pathogen profile was published 10 years ago, studies concerning this plant pathogen have taken a genomic and post-genomic direction. This was pioneered by the first sequenced and annotated genome for a major plant bacterial pathogen and followed by many more genomes in subsequent years. All molecular features studied now have a genomic flavour. In the future, this will help in connecting the classical field of pathology and diversity studies with the gene content of specific strains. In this review, we summarize the recent research on this bacterial pathogen, including strain classification, host range, pathogenicity determinants, regulation of virulence genes, type III effector repertoire, effector-triggered immunity, plant signalling in response to R. solanacearum, as well as a review of different new pathosystems. TAXONOMY Bacteria; Proteobacteria; β subdivision; Ralstonia group; genus Ralstonia. DISEASE SYMPTOMS Ralstonia solanacearum is the agent of bacterial wilt of plants, characterized by a sudden wilt of the whole plant. Typically, stem cross-sections will ooze a slimy bacterial exudate. In the case of Moko disease of banana and brown rot of potato, there is also visible bacterial colonization of banana fruit and potato tuber. DISEASE CONTROL As a soil-borne pathogen, infected fields can rarely be reused, even after rotation with nonhost plants. The disease is controlled by the use of resistant and tolerant plant cultivars. The prevention of spread of the disease has been achieved, in some instances, by the application of strict prophylactic sanitation practices. USEFUL WEBSITES Stock centre: International Centre for Microbial Resources-French Collection for Plant-associated Bacteria CIRM-CFBP, IRHS UMR 1345 INRA-ACO-UA, 42 rue Georges Morel, 49070 Beaucouzé Cedex, France, http://www.angers-nantes.inra.fr/cfbp/. Ralstonia Genome browser: https://iant.toulouse.inra.fr/R.solanacearum. GMI1000 insertion mutant library: https://iant.toulouse.inra.fr/R.solanacearumGMI1000/GenomicResources. MaGe Genome Browser: https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?
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Affiliation(s)
- Nemo Peeters
- INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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