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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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Ijaz S, Ul Haq I, Habib Z, Muti-Ullah, Afzal I, Khan NA, Abdullah. Genome-wide identification, and gene expression analysis of NBS-LRR domain containing R genes in Chenopodium quinoa for unveiling the dynamic contribution in plant immunity against Cercospora cf. chenopodii. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1129-1144. [PMID: 39100881 PMCID: PMC11291812 DOI: 10.1007/s12298-024-01475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 08/06/2024]
Abstract
The plant R genes encode the NLR proteins comprising nucleotide-binding sites (NBS) and variable-length C-terminal leucine-rich repeat domains. The proteins act as intracellular immune receptors and recognize effector proteins of phytopathogens, which convene virulence. Among stresses, diseases contribute majorly to yield loss in crop plants, and R genes confer disease resistance against phytopathogens. We investigated the NLRome of Chenopodium quinoa for intraspecific diversity, characterization, and contribution to immune response regulation against phytopathogens. One eighty-three NBS proteins were identified and grouped into four distinct classes. Exon-intron organization displayed discrimination in gene structure patterns among NLR proteins. Thirty-eight NBS proteins revealed ontology with defense response, ADP binding, and inter alia cellular components. These proteins had shown functional homology with disease-resistance proteins involved in the plant-pathogen interaction pathway. Likewise, expression analysis demonstrated that NLRs encoding genes showed differential expression patterns. However, most genes displayed high expression levels in plant defense response with varying magnitude compared to ADP binding and cellular components. Twenty-four NBS genes were selected based on Heatmap analysis for quantitative polymerase chain reaction under Cercospora disease stress, and their progressive expression pattern provides insights into their functional role under stress conditions. The protein-protein interaction analysis revealed functional enrichment of NLR proteins in regulating hypersensitive, immune, and stress responses. This study, the first to identify and characterize NBS genes in C. quinoa, reveals their contribution to disease response and divulges their dynamic involvement in inducing plant immunity against phytopathogens. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01475-0.
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Affiliation(s)
- Siddra Ijaz
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
| | - Imran Ul Haq
- Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan
| | - Zakia Habib
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
| | - Muti-Ullah
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
| | - Irfan Afzal
- Department of Agronomy, University of Agriculture, University Road, Faisalabad, Pakistan
| | - Nasir Ahmad Khan
- Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan
| | - Abdullah
- Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan
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Ambalavanan A, Mallikarjuna MG, Bansal S, Bashyal BM, Subramanian S, Kumar A, Prakash G. Genome-wide characterization of the NBLRR gene family provides evolutionary and functional insights into blast resistance in pearl millet (Cenchrus americanus (L.) Morrone). PLANTA 2024; 259:143. [PMID: 38704489 DOI: 10.1007/s00425-024-04413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/14/2024] [Indexed: 05/06/2024]
Abstract
MAIN CONCLUSION The investigation is the first report on genome-wide identification and characterization of NBLRR genes in pearl millet. We have shown the role of gene loss and purifying selection in the divergence of NBLRRs in Poaceae lineage and candidate CaNBLRR genes for resistance to Magnaporthe grisea infection. Plants have evolved multiple integral mechanisms to counteract the pathogens' infection, among which plant immunity through NBLRR (nucleotide-binding site, leucine-rich repeat) genes is at the forefront. The genome-wide mining in pearl millet (Cenchrus americanus (L.) Morrone) revealed 146 CaNBLRRs. The variation in the branch length of NBLRRs showed the dynamic nature of NBLRRs in response to evolving pathogen races. The orthology of NBLRRs showed a predominance of many-to-one orthologs, indicating the divergence of NBLRRs in the pearl millet lineage mainly through gene loss events followed by gene gain through single-copy duplications. Further, the purifying selection (Ka/Ks < 1) shaped the expansion of NBLRRs within the lineage of pear millet and other members of Poaceae. Presence of cis-acting elements, viz. TCA element, G-box, MYB, SARE, ABRE and conserved motifs annotated with P-loop, kinase 2, RNBS-A, RNBS-D, GLPL, MHD, Rx-CC and LRR suggests their putative role in disease resistance and stress regulation. The qRT-PCR analysis in pearl millet lines showing contrasting responses to Magnaporthe grisea infection identified CaNBLRR20, CaNBLRR33, CaNBLRR46 CaNBLRR51, CaNBLRR78 and CaNBLRR146 as putative candidates. Molecular docking showed the involvement of three and two amino acid residues of LRR domains forming hydrogen bonds (histidine, arginine and threonine) and salt bridges (arginine and lysine) with effectors. Whereas 14 and 20 amino acid residues of CaNBLRR78 and CaNBLRR20 showed hydrophobic interactions with 11 and 9 amino acid residues of effectors, Mg.00g064570.m01 and Mg.00g006570.m01, respectively. The present investigation gives a comprehensive overview of CaNBLRRs and paves the foundation for their utility in pearl millet resistance breeding through understanding of host-pathogen interactions.
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Affiliation(s)
- Aruljothi Ambalavanan
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sabtharishi Subramanian
- Division of Entomology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India.
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Lynn SC, Dunwell JM, Whitehouse AB, Cockerton HM. Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2024; 15:1376061. [PMID: 38742212 PMCID: PMC11089197 DOI: 10.3389/fpls.2024.1376061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue-specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew.
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Affiliation(s)
- Samantha C. Lynn
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
- Crop Science, University of Reading, Reading, United Kingdom
| | - Jim M. Dunwell
- Crop Science, University of Reading, Reading, United Kingdom
| | - Adam B. Whitehouse
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
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Cao Y, Mo W, Li Y, Xiong Y, Wang H, Zhang Y, Lin M, Zhang L, Li X. Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt. BMC Biol 2024; 22:45. [PMID: 38408951 PMCID: PMC10898138 DOI: 10.1186/s12915-024-01836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung tree. RESULTS Here, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V. fordii and 149 in V. montana. Five VmNBS-LRR paralogous were predicted in V. montana, and 43 orthologous were detected between V. fordii and V. montana. The orthologous gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns in V. fordii and V. montana: Vf11G0978 showed downregulated expression in V. fordii, while its orthologous gene Vm019719 demonstrated upregulated expression in V. montana, indicating that this pair may be responsible for the resistance to Fusarium wilt in V. montana. Vm019719 from V. montana, activated by VmWRKY64, was shown to confer resistance to Fusarium wilt in V. montana by a virus-induced gene silencing (VIGS) experiment. However, in the susceptible V. fordii, its allelic counterpart, Vf11G0978, exhibited an ineffective defense response, attributed to a deletion in the promoter's W-box element. CONCLUSIONS This study provides the first systematic analysis of NBS-LRR genes in the tung tree and identifies a candidate gene that can be utilized for marker-assisted breeding to control Fusarium wilt in V. fordii.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China.
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Wanzhen Mo
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yanli Li
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yao Xiong
- Forestry College, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Mengfei Lin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, 330224, China.
| | - Lin Zhang
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China.
- Hubei Shizhen Laboratory, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Xiaoxu Li
- Beijing Life Science Academy, Beijing, 102209, China.
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Balamurugan A, Mallikarjuna MG, Bansal S, Nayaka SC, Rajashekara H, Chellapilla TS, Prakash G. Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection. BMC PLANT BIOLOGY 2024; 24:75. [PMID: 38281915 PMCID: PMC10823742 DOI: 10.1186/s12870-024-04743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.). RESULTS The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains. CONCLUSION The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.
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Affiliation(s)
- Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - S Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore, 570005, India
| | | | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Singh S, Singh R, Priyadarsini S, Ola AL. Genomics empowering conservation action and improvement of celery in the face of climate change. PLANTA 2024; 259:42. [PMID: 38270699 DOI: 10.1007/s00425-023-04321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024]
Abstract
MAIN CONCLUSION Integration of genomic approaches like whole genome sequencing, functional genomics, evolutionary genomics, and CRISPR/Cas9-based genome editing has accelerated the improvement of crop plants including leafy vegetables like celery in the face of climate change. The anthropogenic climate change is a real peril to the existence of life forms on our planet, including human and plant life. Climate change is predicted to be a significant threat to biodiversity and food security in the coming decades and is rapidly transforming global farming systems. To avoid the ghastly future in the face of climate change, the elucidation of shifts in the geographical range of plant species, species adaptation, and evolution is necessary for plant scientists to develop climate-resilient strategies. In the post-genomics era, the increasing availability of genomic resources and integration of multifaceted genomics elements is empowering biodiversity conservation action, restoration efforts, and identification of genomic regions adaptive to climate change. Genomics has accelerated the true characterization of crop wild relatives, genomic variations, and the development of climate-resilient varieties to ensure food security for 10 billion people by 2050. In this review, we have summarized the applications of multifaceted genomic tools, like conservation genomics, whole genome sequencing, functional genomics, genome editing, pangenomics, in the conservation and adaptation of plant species with a focus on celery, an aromatic and medicinal Apiaceae vegetable. We focus on how conservation scientists can utilize genomics and genomic data in conservation and improvement.
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Affiliation(s)
- Saurabh Singh
- Department of Vegetable Science, Rani Lakshmi Bai Central Agricultural University, Jhansi, UP, 284003, India.
| | - Rajender Singh
- Division of Crop Improvement and Seed Technology, ICAR-Central Potato Research Institute (CPRI), Shimla, India
| | - Srija Priyadarsini
- Institute of Agricultural Sciences, SOA (Deemed to be University), Bhubaneswar, 751029, India
| | - Arjun Lal Ola
- Department of Vegetable Science, Rani Lakshmi Bai Central Agricultural University, Jhansi, UP, 284003, India
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Sirangelo TM. NLR- and mlo-Based Resistance Mechanisms against Powdery Mildew in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2023; 13:105. [PMID: 38202413 PMCID: PMC10780410 DOI: 10.3390/plants13010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Powdery mildew (PM) is one of the most common Cannabis sativa diseases. In spite of this, very few documented studies have characterized the resistance genes involved in PM defense mechanisms, or sources of natural genetic resistance in cannabis. The focus of the present work is on the two primary mechanisms for qualitative resistance against PM. The first is based on resistance (R) genes characterized by conserved nucleotide-binding site and/or leucine-rich repeat domains (NLRs). The second one involves susceptibility (S) genes, and particularly mildew resistance locus o (MLO) genes, whose loss-of-function mutations seem to be a reliable way to protect plants from PM infection. Cannabis defenses against PM are thus discussed, mainly detailing the strategies based on these two mechanisms. Emerging studies about this research topic are also reported and, based on the most significant results, a potential PM resistance model in cannabis plant-pathogen interactions is proposed. Finally, innovative approaches, based on the pyramiding of multiple R genes, as well as on genetic engineering and genome editing methods knocking out S genes, are discussed, to obtain durable PM-resistant cannabis cultivars with a broad-spectrum resistance range.
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Affiliation(s)
- Tiziana M Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123 Rome, Italy
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Tahir ul Qamar M, Sadaqat M, Zhu XT, Li H, Huang X, Fatima K, Almutairi MM, Chen LL. Comparative genomics profiling revealed multi-stress responsive roles of the CC-NBS-LRR genes in three mango cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1285547. [PMID: 37965009 PMCID: PMC10642748 DOI: 10.3389/fpls.2023.1285547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three Mangifera indica cultivars (Alphonso, Hong Xiang Ya, and Tommy atkins) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from H. Xiang Ya, and 1266 genes and 2098 PAVs from T. atkins were added to the reference genome. For the identification of CC-NBS-LRR (CNL) genes in these mango cultivars, this draft pan-genome study has successfully identified 47, 27, and 36 members in Alphonso, H. Xiang Ya, and T. atkins respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All MiCNL genes are unevenly distributed on chromosomes. Both tandem and segmental duplication events played a significant role in the expansion of the CNL gene family. These genes contain cis-elements related to light, stress, hormone, and development. The analysis of protein-protein interactions (PPI) revealed that MiCNL proteins interacted with other defense-responsive proteins. Gene Ontology (GO) analysis indicated that MiCNL genes play a role in defense mechanisms within the organism. The expression level of the identified genes in fruit peel was observed under disease and cold stress which showed that Mi_A_CNL13 and 14 were up-regulated while Mi_A_CNL15, 25, 30, 31, and 40 were down-regulated in disease stress. On the other hand, Mi_A_CNL2, 14, 41, and 45 were up-regulated and Mi_A_CNL47 is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of MiCNLs. It was found that Mi_A_CNL14 is a gene that responds to multiple stress conditions. The CNLs have similar protein structures which show that they are involved in the same function. The above findings provide a foundation for a deeper understanding of the functional characteristics of the mango CNL gene family.
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Affiliation(s)
- Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Xi-Tong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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Sirangelo TM, Ludlow RA, Spadafora ND. Molecular Mechanisms Underlying Potential Pathogen Resistance in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2023; 12:2764. [PMID: 37570918 PMCID: PMC10420965 DOI: 10.3390/plants12152764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Cannabis (Cannabis sativa L.) is one of the earliest cultivated crops, valued for producing a broad spectrum of compounds used in medicinal products and being a source of food and fibre. Despite the availability of its genome sequences, few studies explore the molecular mechanisms involved in pathogen defense, and the underlying biological pathways are poorly defined in places. Here, we provide an overview of Cannabis defence responses against common pathogens, such as Golovinomyces spp., Fusarium spp., Botrytis cinerea and Pythium spp. For each of these pathogens, after a summary of their characteristics and symptoms, we explore studies identifying genes involved in Cannabis resistance mechanisms. Many studies focus on the potential involvement of disease-resistance genes, while others refer to other plants however whose results may be of use for Cannabis research. Omics investigations allowing the identification of candidate defence genes are highlighted, and genome editing approaches to generate resistant Cannabis species based on CRISPR/Cas9 technology are discussed. According to the emerging results, a potential defence model including both immune and defence mechanisms in Cannabis plant-pathogen interactions is finally proposed. To our knowledge, this is the first review of the molecular mechanisms underlying pathogen resistance in Cannabis.
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Affiliation(s)
- Tiziana M. Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123 Rome, Italy
| | - Richard A. Ludlow
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK;
| | - Natasha D. Spadafora
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
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Alsamman AM, Mousa KH, Nassar AE, Faheem MM, Radwan KH, Adly MH, Hussein A, Istanbuli T, Mokhtar MM, Elakkad TA, Kehel Z, Hamwieh A, Abdelsattar M, El Allali A. Identification, characterization, and validation of NBS-encoding genes in grass pea. Front Genet 2023; 14:1187597. [PMID: 37408775 PMCID: PMC10318170 DOI: 10.3389/fgene.2023.1187597] [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: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023] Open
Abstract
Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mostafa M. Faheem
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Monica H. Adly
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Tamer Ahmed Elakkad
- Department of Genetics and Genetic Engineering, Faculty of Agriculture at Moshtohor, Benha University, Benha, Egypt
- Moshtohor Research Park, Molecular Biology Lab, Benha University, Benha, Egypt
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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13
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Li P, Tan X, Liu R, Rahman FU, Jiang J, Sun L, Fan X, Liu J, Liu C, Zhang Y. QTL detection and candidate gene analysis of grape white rot resistance by interspecific grape ( Vitis vinifera L. × Vitis davidii Foex.) crossing. HORTICULTURE RESEARCH 2023; 10:uhad063. [PMID: 37249950 PMCID: PMC10208900 DOI: 10.1093/hr/uhad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/10/2023] [Indexed: 05/31/2023]
Abstract
Grape white rot, a devastating disease of grapevines caused by Coniella diplodiella (Speg.) Sacc., leads to significant yield losses in grape. Breeding grape cultivars resistant to white rot is essential to reduce the regular use of chemical treatments. In recent years, Chinese grape species have gained more attention for grape breeding due to their high tolerance to various biotic and abiotic factors along with changing climatic conditions. In this study, we employed whole-genome resequencing (WGR) to genotype the parents of 'Manicure Finger' (Vitis vinifera, female) and '0940' (Vitis davidii, male), along with 101 F1 mapping population individuals, thereby constructing a linkage genetic map. The linkage map contained 9337 single-nucleotide polymorphism (SNP) markers with an average marker distance of 0.3 cM. After 3 years of phenotypic evaluation of the progeny for white rot resistance, we confirmed one stable quantitative trait locus (QTL) for white rot resistance on chromosome 3, explaining up to 17.9% of the phenotypic variation. For this locus, we used RNA-seq to detect candidate gene expression and identified PR1 as a candidate gene involved in white rot resistance. Finally, we demonstrated that recombinant PR1 protein could inhibit the growth of C. diplodiella and that overexpression of PR1 in susceptible V. vinifera increased grape resistance to the pathogen.
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Affiliation(s)
- Peng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Xibei Tan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Ruitao Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Faiz Ur Rahman
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Jianfu Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Lei Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Xiucai Fan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China
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Yin T, Han P, Xi D, Yu W, Zhu L, Du C, Yang N, Liu X, Zhang H. Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis). Gene 2023; 854:147117. [PMID: 36526123 DOI: 10.1016/j.gene.2022.147117] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The NBS-LRR (nucleotide-binding site-leucine-rich repeat gene) gene family, known as the plant R (resistance) gene family with the most members, plays a significant role in plant resistance to various external adversity stresses. The NBS-LRR gene family has been researched in many plant species. Citrus is one of the most vital global cash crops, the number one fruit group, and the third most traded agricultural product world wild. However, as one of the largest citrus species, a comprehensive study of the NBS-LRR gene family has not been reported on sweet oranges. METHODS In this study, NBS-LRR genes were identified from the Citrus sinensis genome (v3.0), with a comprehensive analysis of this gene family performed, including phylogenetic analysis, gene structure, cis-acting element of a promoter, and chromosomal localization, among others. The expression pattern of NBS-LRR genes was analyzed when sweet orange fruits were infected by Penicillium digitatum, employing experimental data from our research group. It first reported the expression patterns of NBS-LRR genes under abiotic stresses, using three transcript data from NCBI (National Center for Biotechnology Information). RESULTS In this study, 111 NBS-LRR genes were identified in the C. sinensis genome (v3.0) and classified into seven subfamilies according to their N-terminal and C-terminal domains. The phylogenetic tree results indicate that genes containing only the NBS structural domain are more ancient in the sweet orange NBS-LRR gene family. The chromosome localization results showed that 111 NBS-LRR genes were distributed unevenly on nine chromosomes, with the most genes distributed on chromosome 1. In addition, we identified a total of 18 tandem duplication gene pairs in the sweet orange NBS-LRR gene family, and based on the Ka/Ks ratio, all of the tandem duplication genes underwent purifying selection. Transcriptome data analysis showed a significant number of NBS-LRR genes expressed under biotic and abiotic stresses, and some reached significantly different levels of expression. It indicates that the NBS-LRR gene family is vital in resistance to biotic and abiotic stresses in sweet oranges. CONCLUSION Our study provides the first comprehensive framework on the NBS-LRR family of genes, which provides a basis for further in-depth studies on the biological functions of NBS-LRR in growth, development, and response to abiotic stresses in sweet orange.
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Affiliation(s)
- Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Peichen Han
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Dengxian Xi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Wencai Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Ling Zhu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Chaojin Du
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Xiaozhen Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Hanyao Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
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15
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Ribeiro C, Xu J, Hendrich C, Pandey SS, Yu Q, Gmitter FG, Wang N. Seasonal Transcriptome Profiling of Susceptible and Tolerant Citrus Cultivars to Citrus Huanglongbing. PHYTOPATHOLOGY 2023; 113:286-298. [PMID: 36001783 DOI: 10.1094/phyto-05-22-0179-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Citrus huanglongbing (HLB) caused by 'Candidatus Liberibacter asiaticus' (CLas) is the most devastating citrus disease worldwide. Most commercial citrus cultivars are susceptible to HLB, with a few more tolerant exceptions such as 'LB8-9' Sugar Belle mandarin. Transcriptomic analyses have been widely used to investigate the potential mechanisms for disease susceptibility, resistance, or tolerance. Previous transcriptomic studies related to HLB mostly focused on single time point data collection. We hypothesize that changes in day length and temperature throughout the seasons have profound effects on citrus-CLas interactions. Here, we conducted RNA-seq analyses on HLB-susceptible Valencia sweet orange and HLB-tolerant mandarin 'LB8-9' in winter, spring, summer, and fall. Significant variations in differentially expressed genes (DEGs) related to HLB were observed among the four seasons. For both cultivars, the highest number of DEGs were found in the spring. CLas infection stimulates the expression of immune-related genes such as NBS-LRR, RLK, RLCK, CDPK, MAPK pathway, reactive oxygen species (ROS), and PR genes in both cultivars, consistent with the model that HLB is a pathogen-triggered immune disease. HLB-positive mandarin 'LB8-9' trees contained higher concentrations of maltose and sucrose, which are known to scavenge ROS. In addition, mandarin 'LB8-9' showed higher expression of genes involved in phloem regeneration, which might contribute to its HLB tolerance. This study shed light on the pathogenicity mechanism of the HLB pathosystem and the tolerance mechanism against HLB, providing valuable insights into HLB management.
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Affiliation(s)
- Camila Ribeiro
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Connor Hendrich
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Sheo Shankar Pandey
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Qibin Yu
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Frederick G Gmitter
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
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16
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Tong C, Zhang Y, Shi F. Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica. Front Genet 2023; 13:1088763. [PMID: 36704335 PMCID: PMC9871256 DOI: 10.3389/fgene.2022.1088763] [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: 11/03/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which is the largest family of plant disease resistance genes (R genes). A total of 338 NLR genes were identified in the M. ruthenica genome, including 160 typical genes that contained 80 coiled-coil (CC)-NBS-LRR (CNL) genes, 76 toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes, four resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) subclass genes, and 178 atypical NLR genes encoding proteins without at least one important domain. Among its eight chromosomes, M. ruthenica chromosomes 3 and 8 contained most of the NLR genes. More than 40% of all NLR genes were located on these two chromosomes, mainly in multigene clusters. The NLR proteins of M. ruthenica had six highly conserved motifs: P-loop, GLPL, RNBS-D, kinase-2, RNBS-C, and MHDV. Phylogenetic analysis revealed that the NLR genes of M. ruthenica formed three deeply separated clades according to the N-terminal domain of the proteins encoded by these genes. Gene duplication and syntenic analysis suggested four gene duplication types in the NLR genes of M. ruthenica, namely, tandem, proximal, dispersed, and segmental duplicates, which involved 189, 49, 59, and 41 genes, respectively. A total of 41 segmental duplication genes formed 23 NLR gene pairs located on syntenic chromosomal blocks mainly between chromosomes 6 and 7. In addition, syntenic analysis between M. truncatula and M. ruthenica revealed 193 gene pairs located on syntenic chromosomal blocks of the two species. The expression analysis of M. ruthenica NLR genes showed that 303 (89.6%) of the NLR genes were expressed in different varieties. Overall, this study described the full NLR profile of the M. ruthenica genome to provide an important resource for mining disease-resistant genes and disease-resistant breeding.
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Affiliation(s)
- Chunyan Tong
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Yutong Zhang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China,*Correspondence: Fengling Shi,
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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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18
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Khan K, Van Aken O. The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7182-7197. [PMID: 36055768 PMCID: PMC9675596 DOI: 10.1093/jxb/erac351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.
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Affiliation(s)
- Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
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Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis of DcAP2/ERF#96 Associated with Abiotic Stress in Dendrobium catenatum. Int J Mol Sci 2022; 23:ijms232113603. [PMID: 36362389 PMCID: PMC9659080 DOI: 10.3390/ijms232113603] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
APETALA2/Ethylene Responsive Factor (AP2/ERF) family plays important roles in reproductive development, stress responses and hormone responses in plants. However, AP2/ERF family has not been systematically studied in Dendrobium catenatum. In this study, 120 AP2/ERF family members were identified for the first time in D. catenatum, which were divided into four groups (AP2, RAV, ERF and DREB subfamily) according to phylogenetic analysis. Gene structures and conserved motif analysis showed that each DcAP2/ERF family gene contained at least one AP2 domain, and the distribution of motifs varied among subfamilies. Cis-element analysis indicated that DcAP2/ERF genes contained abundant cis-elements related to hormone signaling and stress response. To further identify potential genes involved in drought stress, 12 genes were selected to detect their expression under drought treatment through qRT-PCR analysis and DcAP2/ERF#96, a nuclear localized ethylene-responsive transcription factor, showed a strong response to PEG treatment. Overexpression of DcAP2/ERF#96 in Arabidopsis showed sensitivity to ABA. Molecular, biochemical and genetic assays indicated that DcAP2ERF#96 interacts with DREB2A and directly inhibits the expression of P5CS1 in response to the ABA signal. Taken together, our study provided a molecular basis for the intensive study of DcAP2/ERF genes and revealed the biological function of DcAP2ERF#96 involved in the ABA signal.
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20
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Gong P, Kang J, Sadeghnezhad E, Bao R, Ge M, Zhuge Y, Shangguan L, Fang J. Transcriptional Profiling of Resistant and Susceptible Cultivars of Grapevine ( Vitis L.) Reveals Hypersensitive Responses to Plasmopara viticola. Front Microbiol 2022; 13:846504. [PMID: 35572700 PMCID: PMC9097084 DOI: 10.3389/fmicb.2022.846504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Grapevine downy mildew is the most serious disease of grapevine cultivars that affects the rate of resistance/susceptibility to Plasmopara viticola. In this study, we used the susceptible cultivar "Zitian Seedless" and the resistant cultivar "Kober 5BB" as materials to determine the transcriptome differences and phenotypes of the leaves after inoculation with downy mildew. The differences in microstructures and molecular levels were compared and analyzed. Fluorescence staining and microscopic observations confirmed that hypersensitive cell death occurred around the stomata in "Kober 5BB" infected by downy mildew zoospores. Meanwhile, transcriptomic profiling indicated that there were 11,713 and 6,997 gene expression differences between the resistant and susceptible cultivars at 72 h after inoculation when compared to control (0 h), respectively. The differentially expressed genes of the two cultivars are significantly enriched in different pathways, including response to plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, phenylpropanoid, and flavonoid biosynthesis. Furthermore, the results of functional enrichment analysis showed that H2O2 metabolism, cell death, reactive oxygen response, and carbohydrate metabolism are also involved in the defense response of "Kober 5BB," wherein a total of 322 key genes have been identified. The protein interaction network showed that metacaspases (MCAs), vacuolar processing enzymes (VPEs), and Papain-like cysteine proteases (PLCPs) play an important role in the execution of hypersensitive responses (HR). In conclusion, we demonstrated that HR cell death is the key strategy in the process of grape defense against downy mildew, which may be mediated or activated by Caspase-like proteases.
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Affiliation(s)
- Peijie Gong
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jun Kang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ehsan Sadeghnezhad
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ruoxuan Bao
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Mengqing Ge
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yaxian Zhuge
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
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21
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Fick A, Swart V, Backer R, Bombarely A, Engelbrecht J, van den Berg N. Partially Resistant Avocado Rootstock Dusa ® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Infection. FRONTIERS IN PLANT SCIENCE 2022; 13:793644. [PMID: 35360305 PMCID: PMC8963474 DOI: 10.3389/fpls.2022.793644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Avocado is an important agricultural food crop in many countries worldwide. Phytophthora cinnamomi, a hemibiotrophic oomycete, remains one of the most devastating pathogens within the avocado industry, as it is near impossible to eradicate from areas where the pathogen is present. A key aspect to Phytophthora root rot disease management is the use of avocado rootstocks partially resistant to P. cinnamomi, which demonstrates an increased immune response following infection. In plant species, Nucleotide binding-Leucine rich repeat (NLR) proteins form an integral part of pathogen recognition and Effector triggered immune responses (ETI). To date, a comprehensive set of Persea americana NLR genes have yet to be identified, though their discovery is crucial to understanding the molecular mechanisms underlying P. americana-P. cinnamomi interactions. In this study, a total of 161 PaNLR genes were identified in the P. americana West-Indian pure accession genome. These putative resistance genes were characterized using bioinformatic approaches and grouped into 13 distinct PaNLR gene clusters, with phylogenetic analysis revealing high sequence similarity within these clusters. Additionally, PaNLR expression levels were analyzed in both a partially resistant (Dusa®) and a susceptible (R0.12) avocado rootstock infected with P. cinnamomi using an RNA-sequencing approach. The results showed that the partially resistant rootstock has increased expression levels of 84 PaNLRs observed up to 24 h post-inoculation, while the susceptible rootstock only showed increased PaNLR expression during the first 6 h post-inoculation. Results of this study may indicate that the partially resistant avocado rootstock has a stronger, more prolonged ETI response which enables it to suppress P. cinnamomi growth and combat disease caused by this pathogen. Furthermore, the identification of PaNLRs may be used to develop resistant rootstock selection tools, which can be employed in the avocado industry to accelerate rootstock screening programs.
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Affiliation(s)
- Alicia Fick
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Robert Backer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (IBMCP-CSIC-UPV), Valencia, Spain
| | - Juanita Engelbrecht
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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22
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Zhang H, Ye Z, Liu Z, Sun Y, Li X, Wu J, Zhou G, Wan Y. The Cassava NBS-LRR Genes Confer Resistance to Cassava Bacterial Blight. FRONTIERS IN PLANT SCIENCE 2022; 13:790140. [PMID: 35178059 PMCID: PMC8844379 DOI: 10.3389/fpls.2022.790140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/07/2022] [Indexed: 05/25/2023]
Abstract
Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Genes encoding nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are among the most important disease resistance genes in plants that are specifically involved in the response to diverse pathogens. However, the in vivo roles of NBS-LRR remain unclear in cassava (Manihot esculenta). In this study, we isolated four MeLRR genes and assessed their expression under salicylic acid (SA) treatment and Xam inoculation. Four MeLRR genes positively regulate cassava disease general resistance against Xam via virus-induced gene silencing (VIGS) and transient overexpression. During cassava-Xam interaction, MeLRRs positively regulated endogenous SA and reactive oxygen species (ROS) accumulation and pathogenesis-related gene 1 (PR1) transcripts. Additionally, we revealed that MeLRRs positively regulated disease resistance in Arabidopsis. These pathogenic microorganisms include Pseudomonas syringae pv. tomato, Alternaria brassicicola, and Botrytis cinerea. Our findings shed light on the molecular mechanism underlying the regulation of cassava resistance against Xam inoculation.
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Affiliation(s)
- He Zhang
- 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, China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Zi Ye
- 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, China
| | - Zhixin Liu
- 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, China
| | - Yu 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, China
| | - Xinyu Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Jiao Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Guangzhen Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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23
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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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24
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Xing J, Zhang D, Yin F, Zhong Q, Wang B, Xiao S, Ke X, Wang L, Zhang Y, Zhao C, Lu Y, Chen L, Cheng Z, Chen L. Identification and Fine-Mapping of a New Bacterial Blight Resistance Gene, Xa47(t), in G252, an Introgression Line of Yuanjiang Common Wild Rice ( Oryza rufipogon). PLANT DISEASE 2021; 105:4106-4112. [PMID: 34261357 DOI: 10.1094/pdis-05-21-0939-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F2 population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F2 progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.
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Affiliation(s)
- Jiaxin Xing
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Dunyu Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Fuyou Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Qiaofang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Bo Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Suqin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Xue Ke
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lingxian Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Yun Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Caimei Zhao
- College of Life Science, Yunnan University, Kunming, Yunnan 650091, P.R. China
| | - Yuanda Lu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Zaiquan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lijuan Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
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25
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Takenaka S, Takada A, Kimura Y, Watanabe M, Kuntiya A. Improvement of the halotolerance of a Bacillus serine protease by protein surface engineering. J Basic Microbiol 2021; 62:174-184. [PMID: 34811778 DOI: 10.1002/jobm.202100335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/24/2021] [Accepted: 11/06/2021] [Indexed: 11/07/2022]
Abstract
A moderately halotolerant serine protease was previously isolated from Bacillus subtilis from salted, fermented food. Eight mutation sites on the protein surface were selected for protein engineering based on sequence and structural comparisons with moderately halotolerant proteases and homologous non-halotolerant proteases. The newly constructed multiple mutants with substituted Asp and Arg residues were compared with the recombinant wild type (rApr) and the previously constructed mAla-8 substituted with Ala to analyze the contribution of protein surface charge to the salt adaptation of the protease. The three mutants showed >1.2-fold greater halotolerance than rApr. In addition, the mutants showed a broader range of pH stability than rApr, retaining >80% of their maximum activity in the pH range 5.0-11. The mutants also retained >75% of their activity after incubation for 1 h at pH 8.0 and 55°C or at pH 11.5 and 25°C. The Asp and Arg residues exchanged by multiple substitution probably played a role in increasing protein surface hydration and solubility in high salt conditions. This study illustrated that increasing a high proportion of the negative or positive charge on the surface of the Bacillus serine protease stably improved the protein's salt adaptation.
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Affiliation(s)
- Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Airi Takada
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masanori Watanabe
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Ampin Kuntiya
- Bioprocess Research Cluster, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
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26
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Goyal N, Bhatia G, Garewal N, Upadhyay A, Singh K. Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera. BMC Genomics 2021; 22:776. [PMID: 34717533 PMCID: PMC8556916 DOI: 10.1186/s12864-021-08081-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/10/2021] [Indexed: 12/04/2022] Open
Abstract
Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08081-4.
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Affiliation(s)
- Neetu Goyal
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, -160014, India
| | - Garima Bhatia
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, -160014, India
| | - Naina Garewal
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, -160014, India
| | - Anuradha Upadhyay
- National Research Centre for Grapes, Solapur Road, Pune, Maharashtra, 412 307, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, -160014, India.
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27
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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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28
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Kamble MV, Shahapurkar AB, Adhikari S, Geetha N, Syed A, Ahmed B, Jogaiah S. Identification and Characterization of Downy Mildew-Responsive microRNAs in Indian Vitis vinifera by High-Throughput Sequencing. J Fungi (Basel) 2021; 7:jof7110899. [PMID: 34829189 PMCID: PMC8619265 DOI: 10.3390/jof7110899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Downy mildew (DM) is one of the most devastating diseases disturbing viticulture, mainly during temperate and humid climates. The DM pathogen can attack grapevine leaves and berries differentially, and the disease is managed with recurring applications of fungicides that direct pathogen pressure, develop of resistant strains, and lead to residual soil toxicity and increased pollution effects. Plant microRNAs (miRNAs) are important candidates in physiological regulatory roles in response to biotic stress in plants. In this study, high-throughput sequencing and MiRDeep-P were employed to identify miRNAs in Vitis vinifera. Altogether, 22,492,910, 25,476,471, and 22,448,438 clean reads from the sterile distilled water (SDW)-control, bio-pesticide Trichoderma harzianum (TriH_JSB36)-treated, and downy mildew Plasmopara viticola pathogen libraries, respectively, were obtained. On the basis of the sequencing results and analysis (differential expression analysis), we observed significant differences in 15 miRNAs (5 novel upregulated, and 10 known downregulated) in the pathogen-infected sample (Test) in comparison to the SDW-control sample, with majority of the reads beingin the range of 20-24 bp. This study involves the identification and characterization of vvi-miRNAs that are involved in resistance against downy mildew disease in grapes.
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Affiliation(s)
- Milan V. Kamble
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad 580003, Karnataka, India; (M.V.K.); (A.B.S.); (S.A.)
| | - Abhishek B. Shahapurkar
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad 580003, Karnataka, India; (M.V.K.); (A.B.S.); (S.A.)
| | - Shivakantkumar Adhikari
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad 580003, Karnataka, India; (M.V.K.); (A.B.S.); (S.A.)
| | - Nagaraja Geetha
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Mysore 570005, Karnataka, India;
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Bilal Ahmed
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea;
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad 580003, Karnataka, India; (M.V.K.); (A.B.S.); (S.A.)
- Correspondence: ; Tel.: +91-836-2779533; Fax: +91-836-2747884
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Pimentel D, Amaro R, Erban A, Mauri N, Soares F, Rego C, Martínez-Zapater JM, Mithöfer A, Kopka J, Fortes AM. Transcriptional, hormonal, and metabolic changes in susceptible grape berries under powdery mildew infection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6544-6569. [PMID: 34106234 DOI: 10.1093/jxb/erab258] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Grapevine (Vitis vinifera) berries are extremely sensitive to infection by the biotrophic pathogen Erysiphe necator, causing powdery mildew disease with deleterious effects on grape and wine quality. The combined analysis of the transcriptome and metabolome associated with this common fungal infection has not been previously carried out in any fruit. In order to identify the molecular, hormonal, and metabolic mechanisms associated with infection, healthy and naturally infected V. vinifera cv. Carignan berries were collected at two developmental stages: late green (EL33) and early véraison (EL35). RNA sequencing combined with GC-electron impact ionization time-of-flight MS, GC-electron impact ionization/quadrupole MS, and LC-tandem MS analyses revealed that powdery mildew-susceptible grape berries were able to activate defensive mechanisms with the involvement of salicylic acid and jasmonates and to accumulate defense-associated metabolites (e.g. phenylpropanoids, fatty acids). The defensive strategies also indicated organ-specific responses, namely the activation of fatty acid biosynthesis. However, defense responses were not enough to restrict fungal growth. The fungal metabolic program during infection involves secretion of effectors related to effector-triggered susceptibility, carbohydrate-active enzymes and activation of sugar, fatty acid, and nitrogen uptake, and could be under epigenetic regulation. This study also identified potential metabolic biomarkers such as gallic, eicosanoic, and docosanoic acids and resveratrol, which can be used to monitor early stages of infection.
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Affiliation(s)
- Diana Pimentel
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Nuria Mauri
- Instituto de Ciencias de la Vid y del Vino, CSIC-UR-Gobierno de La Rioja, Ctra. de Burgos km 6, 26007 Logroño, Spain
| | - Flávio Soares
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cecília Rego
- Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - José M Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, CSIC-UR-Gobierno de La Rioja, Ctra. de Burgos km 6, 26007 Logroño, Spain
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max-Planck-Institute for Chemical Ecology, 07745 Jena, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Ana Margarida Fortes
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
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Fayyaz L, Tenscher A, Viet Nguyen A, Qazi H, Walker MA. Vitis Species from the Southwestern United States Vary in Their Susceptibility to Powdery Mildew. PLANT DISEASE 2021; 105:2418-2425. [PMID: 34494871 DOI: 10.1094/pdis-10-20-2103-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The European grapevine (Vitis vinifera L.) has been cultivated in North America for about 500 years. One of the major limitations to its culture is the powdery mildew (PM) fungus, Erysiphe necator Schw. This study reports on the most extensive screening of Vitis species from the southwestern United States and northern Mexico for resistance to PM, testing 147 accessions of 13 Vitis species. In addition, Vitis vinifera cv. Carignane, a highly susceptible wine grape cultivar, was used as a reference to evaluate the effect of the inoculum 14 days postinoculation. Inoculation was done with a vacuum-operated settling tower using a broadly virulent isolate of E. necator, the C-strain. Resistant accessions (nine), moderately susceptible accessions (39), and highly susceptible accessions (99) were detected. The resistant accessions were then inoculated with an additional fungal isolate, e1-101, and they retained their resistance. Vitis species susceptibility was not associated with a North-South gradation, but Western species were more susceptible than Midwestern and Eastern species. All five of the V. monticola accessions were susceptible, as were the accessions of V. treleasei. The species V. acerifolia, V. candicans, V. cinerea, and V. × doaniana had significantly more resistant to moderately susceptible accessions compared with V. arizonica, V. berlandieri, V. californica, V. × champinii, V. girdiana, V. riparia, and V. rupestris, which had relatively more susceptible accessions than the other species. This research identified new sources of PM resistance in Vitis from the southwestern United States that could be incorporated into PM resistance breeding programs throughout the world.
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Affiliation(s)
- Laila Fayyaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616-5270
| | - Alan Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616-5270
| | - Andy Viet Nguyen
- Department of Viticulture and Enology, University of California, Davis, CA 95616-5270
| | - Huma Qazi
- Department of Viticulture and Enology, University of California, Davis, CA 95616-5270
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616-5270
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Bhatia G, Upadhyay SK, Upadhyay A, Singh K. Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection. BMC PLANT BIOLOGY 2021; 21:265. [PMID: 34103007 PMCID: PMC8186045 DOI: 10.1186/s12870-021-03059-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/23/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. RESULTS Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for 'response to stress', 'response to biotic stimulus', 'immune system process', etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. CONCLUSIONS Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.
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Affiliation(s)
- Garima Bhatia
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, 160014, India
| | | | - Anuradha Upadhyay
- National Research Centre for Grapes, Solapur Road, Pune, Maharashtra, 412307, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, 160014, India.
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Bhattarai K, Conesa A, Xiao S, Peres NA, Clark DG, Parajuli S, Deng Z. Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance. BMC PLANT BIOLOGY 2020; 20:539. [PMID: 33256589 PMCID: PMC7706040 DOI: 10.1186/s12870-020-02742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/16/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy is one of the most important flowers in the global floricultural trade, and powdery mildew (PM) is the most important disease of gerbera. Genetic improvement of gerbera PM resistance has become a crucial goal in gerbera breeding. A better understanding of the genetic control of gerbera resistance to PM can expedite the development of PM-resistant cultivars. RESULTS The objectives of this study were to identify gerbera genotypes with contrasting phenotypes in PM resistance and sequence and analyze their leaf transcriptomes to identify disease resistance and susceptibility genes differentially expressed and associated with PM resistance. An additional objective was to identify SNPs and SSRs for use in future genetic studies. We identified two gerbera genotypes, UFGE 4033 and 06-245-03, that were resistant and susceptible to PM, respectively. De novo assembly of their leaf transcriptomes using four complementary pipelines resulted in 145,348 transcripts with a N50 of 1124 bp, of which 67,312 transcripts contained open reading frames and 48,268 were expressed in both genotypes. A total of 494 transcripts were likely involved in disease resistance, and 17 and 24 transcripts were up- and down-regulated, respectively, in UFGE 4033 compared to 06-245-03. These gerbera disease resistance transcripts were most similar to the NBS-LRR class of plant resistance genes conferring resistance to various pathogens in plants. Four disease susceptibility transcripts (MLO-like) were expressed only or highly expressed in 06-245-03, offering excellent candidate targets for gene editing for PM resistance in gerbera. A total of 449,897 SNPs and 19,393 SSRs were revealed in the gerbera transcriptomes, which can be a valuable resource for developing new molecular markers. CONCLUSION This study represents the first transcriptomic analysis of gerbera PM resistance, a highly important yet complex trait in a globally important floral crop. The differentially expressed disease resistance and susceptibility transcripts identified provide excellent targets for development of molecular markers and genetic maps, cloning of disease resistance genes, or targeted mutagenesis of disease susceptibility genes for PM resistance in gerbera.
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Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, IFAS, Gainesville, FL, 32611, USA
- University of Florida, Genetics Institute, Gainesville, FL, 32611, USA
| | - Shunyuan Xiao
- University of Maryland, College of Agriculture and Natural Resources, 4291 Fieldhouse Drive, Rockville, MD, 20850, USA
| | - Natalia A Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, 32611, USA
| | - Saroj Parajuli
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA.
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Barka GD, Caixeta ET, Ferreira SS, Zambolim L. In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach. PLoS One 2020; 15:e0222747. [PMID: 32639982 PMCID: PMC7343155 DOI: 10.1371/journal.pone.0222747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/19/2020] [Indexed: 11/19/2022] Open
Abstract
Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.
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Affiliation(s)
- Geleta Dugassa Barka
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
- Applied Biology Department, Adama Science and Technology University (ASTU), Adama, Oromia, Ethiopia
| | - Eveline Teixeira Caixeta
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
- Embrapa Café, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil
- * E-mail:
| | - Sávio Siqueira Ferreira
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
| | - Laércio Zambolim
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
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Andolfo G, Villano C, Errico A, Frusciante L, Carputo D, Aversano R, Ercolano MR. Inferring RPW8-NLRs's evolution patterns in seed plants: case study in Vitis vinifera. PLANTA 2019; 251:32. [PMID: 31823009 DOI: 10.1007/s00425-019-03324-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/03/2019] [Indexed: 05/20/2023]
Abstract
Genomic and transcriptomic studies in plants and, more in deep, in grapevine reveal that the disease-resistance RNL gene family is highly variable. RNLs (RPW8-NLRs) are a phylogenetically distinct class of nucleotide oligomerization domain (NOD)-like receptors (NLRs) identified in plants. Two RNLs, namely, the NRG1 (N Requirement Gene 1) and the ADR1 (Activated Disease Resistance 1), have been characterized; however, little is known about the RNL evolutionary history in higher plants. To trace the diversification of RNL gene subfamily, we scanned the NLR proteins of 73 plant genomes belonging to 29 taxa, revealing a noticeable diversification across species and within the same genus or botanic family together with a conspicuous expansion in important crop species. To explore the RNL variability in Vitis vinifera and gain information with respect to their structure, evolutionary diversification of five grape genomes ('Aglianico', 'Falanghina', 'Sultanina', 'Tannat', and 'Nebbiolo') has been compared to the reference genome ('Pinot Noir'). The number of RNLs ranged from 6 ('Sultanina') to 14 ('Nebbiolo'), in contrast to the 10 'Pinot Noir' RNLs. The phylogenetic study on grapevine RNLs revealed that all collapsed into NRG1-clade, rather than four. To investigate more in depth the means of intraspecific variability of grape RNL copies, a transcriptomic profiling in response to powdery mildew (PM) infection was carried out through qRT-PCRs and public databases interrogation. The RNL expression variability identified in transcriptome data sets supports the hypothesis of a functional expansion/contraction in grapevine varieties. Although no direct correlations between grapevine PM-resistance and RNL expression was identified, our work can provide good candidates for functional studies able to elucidate the putative "helper" role of RNLs in grape immune signalling.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Clizia Villano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Angela Errico
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Luigi Frusciante
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Domenico Carputo
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy
| | - Riccardo Aversano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy.
| | - Maria R Ercolano
- Department of Agriculture Sciences, University of Naples Federico II, via Università 100, 80055, Portici, NA, Italy.
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Jain A, Sarsaiya S, Wu Q, Lu Y, Shi J. A review of plant leaf fungal diseases and its environment speciation. Bioengineered 2019; 10:409-424. [PMID: 31502497 PMCID: PMC6779379 DOI: 10.1080/21655979.2019.1649520] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/20/2019] [Accepted: 07/24/2019] [Indexed: 11/08/2022] Open
Abstract
There is increasing difficulty in identifying new plant leaf diseases as a result of environmental change. There is a need to identify the factors influencing the emergence and the increasing incidences of these diseases. Here, we present emerging fungal plant leaf diseases and describe their environmental speciation. We considered the factors controlling for local adaptation associated with environmental speciation. We determined that the advent of emergent fungal leaf diseases is closely connected to environmental speciation. Fungal pathogens targeting the leaves may adversely affect the entire plant body. To mitigate the injury caused by these pathogens, it is necessary to be able to detect and identify them early in the infection process. In this way, their distribution, virulence, incidence, and severity could be attenuated.
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Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yuanfu Lu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
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Pirrello C, Mizzotti C, Tomazetti TC, Colombo M, Bettinelli P, Prodorutti D, Peressotti E, Zulini L, Stefanini M, Angeli G, Masiero S, Welter LJ, Hausmann L, Vezzulli S. Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview. FRONTIERS IN PLANT SCIENCE 2019; 10:1394. [PMID: 31824521 PMCID: PMC6883492 DOI: 10.3389/fpls.2019.01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/09/2019] [Indexed: 05/23/2023]
Abstract
The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Chiara Mizzotti
- Department of Biosciences, University of Milan, Milan, Italy
| | - Tiago C. Tomazetti
- Center of Agricultural Sciences, Federal University of Santa Catarina, Rodovia Admar Gonzaga, Florianópolis, Brazil
| | - Monica Colombo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Paola Bettinelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Daniele Prodorutti
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Elisa Peressotti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Luca Zulini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Gino Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milan, Italy
| | - Leocir J. Welter
- Department of Natural and Social Sciences, Federal University of Santa Catarina, Campus of Curitibanos, Rodovia Ulysses Gaboardi, Curitibanos, Brazil
| | - Ludger Hausmann
- Julius Kühn Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
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Zini E, Dolzani C, Stefanini M, Gratl V, Bettinelli P, Nicolini D, Betta G, Dorigatti C, Velasco R, Letschka T, Vezzulli S. R-Loci Arrangement Versus Downy and Powdery Mildew Resistance Level: A Vitis Hybrid Survey. Int J Mol Sci 2019; 20:ijms20143526. [PMID: 31323823 PMCID: PMC6679420 DOI: 10.3390/ijms20143526] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breeding.
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Affiliation(s)
- Elena Zini
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy
| | - Chiara Dolzani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Verena Gratl
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | | | - Daniela Nicolini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Giulia Betta
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Cinzia Dorigatti
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Thomas Letschka
- Laimburg Research Centre, Laimburg 6, 39052 Vadena (BZ), Italy.
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
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