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Chang Y, Liu Y, Wang L, Wang S, Wu J. Global transcriptome analysis reveals resistance genes in the early response of common bean (Phaseolus vulgaris L.) to Colletotrichum lindemuthianum. BMC Genomics 2024; 25:579. [PMID: 38858660 DOI: 10.1186/s12864-024-10497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Disease can drastically impair common bean (Phaseolus vulgaris L.) production. Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara, is one of the diseases that are widespread and cause serious economic loss in common bean. RESULTS Transcriptome analysis of the early response of common bean to anthracnose was performed using two resistant genotypes, Hongyundou and Honghuayundou, and one susceptible genotype, Jingdou. A total of 9,825 differentially expressed genes (DEGs) responding to pathogen infection and anthracnose resistance were identified by differential expression analysis. By using weighted gene coexpression network analysis (WGCNA), 2,051 DEGs were found to be associated with two resistance-related modules. Among them, 463 DEGs related to anthracnose resistance were considered resistance-related candidate genes. Nineteen candidate genes were coexpressed with three resistance genes, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. To further identify resistance genes, 46 candidate genes were selected for experimental validation using salicylic acid (SA) and methyl jasmonate (MeJA). The results indicated that 38 candidate genes that responded to SA/MeJA treatment may be involved in anthracnose resistance in common bean. CONCLUSIONS This study identified 38 resistance-related candidate genes involved in the early response of common bean, and 19 resistance-related candidate genes were coexpressed with anthracnose resistance genes. This study identified putative resistance genes for further resistance genetic investigation and provides an important reference for anthracnose resistance breeding in common bean.
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Affiliation(s)
- Yujie Chang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yonghui Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanfen Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shumin Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Romero G, González S, Royero W, González A. Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean. Genet Mol Biol 2024; 47:e20220263. [PMID: 38593425 PMCID: PMC11003654 DOI: 10.1590/1678-4685-gmb-2022-0263] [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: 09/03/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.
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Affiliation(s)
- German Romero
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
| | - Sandra González
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Wendy Royero
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Adriana González
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
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3
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Badiyal A, Dhiman S, Singh A, Rathour R, Pathania A, Katoch S, Padder BA, Sharma PN. Mapping of adult plant recessive resistance to anthracnose in Indian common bean landrace Baspa/KRC 8. Mol Biol Rep 2024; 51:254. [PMID: 38302755 DOI: 10.1007/s11033-023-09160-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The common bean (Phaseolus vulgaris) has become the food of choice owing to its wealthy nutritional profile, leading to a considerable increase in its cultivation worldwide. However, anthracnose has been a major impediment to production and productivity, as elite bean cultivars are vulnerable to this disease. To overcome barriers in crop production, scientists worldwide are working towards enhancing the genetic diversity of crops. One way to achieve this is by introducing novel genes from related crops, including landraces like KRC 8. This particular landrace, found in the North Western Himalayan region, has shown adult plant resistance against anthracnose and also possesses a recessive resistance gene. METHODS AND RESULTS In this study, a population of 179 F2:9 RIL individuals (Jawala × KRC 8) was evaluated at both phenotypic and genotypic levels using over 830 diverse molecular markers to map the resistance gene present in KRC 8. We have successfully mapped a resistance gene to chromosome Pv01 using four SSR markers, namely IAC 238, IAC 235, IAC 259, and BM 146. The marker IAC 238 is closely linked to the gene with a distance of 0.29 cM, while the other markers flank the recessive resistance gene at 10.87 cM (IAC 259), 17.80 cM (BM 146), and 25.22 cM (IAC 235). Previously, a single recessive anthracnose resistance gene (co-8) has been reported in the common bean accession AB 136. However, when we performed PCR amplification with our tightly linked marker IAC 238, we got different amplicons in AB 136 and KRC 8. Interestingly, the susceptible cultivar Jawala produced the same amplicon as AB 136. This observation indicated that the recessive gene present in KRC 8 is different from co-8. As the gene is located far away from the Co-1 locus, we suggest naming the recessive gene co-Indb/co-19. Fine mapping of co-Indb in KRC 8 may provide new insights into the cloning and characterization of this recessive gene so that it can be incorporated into future bean improvement programs. Further, the tightly linked marker IAC 238 can be utilized in marker assisted introgression in future bean breeding programs. CONCLUSION The novel co-Indb gene present in Himalayan landrace KRC 8, showing adult plant resistance against common bean anthracnose, is independent from all the resistance genes previously located on chromosome Pv01.
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Affiliation(s)
- Anila Badiyal
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Shiwali Dhiman
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Amar Singh
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, 144001, Punjab, India
| | - Shabnam Katoch
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-K Srinagar, Srinagar, 190025, J&K, India.
| | - Prem N Sharma
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India.
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4
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Lateef I, Katoch S, Katoch A, Badiyal A, Pathania A, Dhiman S, Nisa Q, Bashir A, Nabi A, Nabi N, Fayaz T, Gulzar G, Shah MD, Shikari AB, Dar ZA, Itoo H, Shah RA, Sofi TA, Sharma V, Sharma MK, Rathour R, Sharma PN, Padder BA. Fine mapping of a new common bean anthracnose resistance gene (Co-18) to the proximal end of Pv10 in Indian landrace KRC-5. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:32. [PMID: 38270625 DOI: 10.1007/s00122-023-04539-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
KEY MESSAGE Mapping and fine mapping of bean anthracnose resistance genes is a continuous process. We report fine mapping of anthracnose resistance gene Co-18 which is the first anthracnose gene mapped to Pv10. The discovery of resistance gene is a major gain in the bean anthracnose pathosystem research. Among the Indian common bean landraces, KRC-5 exhibit high levels of resistance to the bean anthracnose pathogen Colletotrichum lindemuthianum. To precisely map the anthracnose resistance gene, we used a Recombinant Inbred Line (F2:9 RIL) population (KRC-5 × Jawala). The inheritance test revealed that KRC-5 carries a dominant resistance gene temporarily designated as Co-18. We discovered two RAPD markers linked to Co-18 among 287 RAPD markers. These RAPD markers were eventually developed into SCARs (Sc-OPR15 and Sc-OPF6) and flank Co-18 on chromosome Pv10 at a distance of 5.3 and 4.2 cM, respectively. At 4.0-4.1 Mb on Pv10, we detected a SNP (single-nucleotide polymorphism) signal. We synthesized 58 SSRs and 83 InDels from a pool of 135 SSRs and 1134 InDels, respectively. Five SSRs, four InDels, and two SCARs were used to generate the high-density linkage map, which led to the identification of two SSRs (SSR24 and SSR36) that are tightly linked to Co-18. These two SSRs flank the Co-18 to 178 kb genomic region with 13 candidate genes including five NLR (nucleotide-binding and leucine-rich repeat) genes. The closely linked markers SSR24 and SSR36 will be used in cloning and pyramiding of the Co-18 gene with other R genes to develop durable resistant bean varieties.
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Affiliation(s)
- Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Shabnam Katoch
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Abhishek Katoch
- University Institute of Agricultural Sciences, Chandigarh University, Ajitgarh, India
| | - Anila Badiyal
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, Punjab, 144001, India
| | - Shiwali Dhiman
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mehraj D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Asif B Shikari
- Division of Plant Breeding and Genetics, SKUAST-K, FoA, Wadura, Baramulla, Sopore, India
| | | | - Hamidullah Itoo
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Rafiq A Shah
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Tariq A Sofi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Vivek Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - M K Sharma
- Division of Fruit Science, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - P N Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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5
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Li F, Zhu R, Gao F, Duan T. Prior Infection by Colletotrichum spinaciae Lowers the Susceptibility to Infection by Powdery Mildew in Common Vetch. PLANTS (BASEL, SWITZERLAND) 2023; 13:52. [PMID: 38202360 PMCID: PMC10780821 DOI: 10.3390/plants13010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Anthracnose (Colletotrichum spinaciae) and powdery mildew (Erysiphe pisi) are important diseases of common vetch (Vicia sativa) and often co-occur in the same plant. Here, we evaluate how C. spinaciae infection affects susceptibility to E. pisi, using sterilized and non-sterilized field soil to test the effect of resident soil microorganisms on the plant's immune response. Plants infected with C. spinaciae (C+) exhibited a respective 41.77~44.16% and 72.37~75.27% lower incidence and severity of powdery mildew than uninfected (C-) plants. Moreover, the net photosynthetic rate, transpiration rate, and stomatal conductance were higher in the C- plants than in the C+ plants prior to infection with powdery mildew. These differences were not recorded following powdery mildew infection. Additionally, the activities of superoxide dismutase, polyphenol oxidase, and catalase were higher in the C+ plants than in the C- plants. The resident soil microbiota did not affect the plant responses to both pathogens. By uncovering the mechanistic basis of plant immune response, our study informs integrated disease management in a globally important forage crop.
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Affiliation(s)
- Faxi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China; (F.L.); (R.Z.)
| | - Rui Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China; (F.L.); (R.Z.)
| | - Feng Gao
- Gansu Vocational College of Agriculture, Lanzhou 730020, China
| | - Tingyu Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China; (F.L.); (R.Z.)
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6
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Lovatto M, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Mazucheli J, Vidigal Filho PS, Miranda EGR, Melotto M. Responsiveness of Candidate Genes on CoPv01CDRK/PhgPv01CDRK Loci in Common Bean Challenged by Anthracnose and Angular Leaf Spot Pathogens. Int J Mol Sci 2023; 24:16023. [PMID: 38003212 PMCID: PMC10671028 DOI: 10.3390/ijms242216023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 11/26/2023] Open
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01CDRK/PhgPv01CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01CDRK/PhgPv01CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.
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Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Josmar Mazucheli
- Departamento de Estatística, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | | | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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7
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Monti MM, Mancini I, Gualtieri L, Domingo G, Beccaccioli M, Bossa R, Bracale M, Loreto F, Ruocco M. Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype. PHYSIOLOGIA PLANTARUM 2023; 175:e14044. [PMID: 37882283 DOI: 10.1111/ppl.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/07/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023]
Abstract
We analyzed the changes in the volatilome, proteome, stomatal conductance, salicylic and jasmonic acid contents of a susceptible and a moderately resistant genotype of common bean, Phaseoulus vulgaris L., challenged with Colletotrichum lindemuthianum, the causal agent of fungal anthracnose. Our results indicate differences at both proteome and volatilome levels between the two genotypes, before and after the infection, and different defense strategies. The moderately resistant genotype hindered pathogen infection, invasion, and replication mainly by maintaining epidermal and cell wall structure. The susceptible genotype was not able to limit the early stages of pathogen infection. Rather, stomatal conductance increased in the infected susceptible genotype, and enhanced synthesis of Green Leaf Volatiles and salicylic acid was observed, together with a strong hypersensitive response. Proteomic investigation provided a general framework for physiological changes, whereas observed variations in the volatilome suggested that volatile organic compounds may principally represent stress markers rather than defensive compounds per se.
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Affiliation(s)
- Maurilia M Monti
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
| | - Ilaria Mancini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Liberata Gualtieri
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Marzia Beccaccioli
- Dipartimento di Biologia Ambientale, Università Sapienza Roma, Roma, Italy
| | - Rosanna Bossa
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Francesco Loreto
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Michelina Ruocco
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
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8
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da Silva Dambroz CM, Aono AH, de Andrade Silva EM, Pereira WA. Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean. Sci Rep 2023; 13:13455. [PMID: 37596307 PMCID: PMC10439169 DOI: 10.1038/s41598-023-40054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/03/2023] [Indexed: 08/20/2023] Open
Abstract
Anthracnose, caused by the hemibiotrophic fungus Colletotrichum lindemuthianum, is a damaging disease of common beans that can drastically reduce crop yield. The most effective strategy to manage anthracnose is the use of resistant cultivars. There are many resistance loci that have been identified, mapped and associated with markers in common bean chromosomes. The Leucine-rich repeat kinase receptor protein (LRR-RLK) family is a diverse group of transmembrane receptors, which potentially recognizes pathogen-associated molecular patterns and activates an immune response. In this study, we performed in silico analyses to identify, classify, and characterize common bean LRR-RLKs, also evaluating their expression profile in response to the infection by C. lindemuthianum. By analyzing the entire genome of Phaseolus vulgaris, we could identify and classify 230 LRR-RLKs into 15 different subfamilies. The analyses of gene structures, conserved domains and motifs suggest that LRR-RLKs from the same subfamily are consistent in their exon/intron organization and composition. LRR-RLK genes were found along the 11 chromosomes of the species, including regions of proximity with anthracnose resistance markers. By investigating the duplication events within the LRR-RLK family, we associated the importance of such a family with an expansion resulting from a strong stabilizing selection. Promoter analysis was also performed, highlighting cis-elements associated with the plant response to biotic stress. With regard to the expression pattern of LRR-RLKs in response to the infection by C. lindemuthianum, we could point out several differentially expressed genes in this subfamily, which were associated to specific molecular patterns of LRR-RLKs. Our work provides a broad analysis of the LRR-RLK family in P. vulgaris, allowing an in-depth structural and functional characterization of genes and proteins of this family. From specific expression patterns related to anthracnose response, we could infer a direct participation of RLK-LRR genes in the mechanisms of resistance to anthracnose, highlighting important subfamilies for further investigations.
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Affiliation(s)
| | - Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
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9
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Ariza-Suarez D, Keller B, Spescha A, Aparicio JS, Mayor V, Portilla-Benavides AE, Buendia HF, Bueno JM, Studer B, Raatz B. Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:23-38. [PMID: 35574650 DOI: 10.1111/tpj.15810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.
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Affiliation(s)
- Daniel Ariza-Suarez
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Beat Keller
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Anna Spescha
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Johan Steven Aparicio
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Victor Mayor
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Hector Fabio Buendia
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Juan Miguel Bueno
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Bodo Raatz
- Bean Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Yang M, Zhou C, Yang H, Kuang R, Liu K, Huang B, Wei Y. Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya ( Carica papaya L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1038598. [PMID: 36618670 PMCID: PMC9816866 DOI: 10.3389/fpls.2022.1038598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Colletotrichum brevisporum is an important causal pathogen of anthracnose that seriously affects the fruit quality and yield of papaya (Carica papaya L.). Although many genes and biological processes involved in anthracnose resistance have been reported in other species, the molecular mechanisms involved in the response or resistance to anthracnose in post-harvest papaya fruits remain unclear. In this study, we compared transcriptome changes in the post-harvest fruits of the anthracnose-susceptible papaya cultivar Y61 and the anthracnose-resistant cultivar G20 following C. brevisporum inoculation. More differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElnRNAs) were identified in G20 than in Y61, especially at 24 h post-inoculation (hpi), suggesting a prompt activation of defense responses in G20 in the first 24 h after C. brevisporum inoculation. These DEGs were mainly enriched in plant-pathogen interaction, phenylpropanoid biosynthesis/metabolism, and peroxisome and flavonoid biosynthesis pathways in both cultivars. However, in the first 24 hpi, the number of DEGs related to anthracnose resistance was greater in G20 than in Y61, and changes in their expression levels were faster in G20 than in Y61. We also identified a candidate anthracnose-resistant gene cluster, which consisted of 12 genes, 11 in G20 and Y61, in response to C. brevisporum inoculation. Moreover, 529 resistance gene analogs were identified in papaya genome, most of which responded to C. brevisporum inoculation and were genetically different between papaya cultivars and wild-type populations. The total expression dose of the resistance gene analogs may help papaya resist C. brevisporum infection. This study revealed the mechanisms underlying different anthracnose resistance between the anthracnose-resistant and anthracnose-susceptible cultivars based on gene expression, and identified some potential anthracnose resistance-related candidate genes/major regulatory factors. Our findings provided potential targets for developing novel genetic strategies to overcome anthracnose in papaya.
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Affiliation(s)
- Min Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chenping Zhou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hu Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruibin Kuang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Bingxiong Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuerong Wei
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Boufleur TR, Massola Júnior NS, Becerra S, Baraldi E, Bibiano LBJ, Sukno SA, Thon MR, Baroncelli R. Comparative transcriptomic provides novel insights into the soybean response to Colletotrichum truncatum infection. FRONTIERS IN PLANT SCIENCE 2022; 13:1046418. [PMID: 36507428 PMCID: PMC9732023 DOI: 10.3389/fpls.2022.1046418] [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: 09/16/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Soybean (Glycine max) is among the most important crops in the world, and its production can be threatened by biotic diseases, such as anthracnose. Soybean anthracnose is a seed-borne disease mainly caused by the hemibiotrophic fungus Colletotrichum truncatum. Typical symptoms are pre- and post-emergence damping off and necrotic lesions on cotyledons, petioles, leaves, and pods. Anthracnose symptoms can appear early in the field, causing major losses to soybean production. MATERIAL AND METHODS In preliminary experiments, we observed that the same soybean cultivar can have a range of susceptibility towards different strains of C. truncatum, while the same C. truncatum strain can cause varying levels of disease severity in different soybean cultivars. To gain a better understanding of the molecular mechanisms regulating the early response of different soybean cultivars to different C. truncatum strains, we performed pathogenicity assays to select two soybean cultivars with significantly different susceptibility to two different C. truncatum strains and analyzed their transcriptome profiles at different time points of interaction (0, 12, 48, and 120 h post-inoculation, hpi). RESULTS AND DISCUSSION The pathogenicity assays showed that the soybean cultivar Gm1 is more resistant to C. truncatum strain 1080, and it is highly susceptible to strain 1059, while cultivar Gm2 shows the opposite behavior. However, if only trivial anthracnose symptoms appeared in the more resistant phenotype (MRP; Gm1-1080; Gm2-1059) upon 120 hpi, in the more susceptible phenotype (MSP; Gm-1059; Gm2- 1080) plants show mild symptoms already at 72 hpi, after which the disease evolved rapidly to severe necrosis and plant death. Interestingly, several genes related to different cellular responses of the plant immune system (pathogen recognition, signaling events, transcriptional reprogramming, and defense-related genes) were commonly modulated at the same time points only in both MRP. The list of differentially expressed genes (DEGs) specific to the more resistant combinations and related to different cellular responses of the plant immune system may shed light on the important host defense pathways against soybean anthracnose.
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Affiliation(s)
- Thaís R. Boufleur
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Villamayor, Spain
| | - Nelson S. Massola Júnior
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Sioly Becerra
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Villamayor, Spain
| | - Elena Baraldi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Líllian B. J. Bibiano
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Villamayor, Spain
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Villamayor, Spain
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca (USAL), Villamayor, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
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12
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Rahmanzadeh A, Khahani B, Taghavi SM, Khojasteh M, Osdaghi E. Genome-wide meta-QTL analyses provide novel insight into disease resistance repertoires in common bean. BMC Genomics 2022; 23:680. [PMID: 36192697 PMCID: PMC9531352 DOI: 10.1186/s12864-022-08914-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 09/27/2022] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Common bean (Phaseolus vulgaris) is considered a staple food in a number of developing countries. Several diseases attack the crop leading to substantial economic losses around the globe. However, the crop has rarely been investigated for multiple disease resistance traits using Meta-analysis approach. RESULTS AND CONCLUSIONS In this study, in order to identify the most reliable and stable quantitative trait loci (QTL) conveying disease resistance in common bean, we carried out a meta-QTL (MQTL) analysis using 152 QTLs belonging to 44 populations reported in 33 publications within the past 20 years. These QTLs were decreased into nine MQTLs and the average of confidence interval (CI) was reduced by 2.64 folds with an average of 5.12 cM in MQTLs. Uneven distribution of MQTLs across common bean genome was noted where sub-telomeric regions carry most of the corresponding genes and MQTLs. One MQTL was identified to be specifically associated with resistance to halo blight disease caused by the bacterial pathogen Pseudomonas savastanoi pv. phaseolicola, while three and one MQTLs were specifically associated with resistance to white mold and anthracnose caused by the fungal pathogens Sclerotinia sclerotiorum and Colletotrichum lindemuthianum, respectively. Furthermore, two MQTLs were detected governing resistance to halo blight and anthracnose, while two MQTLs were detected for resistance against anthracnose and white mold, suggesting putative genes governing resistance against these diseases at a shared locus. Comparative genomics and synteny analyses provide a valuable strategy to identify a number of well‑known functionally described genes as well as numerous putative novels candidate genes in common bean, Arabidopsis and soybean genomes.
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Affiliation(s)
- Asma Rahmanzadeh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Bahman Khahani
- Department of Plant Genetics and Production, College of Agriculture, Shiraz University, Shiraz, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, 31587-77871, Iran.
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Jurado M, Campa A, Ferreira JJ. Differentially expressed genes against Colletotrichum lindemuthiamum in a bean genotype carrying the Co-2 gene revealed by RNA-sequencing analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:981517. [PMID: 36311094 PMCID: PMC9615912 DOI: 10.3389/fpls.2022.981517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Anthracnose is responsible for large yield losses in common bean crops. RNA-sequencing was used to investigate the differentially expressed genes (DEGs) in response to race 38 of Colletotrichum lindemuthianum in two near-isogenic lines (A25 and A4804) that differ in the presence of a resistance gene located in the cluster Co-2. Their responses were analyzed at different hours after inoculation (0, 24, and 48) and within and between genotypes. In all, 2,850 DEGs were detected, with 2,373 assigned to at least one functional GO term. Enriched GO terms in the resistant genotype were mainly related to functions as a response to stimulus, hormone signaling, cellular component organization, phosphorylation activities, and transcriptional regulation. The region containing the Co-2 cluster was delimited at the end of chromosome Pv11 (46.65-48.65 Mb) through a comparison with the SNP genotypes, obtained using 'Genotyping by Sequencing,' among seven resistant lines harboring the Co-2 gene and the susceptible line A25. The delimited region contained 23 DEGs, including 8 typical R genes, that showed higher expression levels in the resistant genotype and non-changes in the susceptible genotype after inoculation. Six R genes encoding protein kinases and an LRR domain formed a cluster in a core region between 46.98 and 47.04 Mb. The alignment of the raw transcriptome reads in the core region revealed structural changes that were used to design four potential breeder-friendly DNA markers, and it revealed some alignments with the intergenic regions, suggesting the presence of genes in addition to those annotated in the reference genome.
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Alvarez-Diaz JC, Laugé R, Delannoy E, Huguet S, Paysant-Le Roux C, Gratias A, Geffroy V. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. PLANTS 2022; 11:plants11151995. [PMID: 35956473 PMCID: PMC9370732 DOI: 10.3390/plants11151995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022]
Abstract
Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.
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Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Richard Laugé
- Université Paris-Saclay, INRAE UR 1290 BIOGER, Av. Lucien Bretignières, BP 01, 78850 Thiverval Grignon, France;
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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da Silva LL, Morgan T, Garcia EA, Rosa RO, de Oliveira Mendes TA, de Queiroz MV. Pectinolytic arsenal of Colletotrichum lindemuthianum and other fungi with different lifestyles. J Appl Microbiol 2022; 133:1857-1871. [PMID: 35766136 DOI: 10.1111/jam.15692] [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: 02/17/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
AIM To identify and analyze genes that encode pectinases in the genome of the fungus C. lindemuthianum, evaluate the expression of these genes, and compare putative pectinases found in C. lindemuthianum with pectinases produced by other fungi and oomycetes with different lifestyles. METHODS AND RESULTS Genes encoding pectinases in the genome of C. lindemuthianum were identified and analyzed. The expression of these genes was analyzed. Pectinases from C. lindemuthianum were compared with pectinases from other fungi that have different lifestyles, and the pectinase activity in some of these fungi was quantified. Fifty-eight genes encoding pectinases were identified in C. lindemuthianum. At least six types of enzymes involved in pectin degradation were identified, with pectate lyases and polygalacturonases being the most abundant. Twenty-seven genes encoding pectinases were differentially expressed at some point in C. lindemuthianum during their interactions with their host. For each type of pectinase, there were at least three isoenzyme groups. The number of pectinases present in fungi with different lifestyles seemed to be related more to the lifestyle than to the taxonomic relationship between them. Only phytopathogenic fungi showed pectate lyase activity. CONCLUSIONS The collective results demonstrate the pectinolytic arsenal of C. lindemuthianum, with many and diverse genes encoding pectinases more than that found in other phytopathogens, which suggests that at least part of these pectinases must be important for the pathogenicity of the fungus C. lindemuthianum. SIGNIFICANCE AND IMPACT OF THE STUDY Knowledge of these pectinases could further the understanding of the importance of this broad pectinolytic arsenal in the common bean infection, and could be exploited for biotechnological purposes.
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Affiliation(s)
- Leandro Lopes da Silva
- Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa-, MG, Brasil
| | - Túlio Morgan
- Laboratório de Biotecnologia Molecular, Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa-, MG, Brasil
| | - Ediones Amaro Garcia
- Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa-, MG, Brasil
| | - Rafael Oliveira Rosa
- Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa-, MG, Brasil
| | - Tiago Antônio de Oliveira Mendes
- Laboratório de Biotecnologia Molecular, Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa-, MG, Brasil
| | - Marisa Vieira de Queiroz
- Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa-, MG, Brasil
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Nabi A, Lateef I, Nisa Q, Banoo A, Rasool RS, Shah MD, Ahmad M, Padder BA. Phaseolus vulgaris-Colletotrichum lindemuthianum Pathosystem in the Post-Genomic Era: An Update. Curr Microbiol 2022; 79:36. [PMID: 34982236 DOI: 10.1007/s00284-021-02711-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris-Colletotrichum lindemuthianum is one among the oldest host and pathogen interface. Researchers have taken painstaking efforts across the world for understanding the dialogue during early and late phases of interaction. Collectively, these efforts resulted in the deluge of information that helped the researchers to underpin the interface. The latest molecular biology techniques furnished novel detection methods for the anthracnose pathogen, refined the understanding of pathogen population dynamics, and provided the insights on co-evolutionary common bean resistance and C. lindemuthianum virulence dynamics. One of the important breakthroughs came when the Phaseolus vulgaris and its corresponding anthracnose pathogen (C. lindemuthianum) genomes were decoded in 2014 and 2017, respectively. Availability of both the genomes yielded a significant genomic information that helped bean communities to fine map the economically important traits and to identify the pathogenicity determinants and effector molecules. The interface is in a continuous development as knowledge of the anthracnose resistance genes, their precise physical locations, and the identification of effector proteins; the fungus arsenals are being routinely updated. Hence, we revisited the interface and tried to provide an overview of host pathogen dialogue in the genomic era. Additionally, we compiled the sporadic information on this pathosystem from India and provided its futuristic road map to shape its research in the world and northern India, the major dry bean area in the country.
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Affiliation(s)
- Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rovidha S Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Shafi S, Saini DK, Khan MA, Bawa V, Choudhary N, Dar WA, Pandey AK, Varshney RK, Mir RR. Delineating meta-quantitative trait loci for anthracnose resistance in common bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 13:966339. [PMID: 36092444 PMCID: PMC9453441 DOI: 10.3389/fpls.2022.966339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 05/03/2023]
Abstract
Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean breeding programs, a detailed meta-QTL (MQTL) analysis has been conducted. For the MQTL analysis, 92 QTLs related to anthracnose disease reported in 18 different earlier studies involving 16 mapping populations were compiled and projected on to the consensus map. This meta-analysis led to the identification of 11 MQTLs (each involving QTLs from at least two different studies) on 06 bean chromosomes and 10 QTL hotspots each involving multiple QTLs from an individual study on 07 chromosomes. The confidence interval (CI) of the identified MQTLs was found 3.51 times lower than the CI of initial QTLs. Marker-trait associations (MTAs) reported in published genome-wide association studies (GWAS) were used to validate nine of the 11 identified MQTLs, with MQTL4.1 overlapping with as many as 40 MTAs. Functional annotation of the 11 MQTL regions revealed 1,251 genes including several R genes (such as those encoding for NBS-LRR domain-containing proteins, protein kinases, etc.) and other defense related genes. The MQTLs, QTL hotspots and the potential candidate genes identified during the present study will prove useful in common bean marker-assisted breeding programs and in basic studies involving fine mapping and cloning of genomic regions associated with anthracnose resistance in common beans.
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Affiliation(s)
- Safoora Shafi
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Vanya Bawa
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, India
| | - Neeraj Choudhary
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, India
| | - Waseem Ali Dar
- Mountain Agriculture Research and Extension Station, SKUAST-Kashmir, Bandipora, Jammu and Kashmir, India
| | - Arun K. Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Rajeev Kumar Varshney
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- Rajeev Kumar Varshney,
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
- *Correspondence: Reyazul Rouf Mir,
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The Role of Plant Hormones in the Interaction of Colletotrichum Species with Their Host Plants. Int J Mol Sci 2021; 22:ijms222212454. [PMID: 34830343 PMCID: PMC8620030 DOI: 10.3390/ijms222212454] [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: 10/05/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
Colletotrichum is a plant pathogenic fungus which is able to infect virtually every economically important plant species. Up to now no common infection mechanism has been identified comparing different plant and Colletotrichum species. Plant hormones play a crucial role in plant-pathogen interactions regardless whether they are symbiotic or pathogenic. In this review we analyze the role of ethylene, abscisic acid, jasmonic acid, auxin and salicylic acid during Colletotrichum infections. Different Colletotrichum strains are capable of auxin production and this might contribute to virulence. In this review the role of different plant hormones in plant—Colletotrichum interactions will be discussed and thereby auxin biosynthetic pathways in Colletotrichum spp. will be proposed.
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Nabi A, Banoo A, Rasool RS, Dar MS, Mubashir SS, Masoodi KZ, Shah MD, Khan AA, Khan I, Padder BA. Optimizing the Agrobacterium tumifaciens mediated transformation conditions in Colletotrichum lindemuthianum: A step forward to unravel the functions of pathogenicity arsenals. Lett Appl Microbiol 2021; 75:293-307. [PMID: 34398478 DOI: 10.1111/lam.13552] [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: 12/30/2020] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/28/2022]
Abstract
Colletotrichum lindemuthianum is a hemibiotrophic fungal pathogen that causes bean anthracnose and it is rated among the top 10 important diseases infecting beans. Currently our knowledge on molecular mechanisms underlying C. lindemuthianum pathogenesis is limited. About five pathogenicity genes have been identified in C. lindemuthianum using Restricted Enzyme Mediated Integration (REMI) and the transformation using Agroinfection has not been optimized. In this study, a series of experiments were conducted to optimize the key parameters affecting the Agrobacterium tumefaciens- mediated transformation (ATMT) for C. lindemuthianum. The transformation efficiency increased with increase in spore concentration and co-cultivation time. However, the optimum conditions that yielded significant number of transformants were 106 ml-1 spore concentration, co-cultivation time of 72 h, incubation at 25ºC and using a cellulose membrane filter for the co-cultivation. The optimized protocol resulted in establishment of large mutant library (2400). A few mutants were melanin deficient and a few were unable to produce conidia. To determine the altered pathogenicity, two new approaches such as detached leaf and twig techniques proved reliable and require fewer resources to screen the large mutant libraries in a short time. Among the 1200 transformants tested for virulence, 90% transformants were pathogenically similar to wild type (race 2047), 96 and 24 were reduced and impaired, respectively. The altered avirulent transformants can prove vital for understanding the missing link between growth and developmental stages of pathogen with virulence. This platform will help to develop strategies to determine the potential pathogenicity genes and to decipher molecular mechanisms of host-pathogen interactions in more detail.
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Affiliation(s)
- Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Rovidha S Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - M S Dar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Syed Shoaib Mubashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Khalid Z Masoodi
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Akhtar A Khan
- Division of Entomology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Imran Khan
- Division of Agricultural Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, 190 025
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Cox LD, Munholland S, Mats L, Zhu H, Crosby WL, Lukens L, Pauls KP, Bozzo GG. The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in Phaseolus vulgaris L. Metabolites 2021; 11:433. [PMID: 34357327 PMCID: PMC8306140 DOI: 10.3390/metabo11070433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/17/2022] Open
Abstract
Xanthomonas axonopodis infects common bean (Phaseolus vulgaris L.) causing the disease common bacterial blight (CBB). The aim of this study was to investigate the molecular and metabolic mechanisms underlying CBB resistance in P. vulgaris. Trifoliate leaves of plants of a CBB-resistant P. vulgaris recombinant inbred line (RIL) and a CBB-susceptible RIL were inoculated with X. axonopodis or water (mock treatment). Leaves sampled at defined intervals over a 48-h post-inoculation (PI) period were monitored for alterations in global transcript profiles. A total of 800 genes were differentially expressed between pathogen and mock treatments across both RILs; approximately half were differentially expressed in the CBB-resistant RIL at 48 h PI. Notably, there was a 4- to 32-fold increased transcript abundance for isoflavone biosynthesis genes, including several isoflavone synthases, isoflavone 2'-hydroxylases and isoflavone reductases. Ultra-high performance liquid chromatography-tandem mass spectrometry assessed leaf metabolite levels as a function of the PI period. The concentrations of the isoflavones daidzein and genistein and related metabolites coumestrol and phaseollinisoflavan were increased in CBB-resistant RIL plant leaves after exposure to the pathogen. Isoflavone pathway transcripts and metabolite profiles were unaffected in the CBB-susceptible RIL. Thus, induction of the isoflavone pathway is associated with CBB-resistance in P. vulgaris.
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Affiliation(s)
- Laura D. Cox
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Seth Munholland
- Department of Biological Sciences, University of Windsor, 401 Sunset Ave, Windsor, ON N9B 3P4, Canada; (S.M.); (W.L.C.)
| | - Lili Mats
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada; (L.M.); (H.Z.)
| | - Honghui Zhu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada; (L.M.); (H.Z.)
| | - William L. Crosby
- Department of Biological Sciences, University of Windsor, 401 Sunset Ave, Windsor, ON N9B 3P4, Canada; (S.M.); (W.L.C.)
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Gale G. Bozzo
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
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21
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Phipps S, Delwiche CF, Bisson MA. Salinity-induced Changes in Gene Expression in the Streptophyte Alga Chara: The Critical Role of a Rare Na + -ATPase. JOURNAL OF PHYCOLOGY 2021; 57:1004-1013. [PMID: 33713364 DOI: 10.1111/jpy.13166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The primarily freshwater genus Chara is comprised of many species that exhibit a wide range of salinity tolerance. The range of salt tolerance provides a good platform for investigating the role of transport mechanisms in response to salt stress, and the close evolutionary relationship between Charophytes and land plants can provide broader insights. We investigated the response to salt stress of previously identified transport mechanisms in two species of Chara, Chara longifolia (salt-tolerant), and Chara australis (salt-sensitive): a cation transporter (HKT), a Na+ /H+ antiport (NHX), H+ -ATPase (AHA), and a Na+ -ATPase (ENA). The presence of these candidate genes has been confirmed in both species of Chara, with the exception of the Na+ -ATPase, which is present only in salt-tolerant Chara longifolia. Time-course Illumina transcriptomes were created using RNA from multiple time points (0, 6, 12, 24 and 48 h) after freshwater cultures for each species were exposed to salt stress. These transcriptomes verified our hypotheses of these mechanisms conferring salt tolerance in the two species examined and also aided in identification of specific transcripts representing our genes of interest in both species. The expression of these transcripts was validated through use of qPCR, in a similar experimental set-up used for the RNAseq data described above. The RNAseq and qPCR data showed significant changes of expression mechanisms in C. longifolia (respectively), a down-regulation of HKT and a substantial up-regulation of ENA. Significant responses to salt stress in salt-sensitive C. australis show up-regulation of NHX and AHA.
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Affiliation(s)
- Shaunna Phipps
- Department of Environment & Sustainability, State University at Buffalo, Buffalo, New York, USA
- Department of Biological Sciences, State University at Buffalo, Buffalo, New York, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Mary A Bisson
- Department of Environment & Sustainability, State University at Buffalo, Buffalo, New York, USA
- Department of Biological Sciences, State University at Buffalo, Buffalo, New York, USA
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22
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Richard MMS, Gratias A, Alvarez Diaz JC, Thareau V, Pflieger S, Meziadi C, Blanchet S, Marande W, Bitocchi E, Papa R, Miklas PN, Geffroy V. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3569-3581. [PMID: 33693665 DOI: 10.1093/jxb/erab082] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/05/2021] [Indexed: 05/27/2023]
Abstract
Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x, an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3, an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector.
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Affiliation(s)
- Manon M S Richard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Juan C Alvarez Diaz
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Chouaib Meziadi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Sophie Blanchet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Phillip N Miklas
- USDA ARS, Grain Legume Genet & Physiol Res Unit, Prosser, WA, USA
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
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23
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Banoo A, Nabi A, Rasool RS, Mahiya-Farooq, Shah MD, Ahmad M, Sofi PA, Aasiya-Nabi, Itoo H, Sharma PN, Padder BA. North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:571618. [PMID: 33123180 PMCID: PMC7573075 DOI: 10.3389/fpls.2020.571618] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/04/2020] [Indexed: 08/31/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum. The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.
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Affiliation(s)
- Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Asha Nabi
- Directorate of Extension, SKUAST-Kashmir, Srinagar, India
| | - Rovidha S. Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mahiya-Farooq
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mehraj D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Mushtaq Ahmad
- Directorate of Extension, SKUAST-Kashmir, Srinagar, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, India
| | - Aasiya-Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
| | - Hamidullah Itoo
- Ambri Apple Research Centre, SKUAST-Kashmir, Srinagar, India
| | - P. N. Sharma
- Department of Plant Pathology, CSK HPKV, Palampur, India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Srinagar, India
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Wilker J, Humphries S, Rosas-Sotomayor JC, Gómez Cerna M, Torkamaneh D, Edwards M, Navabi A, Pauls KP. Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean ( Phaseolus vulgaris L.) Landraces and Modern Genotypes. PLANTS 2020; 9:plants9091238. [PMID: 32961677 PMCID: PMC7569834 DOI: 10.3390/plants9091238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/09/2023]
Abstract
Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Sally Humphries
- Department of Sociology and Anthropology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Juan Carlos Rosas-Sotomayor
- Departamento de Ciencia y Producción Agropecuaria, Escuela Agrícola Panamericana, Zamorano, Tegucigalpa 11101, Honduras;
| | - Marvin Gómez Cerna
- Fundación para la Investigación Participativa con Agricultores de Honduras, La Ceiba, Atlántida 561, Honduras;
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Michelle Edwards
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 54136)
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 DOI: 10.21203/rs.3.rs-17010/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. RESULTS We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. CONCLUSIONS This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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26
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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de Vries RP, Mäkelä MR. Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches. Trends Microbiol 2020; 28:487-499. [PMID: 32396827 DOI: 10.1016/j.tim.2020.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
Abstract
Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade plant biomass. This variation is found at many levels and includes genomic adaptation to the preferred biomass component, but also different approaches to degrade this component by diverse sets of activities encoded in the genome. Even larger differences have been observed using transcriptome and proteome studies, even between closely related species, suggesting a high level of adaptation in individual species. A better understanding of the drivers of this diversity could be highly valuable in developing more efficient biotechnology approaches for the enzymatic conversion of plant biomass.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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28
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Hoseinzadeh AH, Soorni A, Shoorooei M, Torkzadeh Mahani M, Maali Amiri R, Allahyari H, Mohammadi R. Comparative transcriptome provides molecular insight into defense-associated mechanisms against spider mite in resistant and susceptible common bean cultivars. PLoS One 2020; 15:e0228680. [PMID: 32017794 PMCID: PMC6999899 DOI: 10.1371/journal.pone.0228680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 01/07/2023] Open
Abstract
Common bean (Phaseolus vulgaris L.) is a major source of proteins and one of the most important edible foods for more than three hundred million people in the world. The common bean plants are frequently attacked by spider mite (Tetranychus urticae Koch), leading to a significant decrease in plant growth and economic performance. The use of resistant cultivars and the identification of the genes involved in plant-mite resistance are practical solutions to this problem. Hence, a comprehensive study of the molecular interactions between resistant and susceptible common bean cultivars and spider mite can shed light into the understanding of mechanisms and biological pathways of resistance. In this study, one resistant (Naz) and one susceptible (Akhtar) cultivars were selected for a transcriptome comparison at different time points (0, 1 and 5 days) after spider mite feeding. The comparison of cultivars in different time points revealed several key genes, which showed a change increase in transcript abundance via spider mite infestation. These included genes involved in flavonoid biosynthesis process; a conserved MYB-bHLH-WD40 (MBW) regulatory complex; transcription factors (TFs) TT2, TT8, TCP, Cys2/His2-type and C2H2-type zinc finger proteins; the ethylene response factors (ERFs) ERF1 and ERF9; genes related to metabolism of auxin and jasmonic acid (JA); pathogenesis-related (PR) proteins and heat shock proteins.
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Affiliation(s)
- Abdul Hadi Hoseinzadeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Marie Shoorooei
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Reza Maali Amiri
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Hossein Allahyari
- Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Rahmat Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
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29
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Menéndez AB, Calzadilla PI, Sansberro PA, Espasandin FD, Gazquez A, Bordenave CD, Maiale SJ, Rodríguez AA, Maguire VG, Campestre MP, Garriz A, Rossi FR, Romero FM, Solmi L, Salloum MS, Monteoliva MI, Debat JH, Ruiz OA. Polyamines and Legumes: Joint Stories of Stress, Nitrogen Fixation and Environment. FRONTIERS IN PLANT SCIENCE 2019; 10:1415. [PMID: 31749821 PMCID: PMC6844238 DOI: 10.3389/fpls.2019.01415] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/11/2019] [Indexed: 05/31/2023]
Abstract
Polyamines (PAs) are natural aliphatic amines involved in many physiological processes in almost all living organisms, including responses to abiotic stresses and microbial interactions. On other hand, the family Leguminosae constitutes an economically and ecologically key botanical group for humans, being also regarded as the most important protein source for livestock. This review presents the profuse evidence that relates changes in PAs levels during responses to biotic and abiotic stresses in model and cultivable species within Leguminosae and examines the unreviewed information regarding their potential roles in the functioning of symbiotic interactions with nitrogen-fixing bacteria and arbuscular mycorrhizae in this family. As linking plant physiological behavior with "big data" available in "omics" is an essential step to improve our understanding of legumes responses to global change, we also examined integrative MultiOmics approaches available to decrypt the interface legumes-PAs-abiotic and biotic stress interactions. These approaches are expected to accelerate the identification of stress tolerant phenotypes and the design of new biotechnological strategies to increase their yield and adaptation to marginal environments, making better use of available plant genetic resources.
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Affiliation(s)
- Ana Bernardina Menéndez
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, UBA-CONICET, Buenos Aires, Argentina
| | | | | | | | - Ayelén Gazquez
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | | | | | | | | | | | - Andrés Garriz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | - Franco Rubén Rossi
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | | | - Leandro Solmi
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | - Maria Soraya Salloum
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Mariela Inés Monteoliva
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Julio Humberto Debat
- Instituto de Patología Vegetal (IPAVE) Ing “Sergio Nome,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Oscar Adolfo Ruiz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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31
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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation. Biochem Genet 2019; 57:747-766. [PMID: 30997627 DOI: 10.1007/s10528-019-09920-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.
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32
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Murube E, Campa A, Ferreira JJ. Integrating genetic and physical positions of the anthracnose resistance genes described in bean chromosomes Pv01 and Pv04. PLoS One 2019; 14:e0212298. [PMID: 30763410 PMCID: PMC6375601 DOI: 10.1371/journal.pone.0212298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/30/2019] [Indexed: 12/21/2022] Open
Abstract
A complex landscape of anthracnose resistance genes (Co-) located at the telomeric regions of the bean chromosomes Pv01 and Pv04 has been reported. The aim of this work was to investigate the genetic and physical positions of genes conferring resistance to races 6, 38, 39, 357, 65, and 73 as well as the relationships among the resistance genes identified herein and the previously described Co- genes in these telomeric regions. The linkage analysis using a genetic map of 497 SNPs from the recombinant inbred line population Xana/BAT93 revealed that the gene conferring resistance to race 65 in cultivar Xana (Co-165-X) was located in the Co-1 cluster, at the distal end of chromosome Pv01. The fine mapping of Co-165-X indicated that it was positioned between the physical positions 49,512,545 and 49,658,821 bp. This delimited physical position agrees with the positions of the previously mapped genes Co- 14, Co-x, Co-14, Co-1HY, and Co-Pa. Responses to races 6, 38, 39, and 357 in BAT93 exhibited co-segregation suggesting that the same gene, or very closely linked genes, were involved in the control. The linkage analysis showed that the resistance gene to race 38 in the genotype BAT93 (Co-338-B) was located at the beginning of chromosome Pv04, in the genetic position of the Co-3 cluster, and was flanked by markers with physical positions between 1,286,490 and 2,047,754 bp. Thus, the genes Co-3, Co-9, Co-10, Co-16, and Co-338-B, found in this work, form part of the same anthracnose resistance cluster at the beginning of chromosome Pv04, which is consistent with the discontinuous distribution of typical R genes annotated in the underlying genomic region. Resistance loci involved in the response to race 73 in the genotypes Xana (R) and BAT93 (R) were mapped to the same positions on clusters Co-1 and Co-3, respectively. The positioning of the resistance genes in the bean genome based on fine linkage mapping should play an important role in the characterization and differentiation of the anthracnose resistance genes. The assignment of Co- genes to clusters of race specific genes can help simplify the current scenario of anthracnose resistance.
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Affiliation(s)
- Ester Murube
- Plant Genetic Group, Area of Horticultural and Forest Crops, SERIDA, Villaviciosa Asturias, Spain
| | - Ana Campa
- Plant Genetic Group, Area of Horticultural and Forest Crops, SERIDA, Villaviciosa Asturias, Spain
| | - Juan José Ferreira
- Plant Genetic Group, Area of Horticultural and Forest Crops, SERIDA, Villaviciosa Asturias, Spain
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Bhat NN, Mahiya-Farooq, Padder BA, Shah M, Dar M, Nabi A, Bano A, Rasool RS, Sana-Surma. Microsatellite mining in the genus Colletotrichum. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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34
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Zhang L, Huang X, He C, Zhang QY, Zou X, Duan K, Gao Q. Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus. FRONTIERS IN PLANT SCIENCE 2018; 9:434. [PMID: 29922301 PMCID: PMC5996897 DOI: 10.3389/fpls.2018.00434] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/21/2018] [Indexed: 05/29/2023]
Abstract
Colletotrichum fructicola, which is part of the C. gloeosporioides species complex, can cause anthracnose diseases in strawberries worldwide. However, the molecular interactions between C. fructicola and strawberry are largely unknown. A deep RNA-sequencing approach was applied to gain insights into the pathogenicity mechanisms of C. fructicola and the defense response of strawberry plants at different stages of infection. The transcriptome data showed stage-specific transcription accompanied by a step-by-step strawberry defense response and the evasion of this defense system by fungus. Fungal genes involved in plant cell wall degradation, secondary metabolism, and detoxification were up-regulated at different stage of infection. Most importantly, C. fructicola infection was accompanied by a large number of highly expressed effectors. Four new identified effectors function in the suppression of Bax-mediated programmed cell death. Strawberry utilizes pathogen-associated molecular patterns (PAMP)-triggered immunity and effector-triggered immunity to prevent C. fructicola invasion, followed by the initiation of downstream innate immunity. The up-regulation of genes related to salicylic acid provided evidence that salicylic acid signaling may serve as the core defense signaling mechanism, while jasmonic acid and ethylene pathways were largely inhibited by C. fructicola. The necrotrophic stage displayed a significant up-regulation of genes involved in reactive oxygen species activation. Collectively, the transcriptomic data of both C. fructicola and strawberry shows that even though plants build a multilayered defense against infection, C. fructicola employs a series of escape or antagonizing mechanisms to successfully infect host cells.
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Affiliation(s)
- Liqing Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xin Huang
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chengyong He
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- College of Food Science, Shanghai Ocean University, Shanghai, China
| | - Qing-Yu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaohua Zou
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ke Duan
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- College of Food Science, Shanghai Ocean University, Shanghai, China
| | - Qinghua Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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35
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Wang Y, Hao X, Lu Q, Wang L, Qian W, Li N, Ding C, Wang X, Yang Y. Transcriptional analysis and histochemistry reveal that hypersensitive cell death and H 2O 2 have crucial roles in the resistance of tea plant ( Camellia sinensis (L.) O. Kuntze) to anthracnose. HORTICULTURE RESEARCH 2018; 5:18. [PMID: 29619229 PMCID: PMC5878829 DOI: 10.1038/s41438-018-0025-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/04/2018] [Accepted: 02/02/2018] [Indexed: 05/04/2023]
Abstract
Anthracnose causes severe losses of tea production in China. Although genes and biological processes involved in anthracnose resistance have been reported in other plants, the molecular response to anthracnose in tea plant is unknown. We used the susceptible tea cultivar Longjing 43 and the resistant cultivar Zhongcha 108 as materials and compared transcriptome changes in the leaves of both cultivars following Colletotrichum fructicola inoculation. In all, 9015 and 8624 genes were differentially expressed between the resistant and susceptible cultivars and their controls (0 h), respectively. In both cultivars, the differentially expressed genes (DEGs) were enriched in 215 pathways, including responses to sugar metabolism, phytohormones, reactive oxygen species (ROS), biotic stimuli and signalling, transmembrane transporter activity, protease activity and signalling receptor activity, but DEG expression levels were higher in Zhongcha 108 than in Longjing 43. Moreover, functional enrichment analysis of the DEGs showed that hydrogen peroxide (H2O2) metabolism, cell death, secondary metabolism, and carbohydrate metabolism are involved in the defence of Zhongcha 108, and 88 key genes were identified. Protein-protein interaction (PPI) network demonstrated that putative mitogen-activated protein kinase (MAPK) cascades are activated by resistance (R) genes and mediate downstream defence responses. Histochemical analysis subsequently validated the strong hypersensitive response (HR) and H2O2 accumulation that occurred around the hyphal infection sites in Zhongcha 108. Overall, our results indicate that the HR and H2O2 are critical mechanisms in tea plant defence against anthracnose and may be activated by R genes via MAPK cascades.
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Affiliation(s)
- Yuchun Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Xinyuan Hao
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Qinhua Lu
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Lu Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Wenjun Qian
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Nana Li
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Changqing Ding
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Xinchao Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
| | - Yajun Yang
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008 People’s Republic of China
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