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Cui W, Fiore N, Figueroa F, Rubilar C, Pizarro L, Pinto M, Pérez S, Beltrán MF, Carreras C, Pimentel P, Zamorano A. Transcriptome Analysis of Sweet Cherry ( Prunus avium L.) Cultivar 'Lapins' upon Infection of Pseudomonas syringae pv. syringae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3718. [PMID: 37960074 PMCID: PMC10647540 DOI: 10.3390/plants12213718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Bacterial canker caused by Pseudomonas syringae pv. syringae (Pss) is responsible for substantial loss to the production of sweet cherry in Chile. To date, the molecular mechanisms of the Pss-sweet cherry interaction and the disease-related genes in the plant are poorly understood. In order to gain insight into these aspects, a transcriptomic analysis of the sweet cherry cultivar 'Lapins' for differentially expressed genes (DEGs) in response to Pss inoculation was conducted. Three Pss strains, A1M3, A1M197, and 11116_b1, were inoculated in young twigs, and RNA was extracted from tissue samples at the inoculation site and distal sections. RNA sequencing and transcriptomic expression analysis revealed that the three strains induced different patterns of responses in local and distal tissues. In the local tissues, A1M3 triggered a much more extensive response than the other two strains, enriching DEGs especially involved in photosynthesis. In the distal tissues, the three strains triggered a comparable extent of responses, among which 11116_b1 induced a group of DEGs involved in defense responses. Furthermore, tissues from various inoculations exhibited an enrichment of DEGs related to carbohydrate metabolism, terpene metabolism, and cell wall biogenesis. This study opened doors to future research on the Pss-sweet cherry interaction, immunity responses, and disease control.
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Affiliation(s)
- Weier Cui
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Nicola Fiore
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Franco Figueroa
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Carlos Rubilar
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Lorena Pizarro
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Manuel Pinto
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Set Pérez
- Laboratorio de Patología Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile;
| | - María Francisca Beltrán
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Claudia Carreras
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Paula Pimentel
- Laboratorio de Fisiología del Estrés, Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas, 882, Rengo 2940000, Chile;
| | - Alan Zamorano
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
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Laribi M, Fredua-Agyeman R, Ben M’Barek S, Sansaloni CP, Dreisigacker S, Gamba FM, Abdedayem W, Nefzaoui M, Araar C, Hwang SF, Yahyaoui AH, Strelkov SE. Genome-wide association analysis of tan spot disease resistance in durum wheat accessions from Tunisia. Front Genet 2023; 14:1231027. [PMID: 37946749 PMCID: PMC10631785 DOI: 10.3389/fgene.2023.1231027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
Background: Tunisia harbors a rich collection of unexploited durum wheat landraces (Triticum durum ssp. durum) that have been gradually replaced by elite cultivars since the 1970s. These landraces represent an important potential source for broadening the genetic background of elite durum wheat cultivars and for the introgression of novel genes for key traits, including disease resistance, into these cultivars. Methods: In this study, single nucleotide polymorphism (SNP) markers were used to investigate the genetic diversity and population structure of a core collection of 235 durum wheat accessions consisting mainly of landraces. The high phenotypic and genetic diversity of the fungal pathogen Pyrenophora tritici-repentis (cause of tan spot disease of wheat) in Tunisia allowed the assessment of the accessions for tan spot resistance at the adult plant stage under field conditions over three cropping seasons. A genome-wide association study (GWAS) was performed using a 90k SNP array. Results: Bayesian population structure analysis with 9191 polymorphic SNP markers classified the accessions into two groups, where groups 1 and 2 included 49.79% and 31.49% of the accessions, respectively, while the remaining 18.72% were admixtures. Principal coordinate analysis, the unweighted pair group method with arithmetic mean and the neighbor-joining method clustered the accessions into three to five groups. Analysis of molecular variance indicated that 76% of the genetic variation was among individuals and 23% was between individuals. Genome-wide association analyses identified 26 SNPs associated with tan spot resistance and explained between 8.1% to 20.2% of the phenotypic variation. The SNPs were located on chromosomes 1B (1 SNP), 2B (4 SNPs), 3A (2 SNPs), 3B (2 SNPs), 4A (2 SNPs), 4B (1 SNP), 5A (2 SNPs), 5B (4 SNPs), 6A (5 SNPs), 6B (2 SNPs), and 7B (1 SNP). Four markers, one on each of chromosomes 1B, and 5A, and two on 5B, coincided with previously reported SNPs for tan spot resistance, while the remaining SNPs were either novel markers or closely related to previously reported SNPs. Eight durum wheat accessions were identified as possible novel sources of tan spot resistance that could be introgressed into elite cultivars. Conclusion: The results highlighted the significance of chromosomes 2B, 5B, and 6A as genomic regions associated with tan spot resistance.
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Affiliation(s)
- Marwa Laribi
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Rudolph Fredua-Agyeman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Sarrah Ben M’Barek
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
- Regional Field Crops Research Center of Beja (CRRGC), Beja, Tunisia
| | | | | | | | - Wided Abdedayem
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
| | - Meriem Nefzaoui
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
| | - Chayma Araar
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Amor H. Yahyaoui
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis, Tunisia
- Borlaug Training Foundation, Colorado State University, Fort Collins, CO, United States
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Joshi B, Singh S, Tiwari GJ, Kumar H, Boopathi NM, Jaiswal S, Adhikari D, Kumar D, Sawant SV, Iquebal MA, Jena SN. Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1252746. [PMID: 37941674 PMCID: PMC10630025 DOI: 10.3389/fpls.2023.1252746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 11/10/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.
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Affiliation(s)
- Babita Joshi
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Singh
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gopal Ji Tiwari
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
| | - Harish Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dibyendu Adhikari
- Plant Ecology and Climate Change Science, CSIR-National Botanical Research Institute, Lucknow, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samir V. Sawant
- Molecular Biology & Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Satya Narayan Jena
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
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Exploration of bacterial diversity in leaves and rhizosphere soil of flood affected and unaffected apricot trees. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Hulin MT, Vadillo Dieguez A, Cossu F, Lynn S, Russell K, Neale HC, Jackson RW, Arnold DL, Mansfield JW, Harrison RJ. Identifying resistance in wild and ornamental cherry towards bacterial canker caused by Pseudomonas syringae. PLANT PATHOLOGY 2022; 71:949-965. [PMID: 35909801 PMCID: PMC9305585 DOI: 10.1111/ppa.13513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 05/31/2023]
Abstract
Bacterial canker is a major disease of stone fruits and is a critical limiting factor to sweet cherry (Prunus avium) production worldwide. One important strategy for disease control is the development of resistant varieties. Partial varietal resistance in sweet cherry is discernible using shoot or whole tree inoculations; however, these quantitative differences in resistance are not evident in detached leaf assays. To identify novel sources of resistance to canker, we used a rapid leaf pathogenicity test to screen a range of wild cherry, ornamental Prunus species and sweet cherry × ornamental cherry hybrids with the canker pathogens, Pseudomonas syringae pvs syringae, morsprunorum races 1 and 2, and avii. Several Prunus accessions exhibited limited symptom development following inoculation with each of the pathogens, and this resistance extended to 16 P. syringae strains pathogenic on sweet cherry and plum. Resistance was associated with reduced bacterial multiplication after inoculation, a phenotype similar to that of commercial sweet cherry towards nonhost strains of P. syringae. Progeny resulting from a cross of a resistant ornamental species Prunus incisa with susceptible sweet cherry (P. avium) exhibited resistance indicating it is an inherited trait. Identification of accessions with resistance to the major bacterial canker pathogens is the first step towards characterizing the underlying genetic mechanisms of resistance and introducing these traits into commercial germplasm.
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Affiliation(s)
- Michelle T. Hulin
- NIAB EMREast MallingUK
- Present address:
The Sainsbury LaboratoryNorwichUK
| | | | | | | | | | - Helen C. Neale
- Centre for Research in BioscienceFaculty of Health and Applied SciencesThe University of the West of EnglandFrenchay CampusBristolUK
| | - Robert W. Jackson
- Birmingham Institute of Forest Research (BIFoR)University of BirminghamBirminghamUK
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Dawn L. Arnold
- Centre for Research in BioscienceFaculty of Health and Applied SciencesThe University of the West of EnglandFrenchay CampusBristolUK
- Harper Adams UniversityNewportShropshireUK
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Hulin MT, Jackson RW, Harrison RJ, Mansfield JW. Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits. PLANT PATHOLOGY 2020; 69:962-978. [PMID: 32742023 PMCID: PMC7386918 DOI: 10.1111/ppa.13189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 05/10/2023]
Abstract
Bacterial canker disease is a major limiting factor in the growing of cherry and other Prunus species worldwide. At least five distinct clades within the bacterial species complex Pseudomonas syringae are known to be causal agents of the disease. The different pathogens commonly coexist in the field. Reducing canker is a challenging prospect as the efficacy of chemical controls and host resistance may vary against each of the diverse clades involved. Genomic analysis has revealed that the pathogens use a variable repertoire of virulence factors to cause the disease. Significantly, strains of P. syringae pv. syringae possess more genes for toxin biosynthesis and fewer encoding type III effector proteins. There is also a shared pool of key effector genes present on mobile elements such as plasmids and prophages that may have roles in virulence. By contrast, there is evidence that absence or truncation of certain effector genes, such as hopAB, is characteristic of cherry pathogens. Here we highlight how recent research, underpinned by the earlier epidemiological studies, is allowing significant progress in our understanding of the canker pathogens. This fundamental knowledge, combined with emerging insights into host genetics, provides the groundwork for development of precise control measures and informed approaches to breed for disease resistance.
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Affiliation(s)
| | - Robert W. Jackson
- Birmingham Institute of Forest Research (BIFoR), University of BirminghamBirminghamUK
- School of Biosciences, University of BirminghamBirminghamUK
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