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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Gong C, Wang Z, Li Z, Sun B, Luo W, Luo S, Chen S, Mai P, Li Z, Li Y, Wang Y, Li T. A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt. HORTICULTURE RESEARCH 2024; 11:uhad272. [PMID: 38333730 PMCID: PMC10852381 DOI: 10.1093/hr/uhad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.
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Affiliation(s)
- Chao Gong
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhiliang Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Baojuan Sun
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Wenlong Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shanwei Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shuting Chen
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Peiting Mai
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenxing Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Ye Li
- Harbin Academy of Agricultural Sciences, Harbin, Heilongjiang, 150029, China
| | - Yikui Wang
- Institute of Vegetable, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Tao Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
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Miao Y, Wu L, Xue Q, Zhang Q, Zou H. Ralstonia solanacearum type III effector RipAA targets chloroplastic AtpB to modulate an incompatible interaction on Nicotiana benthamiana. Front Microbiol 2023; 14:1179824. [PMID: 37275133 PMCID: PMC10232776 DOI: 10.3389/fmicb.2023.1179824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/30/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction The type III effector RipAA of Ralstonia solanacearum GMI1000 plays a critical role in the incompatible interaction on Nicotiana benthamiana. Methods The RipAA was transiently expressed in N. benthamiana by Agrobacterium-mediated transformation. Chemical staining with trypan blue and DAB were conducted to examine the cell death and the accumulation of hydrogen peroxide (H2O2), respectively. The expression of the marker genes for salicylic acid (SA) and jasmonic acid (JA) signaling was evaluated by quantitative reverse transcription PCR (qRT-PCR). The proteins interacted with RipAA was identified from N. benthamiana by yeast two-hybrid and pull-down assays. A TRV-mediated gene silencing was used to assess the role of host gene in response to RipAA expression and R. solanacearum infection. Results and discussion RipAA induced the accumulation of hydrogen peroxide (H2O2) and genome DNA degradation in N. benthamiana, which were accompanied by a hypersensitive reaction. Simultaneously, the marker genes for salicylic acid (SA) signaling were induced and those for jasmonic acid (JA) signaling were reduced. N. benthamiana chloroplastic AtpB, the ATPase β subunit, was identified as an interactor with RipAA. The silencing of atpB in N. benthamiana resulted in the inability of RipAA to induce a hypersensitive response, a compatible interaction with GMI1000, and an enhanced sensitivity to bacterial wilt. Our data support the concept that RipAA determines host-range specificity by targeting the host chloroplastic AtpB.
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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Kapadia C, Datta R, Mahammad SM, Tomar RS, Kheni JK, Ercisli S. Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant ( Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection. ACS OMEGA 2023; 8:2648-2657. [PMID: 36687045 PMCID: PMC9851032 DOI: 10.1021/acsomega.2c07097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/27/2022] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), a type of short noncoding RNA molecule (21-23 nucleotides), mediate repressive gene regulation through RNA silencing at the posttranscriptional level and play an important role in the defense response to abiotic and biotic stresses. miRNAs of the plant system have been studied in model crops for their diverse regulatory role while less is known about their significance in other plants whose genome and transcriptome data are scarce in the database, including eggplant (Solanum melongena L.). In the present study, a next-generation sequencing platform was used for the sequencing of miRNA, and real-time quantitative PCR for miRNAs was used to validate the gene expression patterns of miRNAs in Solanum melongena plantlets infected with the bacterial wilt-causing pathogen Ralstonia solanacearum (R. solanacearum). Sequence analyses showed the presence of 375 miRNAs belonging to 29 conserved families. The miR414 is highly conserved miRNA across the plant system while miR5658 and miR5021 were found exclusively in Arabidopsis thaliana surprisingly, these miRNAs were found in eggplants too. The most abundant families were miR5658 and miR414. Ppt-miR414, hvu-miR444b, stu-miR8020, and sly miR5303 were upregulated in Pusa purple long (PPL) (susceptible) at 48 h postinfection, followed by a decline after 96 h postinfection. A similar trend was obtained in ath-miR414, stu-mir5303h, alymiR847-5p, far-miR1134, ath-miR5021, ath-miR5658, osa-miR2873c, lja-miR7530, stu-miR7997c, and gra-miR8741 but at very low levels after infection in the susceptible variety, indicating their negative role in the suppression of host immunity. On the other hand, osa-miR2873c was found to be slightly increased after 96 hpi from 48 hpi. Most of the miRNAs under study showed relatively lower expression in the resistant variety Arka Nidhi after infection than in the susceptible variety. These results shed light on a deeper regulatory role of miRNAs and their targets in regulation of the plant response to bacterial infection. The present experiment and their results suggested that the higher expression of miRNA leads to a decline in host mRNA and thus shows susceptibility.
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Affiliation(s)
- Chintan Kapadia
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rahul Datta
- Department
of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Saiyed Mufti Mahammad
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rukam Singh Tomar
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Jasmin Kumar Kheni
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Sezai Ercisli
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
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Xiao XO, Lin W, Feng E, Ou X. Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection. PeerJ 2023; 11:e14658. [PMID: 36647448 PMCID: PMC9840387 DOI: 10.7717/peerj.14658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant.
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Affiliation(s)
- Xi Ou Xiao
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
| | - Wenqiu Lin
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
| | - Enyou Feng
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Xiongchang Ou
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
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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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Habe I, Miyatake K. Identification and characterization of resistance quantitative trait loci against bacterial wilt caused by the Ralstonia solanacearum species complex in potato. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:50. [PMID: 37313419 PMCID: PMC10248640 DOI: 10.1007/s11032-022-01321-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) represents one of the most serious diseases affecting potato cultivation. The development of BW-resistant cultivars represents the most efficient strategy to control this disease. The resistance-related quantitative trait loci (QTLs) in plants against different RSSC strains have not been studied extensively. Therefore, we performed QTL analysis for evaluating BW resistance using a diploid population derived from Solanum phureja, S. chacoense, and S. tuberosum. Plants cultivated in vitro were inoculated with different strains (phylotype I/biovar 3, phylotype I/biovar 4, and phylotype IV/biovar 2A) and incubated at 24 °C or 28 °C under controlled conditions. Composite interval mapping was performed for the disease indexes using a resistant parent-derived map and a susceptible parent-derived map consisting of single-nucleotide polymorphism markers. We identified five major and five minor resistance QTLs on potato chromosomes 1, 3, 5, 6, 7, 10, and 11. The major QTLs PBWR-3 and PBWR-7 conferred stable resistance against Ralstonia pseudosolanacearum (phylotype I) and Ralstonia syzygii (phylotype IV), whereas PBWR-6b was a strain-specific major resistance QTL against phylotype I/biovar 3 and was more effective at a lower temperature. Therefore, we suggest that broad-spectrum QTLs and strain-specific QTLs can be combined to develop the most effective BW-resistant cultivars for specific areas. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01321-9.
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Affiliation(s)
- Ippei Habe
- Nagasaki Agriculture and Forestry Technical Development Center, 3118 Kaizu, Isahaya, Nagasaki, 854-0063 Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO, Kusawa 360, Mie, Tsu, 514-2392 Japan
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9
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Hemara LM, Jayaraman J, Sutherland PW, Montefiori M, Arshed S, Chatterjee A, Chen R, Andersen MT, Mesarich CH, van der Linden O, Yoon M, Schipper MM, Vanneste JL, Brendolise C, Templeton MD. Effector loss drives adaptation of Pseudomonas syringae pv. actinidiae biovar 3 to Actinidia arguta. PLoS Pathog 2022; 18:e1010542. [PMID: 35622878 PMCID: PMC9182610 DOI: 10.1371/journal.ppat.1010542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/09/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
A pandemic isolate of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has devastated kiwifruit orchards growing cultivars of Actinidia chinensis. In contrast, A. arguta (kiwiberry) is not a host of Psa3. Resistance is mediated via effector-triggered immunity, as demonstrated by induction of the hypersensitive response in infected A. arguta leaves, observed by microscopy and quantified by ion-leakage assays. Isolates of Psa3 that cause disease in A. arguta have been isolated and analyzed, revealing a 51 kb deletion in the exchangeable effector locus (EEL). This natural EEL-mutant isolate and strains with synthetic knockouts of the EEL were more virulent in A. arguta plantlets than wild-type Psa3. Screening of a complete library of Psa3 effector knockout strains identified increased growth in planta for knockouts of four effectors–AvrRpm1a, HopF1c, HopZ5a, and the EEL effector HopAW1a –suggesting a resistance response in A. arguta. Hypersensitive response (HR) assays indicate that three of these effectors trigger a host species-specific HR. A Psa3 strain with all four effectors knocked out escaped host recognition, but a cumulative increase in bacterial pathogenicity and virulence was not observed. These avirulence effectors can be used in turn to identify the first cognate resistance genes in Actinidia for breeding durable resistance into future kiwifruit cultivars. Clonally propagated monoculture crop plants facilitate the emergence and spread of new diseases. Plant pathogens cause disease by the secretion of effectors that function by repressing the host defense response. While the last few decades have seen a huge increase in our understanding of the role effectors play in mediating plant-pathogen interactions, the combinations of effectors required for the establishment of plant disease and that account for host specificity are less well understood. Breeding genetic resistance is often used to protect plants from disease but it is frequently evaded by rapidly evolving pathogens. Pseudomonas syringae pv. actinidiae (Psa) which causes bacterial canker disease of kiwifruit has spread rapidly throughout the world’s kiwifruit orchards, particularly those growing cultivars of Actinidia chinensis. Other Actinidia species including A. arguta display strong resistance conferred by recognition of effectors delivered by Psa. We explore the depth and dynamics of Psa effector recognition by A. arguta and show that there is a trade-off between losses of effector recognition by A. arguta versus the retention of pathogenicity. Our findings should aid in the understanding of how to breed durable resistance into perennial plants challenged by swiftly evolving pathogens.
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Affiliation(s)
- Lauren M. Hemara
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
| | - Paul W. Sutherland
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Mirco Montefiori
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Saadiah Arshed
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Ronan Chen
- The New Zealand Institute for Plant and Food Research Limited, Food Industry Science Centre, Palmerston North, New Zealand
| | - Mark T. Andersen
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Carl H. Mesarich
- Bioprotection Aoteoroa, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Otto van der Linden
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Minsoo Yoon
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Magan M. Schipper
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Joel L. Vanneste
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Campus, Hamilton, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Bioprotection Aoteoroa, New Zealand
- * E-mail: ,
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10
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Salinier J, Lefebvre V, Besombes D, Burck H, Causse M, Daunay MC, Dogimont C, Goussopoulos J, Gros C, Maisonneuve B, McLeod L, Tobal F, Stevens R. The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030347. [PMID: 35161327 PMCID: PMC8838894 DOI: 10.3390/plants11030347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 05/14/2023]
Abstract
The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, France. Accessions from the collections have geographically diverse origins, are generally well-described and fixed for traits of agronomic or scientific interest and have available passport data. In addition to currently conserving over 10,000 accessions (between 900 and 3000 accessions per crop), the centre maintains scientific collections such as core collections and bi- or multi-parental populations, which have also been genotyped with SNP markers. Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality traits and environmental stress tolerance.
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11
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Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.). BMC Genomics 2021; 22:356. [PMID: 34000992 PMCID: PMC8130101 DOI: 10.1186/s12864-021-07662-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). RESULTS A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima's D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. CONCLUSIONS Genetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.
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12
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Miyatake K, Saito T, Nunome T, Yamaguchi H, Negoro S, Ohyama A, Wu J, Katayose Y, Fukuoka H. Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection. BREEDING SCIENCE 2020; 70:438-448. [PMID: 32968346 PMCID: PMC7495204 DOI: 10.1270/jsbbs.20004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/02/2020] [Indexed: 05/29/2023]
Abstract
As prickles cause labour inefficiency during cultivation and scratches on the skin of fruits during transportation, they are considered undesirable traits of eggplant (Solanum melongena L.). Because the molecular basis of prickle emergence has not been entirely revealed in plants, we mapped an eggplant semi-dominant Prickle (Pl) gene locus, which causes the absence of prickles, on chromosome 6 of a linkage map of the F2 population derived from crossing the no-prickly cultivar 'Togenashi-senryo-nigo' and the prickly line LS1934. By performing synteny mapping with tomato, the genomic region corresponding to the eggplant Pl locus was identified. Through bacterial artificial chromosome (BAC) screening, positive BAC clones and the contig sequence that harbour the Pl locus in the prickly eggplant genome were revealed. The BAC contig length was 133 kb, and it contained 16 predicted genes. Among them, a characteristic 0.5-kb insertion/deletion was detected. As the 0.5-kb insertion was commonly identified with the prickly phenotype worldwide, a primer pair that amplifies the insertion/deletion could be used for marker-assisted selection of the no-prickly phenotype. Such findings contribute to map-based-cloning of the Pl gene and the understanding of gene function, ultimately providing new insights into the regulatory molecular mechanisms underlying prickle emergence in plants.
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Affiliation(s)
- Koji Miyatake
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Takeo Saito
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hirotaka Yamaguchi
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satomi Negoro
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Ohyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Jianzhong Wu
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Yuichi Katayose
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroyuki Fukuoka
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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Li D, Li S, Li W, Liu A, Jiang Y, Gan G, Li W, Liang X, Yu N, Chen R, Wang Y. Comparative transcriptome analysis provides insights into the molecular mechanism underlying double fertilization between self-crossed Solanum melongena and that hybridized with Solanum aethiopicum. PLoS One 2020; 15:e0235962. [PMID: 32760091 PMCID: PMC7410197 DOI: 10.1371/journal.pone.0235962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/26/2020] [Indexed: 11/18/2022] Open
Abstract
Wild relatives represent a source of variation for many traits of interest for eggplant (Solanum melongena) breeding, as well as for broadening its genetic base. However, interspecific hybridization with wild relatives has been barely used in eggplant breeding programs, and reproductive barriers have resulted in reduced seed numbers in interspecific combinations. The mechanism underlying this phenomenon remains unclear. We hybridized females of cultivated eggplant 177 (Solanum melongena) with males of wild relatives 53 and Y11 (Solanum aethiopicum). Self-crossed 177 was the control. The seed number per control fruit was significantly higher than that of the hybrids. Paraffin sections showed no significant difference between control and 177×53 and 177×Y11. Double fertilization began 4 days post-pollination. Sperm cells were fused with egg cells 6 days post-pollination. To understand the differences in molecular mechanisms underlying this process, transcriptomes of ovaries at 0, 4, and 6 days after self-crossing and hybridization were analyzed. We screened 22,311 differentially expressed genes (DEGs) between the control and hybrids 4 and 6 days post-pollination. A total of 497 DEGs were shared among all pollination combinations. These DEGs were enriched in plant hormone transduction, cell senescence, metabolism, and biosynthesis pathways. DEG clustering analysis indicated distinct expression patterns between the control and hybrids but not between the hybrids. The DEGs in hybrids involved secondary metabolic process, phenylpropanoid metabolic process, and carboxypeptidase activity, while those in the control involved xyloglucan metabolic process, auxin-activated signaling pathway, cell wall polysaccharide metabolic process, and xyloglucosyl transferase activity. Additionally, 1683 transcription factors, including members of the AP2-ERF, MYB, bHLH, and B3 families may play important roles in self-crossing and hybridization. Our results provide insights into the regulatory mechanisms underlying variations between ovaries of self-crossed and hybrid eggplants and a basis for future studies on crossbreeding Solanum and genetic mechanisms underlying double fertilization.
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Affiliation(s)
- Dandan Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Siqi Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Wenjia Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Ake Liu
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Xuyu Liang
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Ning Yu
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Vegetable Breeding and New Technology Development, Nanning, China
| | - Riyuan Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- * E-mail: (YW); (RC)
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
- * E-mail: (YW); (RC)
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Choi K, Choi J, Lee PA, Roy N, Khan R, Lee HJ, Weon HY, Kong HG, Lee SW. Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant. FRONTIERS IN PLANT SCIENCE 2020; 11:1186. [PMID: 32849735 PMCID: PMC7427413 DOI: 10.3389/fpls.2020.01186] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/22/2020] [Indexed: 05/21/2023]
Abstract
Plant-associated microbiota plays an important role in plant disease resistance. Bacterial wilt resistance of tomato is a function of the quantitative trait of tomato plants; however, the mechanism underlying quantitative resistance is unexplored. In this study, we hypothesized that rhizosphere microbiota affects the resistance of tomato plants against soil-borne bacterial wilt caused by Ralstonia solanacearum. This hypothesis was tested using a tomato cultivar grown in a defined soil with various microbiota transplants. The bacterial wilt-resistant Hawaii 7996 tomato cultivar exhibited marked suppression and induction of disease severity after treatment with upland soil-derived and forest soil-derived microbiotas, respectively, whereas the transplants did not affect the disease severity in the susceptible tomato cultivar Moneymaker. The differential resistance of Hawaii 7996 to bacterial wilt was abolished by diluted or heat-killed microbiota transplantation. Microbial community analysis revealed the transplant-specific distinct community structure in the tomato rhizosphere and the significant enrichment of specific microbial operational taxonomic units (OTUs) in the rhizosphere of the upland soil microbiota-treated Hawaii 7996. These results suggest that the specific transplanted microbiota alters the bacterial wilt resistance in the resistant cultivar potentially through a priority effect.
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Affiliation(s)
- Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Jinhee Choi
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Pyeong An Lee
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
- School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Hang Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Hyun Gi Kong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
- *Correspondence: Seon-Woo Lee,
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Bragard C, Dehnen-Schmutz K, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Van der Wolf J, Kaluski T, Pautasso M, Jacques MA. Pest categorisation of the Ralstonia solanacearum species complex. EFSA J 2019; 17:e05618. [PMID: 32626235 PMCID: PMC7009105 DOI: 10.2903/j.efsa.2019.5618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of the Ralstonia solanacearum species complex (RSSC), a distinguishable cosmopolitan group of bacterial plant pathogens (including R. solanacearum, Ralstonia pseudosolanacearum and two subspecies of Ralstonia syzygii) of the family Burkholderiaceae. The RSSC causes bacterial wilt in solanaceous crops, such as potato, tomato and pepper, but can also cause wilts in other important food crops such as fruit banana, plantain banana and cassava. The pest survives in the soil, and a number of weed species can also be infected by the pest, often asymptomatically. The RSSC is regulated in Council Directive 2000/29/EC (Annex IAII) (indicated by its former name R. solanacearum, as delimited by Yabuuchi et al.) as a harmful organism whose introduction into the EU is banned. In addition, Council Directive 1998/57/EC (amended by Commission Directive 2006/63/CE) concerns the measures to be taken within EU Member States (MS) against the RSSC to (a) detect it and determine its distribution, (b) prevent its occurrence and spread, and (c) control it with the aim of eradication. The pest is present in several EU MS, but in all cases with a restricted distribution and under official control. New phylotypes of the RSSC could enter the EU primarily via host plants for planting (including seed tubers). The pest could establish in the EU, as climatic conditions are favourable, hosts are common and the pathogen has high adaptability. Spread is mainly via plants for planting. Substantial crop losses in the EU would occur in the presence of RSSC epidemics. The RSSC is regarded as one of the world's most important phytopathogenic bacteria due to its broad geographical distribution, large host range, aggressiveness, genetic diversity and long persistence in soil and water. The list of hosts and commodities for which the pest is regulated is incomplete due to the high diversity of hosts and the lack of knowledge of the complete host range. Moreover, the comparative epidemiology of the different pathogen species has not yet been studied. The criteria assessed by the Panel for consideration of the RSSC as potential quarantine pest are met, while, for regulated non-quarantine pests, the criterion on the widespread presence in the EU is not met.
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17
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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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Kim B, Hwang IS, Lee HJ, Lee JM, Seo E, Choi D, Oh CS. Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1017-1030. [PMID: 29352323 DOI: 10.1007/s00122-018-3054-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/12/2018] [Indexed: 06/07/2023]
Abstract
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease. In total, 5259 non-synonymous SNPs were found between the two groups. Among them, only 265 SNPs were located in the coding DNA sequences, and the majority of these SNPs were located on chromosomes 6 and 12. The genes that both carry SNP(s) and are near Bwr-6 and Bwr-12 were selected. In particular, four genes in chromosome 12 encode putative leucine-rich repeat (LRR) receptor-like proteins. SNPs within these four genes were used to develop SNP markers, and each SNP marker was validated by a high-resolution melting method. Consequently, one SNP marker, including a functional SNP in a gene, Solyc12g009690.1, could efficiently distinguish tomato varieties resistant to bacterial wilt from susceptible varieties. These results indicate that Solyc12g009690.1, the gene encoding a putative LRR receptor-like protein, might be tightly linked to Bwr-12, and the SNP marker developed in this study will be useful for selection of tomato cultivars resistant to bacterial wilt.
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Affiliation(s)
- Boyoung Kim
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, South Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, South Korea
| | - Hyung Jin Lee
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Seoul National University, Seoul, 08826, South Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul, 08826, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, 17104, South Korea.
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Salgon S, Raynal M, Lebon S, Baptiste JM, Daunay MC, Dintinger J, Jourda C. Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.). Int J Mol Sci 2018; 19:E357. [PMID: 29370090 PMCID: PMC5855579 DOI: 10.3390/ijms19020357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/02/2022] Open
Abstract
Eggplant cultivation is limited by numerous diseases, including the devastating bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC). Within the RSSC, Ralstonia pseudosolanacearum (including phylotypes I and III) causes severe damage to all solanaceous crops, including eggplant. Therefore, the creation of cultivars resistant to R. pseudosolanacearum strains is a major goal for breeders. An intraspecific eggplant population, segregating for resistance, was created from the cross between the susceptible MM738 and the resistant EG203 lines. The population of 123 doubled haploid lines was challenged with two strains belonging to phylotypes I (PSS4) and III (R3598), which both bypass the published EBWR9 BW-resistance quantitative trait locus (QTL). Ten and three QTLs of resistance to PSS4 and to R3598, respectively, were detected and mapped. All were strongly influenced by environmental conditions. The most stable QTLs were found on chromosomes 3 and 6. Given their estimated physical position, these newly detected QTLs are putatively syntenic with BW-resistance QTLs in tomato. In particular, the QTLs' position on chromosome 6 overlaps with that of the major broad-spectrum tomato resistance QTL Bwr-6. The present study is a first step towards understanding the complex polygenic system, which underlies the high level of BW resistance of the EG203 line.
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Affiliation(s)
- Sylvia Salgon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
- Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), Université de la Réunion, F-97410 Saint-Pierre, France.
- Association Réunionnaise pour la Modernisation de l'Economie Fruitière Légumière et Horticole (ARMEFLHOR), F-97410 Saint-Pierre, France.
| | | | - Sylvain Lebon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Jean-Michel Baptiste
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Marie-Christine Daunay
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génétique et Amélioration des Fruits et Légumes (UR GAFL), F-84143 Montfavet, France.
| | - Jacques Dintinger
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Cyril Jourda
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
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