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Li S, Zhao Y, Wu P, Grierson D, Gao L. Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39016673 DOI: 10.1111/jipb.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high-quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis-related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening-related and defense-related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non-climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high-quality fruit and decrease food waste and related economic losses.
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Affiliation(s)
- Shan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yu Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pan Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Donald Grierson
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Lei Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Chelliah A, Arumugam C, Suthanthiram B, Raman T, Subbaraya U. Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp. Funct Integr Genomics 2022; 23:7. [PMID: 36538175 DOI: 10.1007/s10142-022-00925-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.
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Affiliation(s)
- Anuradha Chelliah
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India.
| | - Chandrasekar Arumugam
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Backiyarani Suthanthiram
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Thangavelu Raman
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Uma Subbaraya
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
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Juškytė AD, Mažeikienė I, Stanys V. Analysis of R Genes Related to Blackcurrant Reversion Virus Resistance in the Comparative Transcriptome of Ribes nigrum cv. Aldoniai. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223137. [PMID: 36432866 PMCID: PMC9692259 DOI: 10.3390/plants11223137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 05/14/2023]
Abstract
Blackcurrant reversion virus (BRV) is the most destructive mite-transmitted pathogen in blackcurrants. The understanding of the resistance to BRV is limited, hindering and delaying the selection process. To identify the resistance (R) gene for BRV resistance, a gene expression analysis based on de novo blackcurrant cv. Aldoniai comparative transcriptome analysis (mock- and BRV-inoculated samples at 2 and 4 days post-inoculation (dpi)) was performed. In this study, 111 annotated clusters associated with pathogenesis according to conservative R gene domains were identified. In virus-infected samples, only Cluster-12591.33361 showed significant expression at 4 dpi. The expression profiles of this cluster were significantly associated with the presence of BRV particles in plant tissues, making it a putative R gene in the dominant resistance strategy in the BRV-Ribes nigrum interaction. The newly identified gene R.nigrum_R belongs to the CC-NBS-LRR class and has 63.9% identity with RPM1 in Populus spp. This study provides new insights on dominant putative R genes related to resistance to BRV in R. nigrum, which could aid targeted research and genetic improvement in breeding programs of blackcurrants.
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Yang J, Xiong C, Li S, Zhou C, Li L, Xue Q, Liu W, Niu Z, Ding X. Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment. BMC PLANT BIOLOGY 2022; 22:529. [PMID: 36376794 PMCID: PMC9661794 DOI: 10.1186/s12870-022-03904-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Dendrobium officinale Kimura et Migo, which contains rich polysaccharides, flavonoids and alkaloids, is a Traditional Chinese Medicine (TCM) with important economic benefits, while various pathogens have brought huge losses to its industrialization. NBS gene family is the largest class of plant disease resistance (R) genes, proteins of which are widely distributed in the upstream and downstream of the plant immune systems and are responsible for receiving infection signals and regulating gene expression respectively. It is of great significance for the subsequent disease resistance breeding of D. officinale to identify NBS genes by using the newly published high-quality chromosome-level D. officinale genome. RESULTS In this study, a total of 655 NBS genes were uncovered from the genomes of D. officinale, D. nobile, D. chrysotoxum, V. planifolia, A. shenzhenica, P. equestris and A. thaliana. The phylogenetic results of CNL-type protein sequences showed that orchid NBS-LRR genes have significantly degenerated on branches a and b. The Dendrobium NBS gene homology analysis showed that the Dendrobium NBS genes have two obvious characteristics: type changing and NB-ARC domain degeneration. Because the NBS-LRR genes have both NB-ARC and LRR domains, 22 D. officinale NBS-LRR genes were used for subsequent analyses, such as gene structures, conserved motifs, cis-elements and functional annotation analyses. All these results suggested that D. officinale NBS-LRR genes take part in the ETI system, plant hormone signal transduction pathway and Ras signaling pathway. Finally, there were 1,677 DEGs identified from the salicylic acid (SA) treatment transcriptome data of D. officinale. Among them, six NBS-LRR genes (Dof013264, Dof020566, Dof019188, Dof019191, Dof020138 and Dof020707) were significantly up-regulated. However, only Dof020138 was closely related to other pathways from the results of WGCNA, such as pathogen identification pathways, MAPK signaling pathways, plant hormone signal transduction pathways, biosynthetic pathways and energy metabolism pathways. CONCLUSION Our results revealed that the NBS gene degenerations are common in the genus Dendrobium, which is the main reason for the diversity of NBS genes, and the NBS-LRR genes generally take part in D. officinale ETI system and signal transduction pathways. In addition, the D. officinale NBS-LRR gene Dof020138, which may have an important breeding value, is indirectly activated by SA in the ETI system.
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Affiliation(s)
- Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Caijun Xiong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Siyuan Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Cheng Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Lingli Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, 210023, China.
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5
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Si Z, Qiao Y, Zhang K, Ji Z, Han J. Genome-wide identification and characterization of NBS-encoding genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.). Open Life Sci 2022; 17:497-511. [PMID: 35647293 PMCID: PMC9102303 DOI: 10.1515/biol-2022-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/24/2022] [Accepted: 03/03/2022] [Indexed: 11/15/2022] Open
Abstract
The most predominant type of resistance (R) genes contain nucleotide-binding sites and leucine-rich repeat (NBS-LRR) domains, characterization of which is helpful for plant resistance improvement. However, the NBS genes of Ipomoea trifida (H.B.K.) remain insufficient to date. In this study, a genome-wide analysis of the NBS-encoding gene in I. trifida (H.B.K.) was carried out. A total of 442 NBS encoding genes were identified, amounting to 1.37% of the total genes of I. trifida (H.B.K.). Based on the analysis of the domains, the identified ItfNBS genes were further classified into seven groups: CNL, NL, CN, N, TNL, TN, and RNL. Phylogenetic analysis showed that the I. trifida NBS genes clustered into three independent clades: RNL, TNL, and CNL. Chromosome location analysis revealed that the distribution of ItfNBS genes in chromosomes was uneven, with a number ranging from 3 to 45. Multiple stress-related regulatory elements were detected in the promoters of the NBS-encoding genes, and their expression profiles were obtained. The qRT-PCR analysis revealed that IbNBS10, IbNBS20, IbNBS258, and IbNBS88 responded to stem nematode infection. These results provide critical proof for further characterization and analysis of NBS-encoding genes with important functions.
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Affiliation(s)
- Zengzhi Si
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology , Qinghuangdao , 066000, Hebei Province , China
| | - Yake Qiao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology , Qinghuangdao , 066000, Hebei Province , China
| | - Kai Zhang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology , Qinghuangdao , 066000, Hebei Province , China
| | - Zhixin Ji
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology , Qinghuangdao , 066000, Hebei Province , China
| | - Jinling Han
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology , Qinghuangdao , 066000, Hebei Province , China
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6
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Edger PP, Iorizzo M, Bassil NV, Benevenuto J, Ferrão LFV, Giongo L, Hummer K, Lawas LMF, Leisner CP, Li C, Munoz PR, Ashrafi H, Atucha A, Babiker EM, Canales E, Chagné D, DeVetter L, Ehlenfeldt M, Espley RV, Gallardo K, Günther CS, Hardigan M, Hulse-Kemp AM, Jacobs M, Lila MA, Luby C, Main D, Mengist MF, Owens GL, Perkins-Veazie P, Polashock J, Pottorff M, Rowland LJ, Sims CA, Song GQ, Spencer J, Vorsa N, Yocca AE, Zalapa J. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. HORTICULTURE RESEARCH 2022; 9:uhac083. [PMID: 35611183 PMCID: PMC9123236 DOI: 10.1093/hr/uhac083] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/22/2022] [Indexed: 06/02/2023]
Abstract
The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nahla V Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Juliana Benevenuto
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lara Giongo
- Fondazione Edmund Mach - Research and Innovation CentreItaly
| | - Kim Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Lovely Mae F Lawas
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changying Li
- Phenomics and Plant Robotics Center, College of Engineering, University of Georgia, Athens, USA
| | - Patricio R Munoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Amaya Atucha
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ebrahiem M Babiker
- USDA-ARS Southern Horticultural Laboratory, Poplarville, MS 39470-0287, USA
| | - Elizabeth Canales
- Department of Agricultural Economics, Mississippi State University, Mississippi State, MS 39762, USA
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Lisa DeVetter
- Department of Horticulture, Washington State University Northwestern Washington Research and Extension Center, Mount Vernon, WA, 98221, USA
| | - Mark Ehlenfeldt
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Karina Gallardo
- School of Economic Sciences, Washington State University, Puyallup, WA 98371, USA
| | - Catrin S Günther
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, New Zealand
| | - Michael Hardigan
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Amanda M Hulse-Kemp
- USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - MacKenzie Jacobs
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Claire Luby
- USDA-ARS, Horticulture Crops Research Unit, Corvallis, OR 97333, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
| | - Molla F Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | | | | | - James Polashock
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Marti Pottorff
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC USA
| | - Lisa J Rowland
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705, USA
| | - Charles A Sims
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Guo-qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Jessica Spencer
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Nicholi Vorsa
- SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 USA
| | - Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Juan Zalapa
- USDA-ARS, VCRU, Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Xu X, Chen Y, Li B, Zhang Z, Qin G, Chen T, Tian S. Molecular mechanisms underlying multi-level defense responses of horticultural crops to fungal pathogens. HORTICULTURE RESEARCH 2022; 9:uhac066. [PMID: 35591926 PMCID: PMC9113409 DOI: 10.1093/hr/uhac066] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 05/21/2023]
Abstract
The horticultural industry helps to enrich and improve the human diet while contributing to growth of the agricultural economy. However, fungal diseases of horticultural crops frequently occur during pre- and postharvest periods, reducing yields and crop quality and causing huge economic losses and wasted food. Outcomes of fungal diseases depend on both horticultural plant defense responses and fungal pathogenicity. Plant defense responses are highly sophisticated and are generally divided into preformed and induced defense responses. Preformed defense responses include both physical barriers and phytochemicals, which are the first line of protection. Induced defense responses, which include innate immunity (pattern-triggered immunity and effector-triggered immunity), local defense responses, and systemic defense signaling, are triggered to counterstrike fungal pathogens. Therefore, to develop regulatory strategies for horticultural plant resistance, a comprehensive understanding of defense responses and their underlying mechanisms is critical. Recently, integrated multi-omics analyses, CRISPR-Cas9-based gene editing, high-throughput sequencing, and data mining have greatly contributed to identification and functional determination of novel phytochemicals, regulatory factors, and signaling molecules and their signaling pathways in plant resistance. In this review, research progress on defense responses of horticultural crops to fungal pathogens and novel regulatory strategies to regulate induction of plant resistance are summarized, and then the problems, challenges, and future research directions are examined.
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Affiliation(s)
- Xiaodi Xu
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- Corresponding authors. E-mail: ;
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding authors. E-mail: ;
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8
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Yu X, Zhong S, Yang H, Chen C, Chen W, Yang H, Guan J, Fu P, Tan F, Ren T, Shen J, Zhang M, Luo P. Identification and Characterization of NBS Resistance Genes in Akebia trifoliata. FRONTIERS IN PLANT SCIENCE 2021; 12:758559. [PMID: 34777439 PMCID: PMC8585750 DOI: 10.3389/fpls.2021.758559] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 05/26/2023]
Abstract
Akebia trifoliata is an important multiuse perennial plant that often suffers attacks from various pathogens due to its long growth cycle, seriously affecting its commercial value. The absence of research on the resistance (R) genes of A. trifoliata has greatly limited progress in the breeding of resistant varieties. Genes encoding proteins containing nucleotide binding sites (NBSs) and C-terminal leucine-rich repeats (LRRs), the largest family of plant resistance (R) genes, are vital for plant disease resistance. A comprehensive genome-wide analysis showed that there were only 73 NBS genes in the A. trifoliata genome, including three main subfamilies (50 coiled coil (CC)-NBS-LRR (CNL), 19 Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and four resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) genes). Additionally, 64 mapped NBS candidates were unevenly distributed on 14 chromosomes, most of which were assigned to the chromosome ends; 41 of these genes were located in clusters, and the remaining 23 genes were singletons. Both the CNLs and TNLs were further divided into four subgroups, and the CNLs had fewer exons than the TNLs. Structurally, all eight previously reported conserved motifs were identified in the NBS domains, and both their order and their amino acid sequences exhibited high conservation. Evolutionarily, tandem and dispersed duplications were shown to be the two main forces responsible for NBS expansion, producing 33 and 29 genes, respectively. A transcriptome analysis of three fruit tissues at four developmental stages showed that NBS genes were generally expressed at low levels, while a few of these genes showed relatively high expression during later development in rind tissues. Overall, this research is the first to identify and characterize A. trifoliata NBS genes and is valuable for both the development of new resistant cultivars and the study of molecular mechanisms of resistance.
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Affiliation(s)
- Xiaojiao Yu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Wei Chen
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Hao Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Ju Guan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peng Fu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Tianheng Ren
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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Si Z, Qiao Y, Zhang K, Ji Z, Han J. Characterization of Nucleotide Binding -Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses. Cytogenet Genome Res 2021; 161:257-271. [PMID: 34320507 DOI: 10.1159/000515834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 11/19/2022] Open
Abstract
Sweetpotato, Ipomoea batatas (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes' expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that IbNBS75, IbNBS219, and IbNBS256 respond to stem nematode infection; Ib-NBS240, IbNBS90, and IbNBS80 respond to cold stress, while IbNBS208, IbNBS71, and IbNBS159 respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.
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Affiliation(s)
- Zengzhi Si
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yake Qiao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Kai Zhang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Zhixin Ji
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jinling Han
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Li T, Zhang Q, Jiang X, Li R, Dhar N. Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species. FRONTIERS IN PLANT SCIENCE 2021; 12:695691. [PMID: 34567025 PMCID: PMC8456104 DOI: 10.3389/fpls.2021.695691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/11/2021] [Indexed: 05/16/2023]
Abstract
Verticillium wilt (VW) is a destructive disease in cotton caused by Verticillium dahliae and has a significant impact on yield and quality. In the absence of safe and effective chemical control, VW is difficult to manage. Thus, at present, developing resistant varieties is the most economical and effective method of controlling Verticillium wilt of cotton. The CC-NBS-LRR (CNL) gene family is an important class of plant genes involved in disease resistance. This study identified 141 GbCNLs in Gossypium barbadense genome, with 37.5% (53 genes) GbCNLs enriched in 12 gene clusters (GC01-GC12) based on gene distribution in the chromosomes. Especially, seven GbCNLs from two largest clusters (GC11 and GC12) were significantly upregulated in the resistant cultivar (Hai No. 7124) and the susceptible (Giza No. 57). Virus-induced gene silencing of GbCNL130 in G. barbadense, one typical gene in the gene cluster 12 (GC12), significantly altered the response to VW, compromising plant resistance to V. dahliae. In contrast, GbCNL130 overexpression significantly increased the resistance to VW in the wild-type Arabidopsis thaliana. Based on our research findings presented here, we conclude that GbCNL130 promotes resistance to VW by activating the salicylic acid (SA)-dependent defense response pathway resulting in strong accumulation of reactive oxygen species and upregulation of pathogenesis-related (PR) genes. In conclusion, our study resulted in the discovery of a new CNL resistance gene in cotton, GbCNL130, that confers resistance to VW across different hosts.
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Affiliation(s)
- Tinggang Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, China
- *Correspondence: Tinggang Li,
| | - Qianqian Zhang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xilong Jiang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ran Li
- Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nikhilesh Dhar
- Department of Plant Pathology, University of California, Davis, Salinas, CA, United States
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11
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Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome. PLANTS 2020; 9:plants9101350. [PMID: 33065969 PMCID: PMC7601643 DOI: 10.3390/plants9101350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022]
Abstract
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present study, we identified 100 NBS-LRR genes in the kiwifruit genome and they were grouped into six distinct classes based on their domain architecture. Of the 100 genes, 79 are truncated non-regular NBS-LRR genes. Except for 37 NBS-LRR genes with no location information, the remaining 63 genes are distributed unevenly across 18 kiwifruit chromosomes and 38.01% of them are present in clusters. Seventeen families of cis-acting elements were identified in the promoters of the NBS-LRR genes, including AP2, NAC, ERF and MYB. Pseudomonas syringae pv. actinidiae (pathogen of the kiwifruit bacterial canker) infection induced differential expressions of 16 detected NBS-LRR genes and three of them are involved in plant immunity responses. Our study provides insight of the NBS-LRR genes in kiwifruit and a resource for the identification of new R-genes in the fruit.
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Liu Z, Xie J, Wang H, Zhong X, Li H, Yu J, Kang J. Identification and expression profiling analysis of NBS-LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage. 3 Biotech 2019; 9:202. [PMID: 31065502 PMCID: PMC6500516 DOI: 10.1007/s13205-019-1714-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/11/2019] [Indexed: 10/26/2022] Open
Abstract
As one of the most important resistance (R) gene families in plants, the NBS-LRR genes, encoding proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains, play significant roles in resisting pathogens. The published genomic data for cabbage (Brassica oleracea L.) provide valuable data to identify and characterize the genomic organization of cabbage NBS-LRR genes. Ultimately, we identified 105 TIR (N-terminal Toll/interleukin-1 receptor)-NBS-LRR (TNL) genes and 33 CC (coiled-coil)-NBS-LRR (CNL) genes. Further research indicated that 50.7% of the 138 NBS-LRR genes exist in 27 clusters and there are large differences among the gene structures and protein characteristics. Conserved motif and phylogenetic analysis showed that the structures of TNLs and CNLs were similar, with some differences. These NBS-LRRs are evolved under negative selection and mostly arose from whole-genome duplication events during evolution. Tissue-expression profiling of NBS-LRR genes revealed that 37.1% of the TNL genes are highly or specifically expressed in roots, especially the genes on chromosome 7 (76.5%). Digital gene expression and reverse transcription PCR analyses revealed the expression patterns of the NBS-LRR genes upon challenge by Fusarium oxysporum f.sp. conglutinans: nine genes were upregulated, and five were downregulated. The major resistance gene Foc1 probably works together with the other four genes in the same cluster to resist F. oxysporum infection.
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Affiliation(s)
- Zeci Liu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070 People’s Republic of China
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097 People’s Republic of China
| | - Jianming Xie
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070 People’s Republic of China
| | - Huiping Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097 People’s Republic of China
| | - Xionghui Zhong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097 People’s Republic of China
| | - Hailong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097 People’s Republic of China
| | - Jihua Yu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070 People’s Republic of China
| | - Jungen Kang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097 People’s Republic of China
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Die JV, Castro P, Millán T, Gil J. Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome. Genes (Basel) 2018; 9:E568. [PMID: 30477134 PMCID: PMC6316259 DOI: 10.3390/genes9120568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/07/2018] [Accepted: 11/19/2018] [Indexed: 11/21/2022] Open
Abstract
Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (R). The most predominant R-genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The NBS genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of cis-regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus.
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Affiliation(s)
- Jose V Die
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Patricia Castro
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Teresa Millán
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Juan Gil
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
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Neupane S, Andersen EJ, Neupane A, Nepal MP. Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.). Genes (Basel) 2018; 9:genes9080384. [PMID: 30061549 PMCID: PMC6115920 DOI: 10.3390/genes9080384] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 01/08/2023] Open
Abstract
Nucleotide Binding Site—Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants’ defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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