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Long H, Sun Y, Chen Y, Pei Y, Feng T, Che H. Occurrence of Root-Knot Nematode ( Meloidogyne spp.) on Peppers in Hainan, China, and M. enterolobii and M. incognita Resistance of Common Cultivars. PLANT DISEASE 2023; 107:3148-3154. [PMID: 37026625 DOI: 10.1094/pdis-02-23-0281-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are the most economically damaging group of plant-parasitic nematodes. They are considered to be a major constraint of pepper (Capsicum annuum L.) crops worldwide. In China, Hainan Island is the main producer of pepper, where the climatic conditions and cropping patterns are favorable for infection by Meloidogyne spp. In this study, we conducted a detailed investigation of the occurrence, severity, and population distribution of root-knot nematodes infesting pepper throughout Hainan Island. We also tested the level of resistance to M. enterolobii and M. incognita of the common pepper cultivars in Hainan. Our results showed that root-knot nematodes belonging to M. enterolobii, M. incognita, and M. javanica were found in Hainan, and the dominant population was M. enterolobii, which is the predominant species in the tropical area. Notably, all the pepper cultivars in this study were highly susceptible to M. enterolobii, which is probably a reason for its rapid spread throughout Hainan. The pepper cultivars exhibited different levels of resistance to M. incognita. This study promotes the comprehensive understanding of the root-knot nematode distribution and host resistance level of Meloidogyne in Hainan, which will guide the effective control of root-knot nematodes.
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Affiliation(s)
- Haibo Long
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Yanfang Sun
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yuan Chen
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yueling Pei
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Tuizi Feng
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haiyan Che
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Elarabi NI, Abdel-Rahman AA, Abdel-Haleem H, Abdel-Hakeem M. Silver and zinc oxide nanoparticles disrupt essential parasitism, neuropeptidergic, and expansion-like proteins genes in Meloidogyne incognita. Exp Parasitol 2022; 243:108402. [DOI: 10.1016/j.exppara.2022.108402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/14/2022] [Accepted: 10/02/2022] [Indexed: 11/04/2022]
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Lee JH, Venkatesh J, Jo J, Jang S, Kim GW, Kim JM, Han K, Ro N, Lee HY, Kwon JK, Kim YM, Lee TH, Choi D, Van Deynze A, Hill T, Kfir N, Freiman A, Davila Olivas NH, Elkind Y, Paran I, Kang BC. High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers. HORTICULTURE RESEARCH 2022; 9:uhac210. [PMID: 36467270 PMCID: PMC9715575 DOI: 10.1093/hr/uhac210] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.
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Affiliation(s)
| | | | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Siyoung Jang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Doil Choi
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Nir Kfir
- NRGene, 5 Golda Meir St., Ness Ziona 7403649, Israel
| | - Aviad Freiman
- Top Seeds International Ltd. Moshav Sharona, 1523200, Israel
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Rutter WB, Franco J, Gleason C. Rooting Out the Mechanisms of Root-Knot Nematode-Plant Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:43-76. [PMID: 35316614 DOI: 10.1146/annurev-phyto-021621-120943] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKNs; Meloidogyne spp.) engage in complex parasitic interactions with many different host plants around the world, initiating elaborate feeding sites and disrupting host root architecture. Although RKNs have been the focus of research for many decades, new molecular tools have provided useful insights into the biological mechanisms these pests use to infect and manipulate their hosts. From identifying host defense mechanisms underlying resistance to RKNs to characterizing nematode effectors that alter host cellular functions, the past decade of research has significantly expanded our understanding of RKN-plant interactions, and the increasing number of quality parasite and host genomes promises to enhance future research efforts into RKNs. In this review, we have highlighted recent discoveries, summarized the current understanding within the field, and provided links to new and useful resources for researchers. Our goal is to offer insights and tools to support the study of molecular RKN-plant interactions.
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Affiliation(s)
- William B Rutter
- US Vegetable Laboratory, USDA Agricultural Research Service, Charleston, South Carolina, USA
| | - Jessica Franco
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA;
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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Han WH, Wang JX, Zhang FB, Liu YX, Wu H, Wang XW. Small RNA and Degradome Sequencing Reveal Important MicroRNA Function in Nicotiana tabacum Response to Bemisia tabaci. Genes (Basel) 2022; 13:361. [PMID: 35205405 PMCID: PMC8871844 DOI: 10.3390/genes13020361] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, are key molecules in many biological and metabolic processes of plant growth, development and stress response via targeting mRNAs. The phloem-feeding insect whitefly Bemisia tabaci (Hemiptera, Aleyrodidae) is a serious pest that causes devastating harm to agricultural production worldwide. However, the function of host miRNAs in the response to whitefly infestation remains unclear. Here, we sequenced the small RNA and degradome of tobacco (Nicotiana tabacum L.), after and before infestation by B. tabaci. We identified 1291 miRNAs belonging to 138 miRNA families including 706 known miRNAs and 585 novel miRNAs. A total of 47 miRNAs were differentially expressed, of which 30 were upregulated and 17 were downregulated by whitefly exposure. Then, computational analysis showed that the target genes of differential miRNAs were involved in R gene regulation, plant innate immunity, plant pathogen defense, the plant hormone signal pathway and abiotic stress tolerance. Furthermore, degradome analysis demonstrated that 253 mRNAs were cleaved by 66 miRNAs. Among them, the targets cleaved by upregulated miR6025, miR160, miR171, miR166 and miR168 are consistent with our prediction, suggesting that pathogen-related miRNAs may function in plant defense against whitefly. Moreover, our results show that plant miRNA response and miRNA-mediated post-transcriptional regulation for phloem-feeding insect infestation are similar to pathogen invasion. Our study provides additional data to further elucidate how host plants respond and defend the phloem-feeding insects.
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Affiliation(s)
| | | | | | | | | | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (W.-H.H.); (J.-X.W.); (F.-B.Z.); (Y.-X.L.); (H.W.)
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A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode. Genes (Basel) 2020; 11:genes11121507. [PMID: 33333784 PMCID: PMC7765216 DOI: 10.3390/genes11121507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.
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