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Brochu AS, Dumonceaux T, Valenzuela M, Bélanger RR, Pérez-López E. A New Multiplex TaqMan qPCR for Precise Detection and Quantification of Clavibacter michiganensis in Seeds and Plant Tissue. Plant Dis 2024. [PMID: 38381965 DOI: 10.1094/pdis-06-23-1194-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, is the ability of Cm to infect seeds and plants without causing symptoms what makes it an even more dangerous pathogen. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay is able to discriminate Cm strains from other related bacteria. The assay was validated on tissue and seed samples following artificial infection and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves, and roots. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.
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Affiliation(s)
- Anne-Sophie Brochu
- Université Laval, 4440, Plant Sciences, 2480 Boulevard Hochelaga, Québec, Quebec, Canada, G1V 0A6;
| | - Tim Dumonceaux
- Agriculture and Agri-Food Canada, Bio-products and processes, 107 Science Place, Saskatoon, Saskatchewan, Canada, S7N0X2
- Agriculture and Agri-Food Canada;
| | | | - Richard R Bélanger
- Université Laval, Phytologie, 2425 rue de l'Agriculture, Pavillon Comtois, Québec, Quebec, Canada, G1V0A6;
| | - Edel Pérez-López
- Universite Laval, 4440, Phytologie, 2480, Boul. Hochelaga, Quebec, Quebec, Canada, G1V 0A6;
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Bragard C, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Migheli Q, Stefani E, Vloutoglou I, Czwienczek E, Maiorano A, Streissl F, Reignault PL. Pest categorisation of Xanthomonas citri pv. viticola. EFSA J 2021; 19:e06929. [PMID: 34963789 PMCID: PMC8675326 DOI: 10.2903/j.efsa.2021.6929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The EFSA Plant Health Panel performed a pest categorisation of Xanthomonas citri pv. viticola (Nayudu) Dye, a Gram-negative bacterium belonging to the Xanthomonadaceae family. The pathogen is a well-defined taxonomic unit and is the causal agent of the leaf spot and bacterial canker of Vitis vinifera. This bacterium is present in India and Brazil, where it affects table grape cultivation; the same pathogen is able to cause a disease on Azadirachta indica and on some weed species. Reports indicate that the bacterium is present in Thailand as well. The pathogen has never been reported from the EU territory and it is not included in EU Commission Implementing Regulation 2019/2072. The pathogen can be detected on its host plants using direct isolation, serological or PCR-based methods. Its identification is achieved using biochemical and nutritional assays, together with a multilocus sequence analysis based on seven housekeeping genes. The main pathway for the entry of the pathogen into the EU territory is plant propagation material. In the EU, there is large availability of host plants, with grapevine being one of the most important crops in Europe and more specifically in its Mediterranean areas. Since X. citri pv. viticola is only reported in tropical and subtropical areas (BSh and Aw climatic zones according to the Köppen-Geiger classification), there is uncertainty whether the climatic conditions in the EU territory are suitable for its establishment. Nevertheless, due to the great importance of grapevine for the EU agriculture, any disease outbreak may have a high-economic impact. Phytosanitary measures are available to prevent the introduction of the pathogen into the EU. X. citri pv. viticola satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest.
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Basim H, Basim E, Tombuloglu H, Unver T. Comparative transcriptome analysis of resistant and cultivated tomato lines in response to Clavibacter michiganensis subsp. michiganensis. Genomics 2021; 113:2455-2467. [PMID: 34052318 DOI: 10.1016/j.ygeno.2021.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022]
Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive bacterium causing destructive bacterial wilt and canker disease in tomato. Herein, a comparative transcriptome analysis was performed on Cmm-resistant and -susceptible tomato lines. Tomato seedlings were inoculated with Cmm and harvested for transcriptome analysis after 4 and 8 day time-points. Twenty-four transcriptome libraries were profiled by RNA sequencing approach. Total of 545 million clean reads was generated. 1642 and 2715 differentially expressed genes (DEG) were identified in susceptible lines within 4 and 8 days after inoculation (DAI), respectively. In resistant lines, 1731 and 1281 DEGs were found following 4 and 8 DAI, respectively. Gene Ontology analysis resulted in a higher number of genes involved in biological processes and molecular functions in susceptible lines. On the other hand, such biological processes, "defense response", and "response to stress" were distinctly indicated in resistant lines which were not found in susceptible ones upon inoculation, according to the gene set enrichment analyses. Upon Cmm-inoculation, several defense responsive genes were found to be differentially expressed. Of which 26 genes were in the resistant line and three were in the susceptible line. This study helps to understand the transcriptome response of Cmm-resistant and -susceptible tomato lines. The results provide comprehensive data for molecular breeding studies, for the purpose to control of the pathogen in tomato.
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Affiliation(s)
- Huseyin Basim
- Department of Plant Protection, Faculty of Agriculture, Akdeniz University, 07070 Antalya, Turkey.
| | - Esin Basim
- Department of Organic Agriculture, Technical Sciences Vocational School, Akdeniz University, 07070 Antalya, Turkey
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Turgay Unver
- Ficus Biotechnology, Ostim OSB Mah, 100. Yil Blv, No:55, Yenimahalle, Ankara, Turkey
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Faize M, Faize L, Alburquerque N, Venisse JS, Burgos L. Hydrogen peroxide generated by over-expression of cytosolic superoxide dismutase in transgenic plums enhances bacterial canker resistance and modulates plant defence responses. Mol Biol Rep 2020; 47:5889-901. [PMID: 32661871 DOI: 10.1007/s11033-020-05660-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
H2O2 generated during the oxidative burst, plays important roles in plant defenses responses against pathogens. In this study we examined the role of H2O2 on bacterial canker resistance in transgenic plums over-expressing cytosolic superoxide dismutase. Three transgenic lines (C64, C66 and F12) with elevated levels of H2O2 accumulation showed enhanced resistance against bacterial canker disease caused by Pseudomonas syringae pv. syringae, when compared to the non-transformed control. Analysis of the expression of several genes involved in the plant-pathogen interaction showed that the expression of those involved in SA pathway (pr1 and npr1) and JA (lox3) were activated earlier and transiently in transgenic lines C66 and F12 when compared to the wild type. However, the expression of genes involved in anthocyanin synthesis (chi, chs, f3h, dfr, atcs, myb10) and ethylene (acs) was induced at very low levels whereas it was activated by the pathogen at exaggerated levels in the non-transformed line. These results suggest that resistance observed in transgenic lines over-producing H2O2 is correlated with an early and transient induction of defense genes associated with the SA and JA pathways and inhibition of gene expression associated with ethylene and anthocyanin biosynthesis.
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Cellini A, Donati I, Fiorentini L, Vandelle E, Polverari A, Venturi V, Buriani G, Vanneste JL, Spinelli F. N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae. Microb Ecol 2020; 79:383-396. [PMID: 31359073 DOI: 10.1007/s00248-019-01416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.
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Affiliation(s)
- Antonio Cellini
- Department of Agricultural and Food Science, Alma Mater Studiorum - Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Irene Donati
- Department of Agricultural and Food Science, Alma Mater Studiorum - Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Luca Fiorentini
- Department of Agricultural and Food Science, Alma Mater Studiorum - Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Elodie Vandelle
- Department of Biotechnology, Università degli Studi di Verona, Verona, Italy
| | - Annalisa Polverari
- Department of Biotechnology, Università degli Studi di Verona, Verona, Italy
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giampaolo Buriani
- Department of Agricultural and Food Science, Alma Mater Studiorum - Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy
| | - Joel L Vanneste
- The New Zealand Institute for Plant & Food Research, Hamilton, New Zealand
| | - Francesco Spinelli
- Department of Agricultural and Food Science, Alma Mater Studiorum - Università di Bologna, Viale Fanin 44, 40127, Bologna, Italy.
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Park J, Lim JA, Yu JG, Oh CS. Genomic Features and Lytic Activity of the Bacteriophage PPPL-1 Effective against Pseudomonas syringae pv. actinidiae, a Cause of Bacterial Canker in Kiwifruit. J Microbiol Biotechnol 2019; 28:1542-1546. [PMID: 30369117 DOI: 10.4014/jmb.1806.06055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Bacterial canker in kiwifruit is caused by Pseudomonas syringae pv. actinidiae (Psa). In this study, the bacteriophage PPPL-1 effective against Psa was characterized. Belonging to the Podoviridae family, PPPL-1 was effective against most Psa strains as well as most Pseudomonas syringae pathovars. PPPL-1 carries a 41,149-bp genome with 49 protein coding sequences and is homologous to the previously reported phiPSA2 bacteriophage. The lytic activity of PPPL-1 was stable up to 40°C, within a range of pH 3-11 and under 365 nm UV light. These results indicate that the bacteriophage PPPL-1 might be useful to control Psa in the kiwifruit field.
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Affiliation(s)
- Jungkum Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jeong-A Lim
- Research Group of Food Safety, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Ji-Gang Yu
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin 17104, Republic of Korea
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Ruinelli M, Blom J, Smits THM, Pothier JF. Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp. BMC Genomics 2019; 20:172. [PMID: 30836956 PMCID: PMC6402114 DOI: 10.1186/s12864-019-5555-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 02/22/2019] [Indexed: 11/22/2022] Open
Abstract
Background Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe lack of genomic information of these pathogens. The high phylogenetic diversity observed within strains causing disease on Prunus spp. in nature, raised the question whether other strains or species within the P. syringae species complex were potentially pathogenic on Prunus spp. Results To gain insight into the genomic potential of adaptation and virulence in Prunus spp., a total of twelve de novo whole genome sequences of P. syringae pathovars and species found in association with diseases on cherry (sweet, sour and ornamental-cherry) and peach were sequenced. Strains sequenced in this study covered three phylogroups and four clades. These strains were screened in vitro for pathogenicity on Prunus spp. together with additional genome sequenced strains thus covering nine out of thirteen of the currently defined P. syringae phylogroups. Pathogenicity tests revealed that most of the strains caused symptoms in vitro and no obvious link was found between presence of known virulence factors and the observed pathogenicity pattern based on comparative genomics. Non-pathogenic strains were displaying a two to three times higher generation time when grown in rich medium. Conclusion In this study, the first set of complete genomes of cherry associated P. syringae strains as well as the draft genome of the quarantine peach pathogen P. syringae pv. persicae were generated. The obtained genomic data were matched with phenotypic data in order to determine factors related to pathogenicity to Prunus spp. Results of this study suggest that the inability to cause disease on Prunus spp. in vitro is not the result of host specialization but rather linked to metabolic impairments of individual strains. Electronic supplementary material The online version of this article (10.1186/s12864-019-5555-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michela Ruinelli
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland.
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland
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Dharmaraj K, Cui W, Rikkerink EHA, Templeton MD. Construction of a kiwifruit yeast two-hybrid cDNA library to identify host targets of the Pseudomonas syringae pv. actinidiae effector AvrPto5. BMC Res Notes 2019; 12:63. [PMID: 30691538 PMCID: PMC6350409 DOI: 10.1186/s13104-019-4102-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/19/2019] [Indexed: 11/10/2022] Open
Abstract
Objective Bacterial canker is a destructive disease of kiwifruit caused by the Gram-negative bacterium Pseudomonas syringae pv. actinidiae (Psa). To understand the disease-causing mechanism of Psa, a kiwifruit yeast two-hybrid cDNA library was constructed to identify putative host targets of the Psa Type Three Secreted Effector AvrPto5. Results In this study, we used the Mate & Plate™ yeast two-hybrid library method for constructing a kiwifruit cDNA library from messenger RNA of young leaves. The constructed library consisted of 2.15 × 106 independent clones with an average insert size of 1.52 kb. The screening of the kiwifruit yeast two-hybrid cDNA library with Psa AvrPto5 revealed the interaction of a V-type proton ATPase subunit-H, a proline rich-protein and heavy metal-associated isoprenylated plant protein 26. Among these, heavy metal-associated isoprenylated plant protein 26 showed a positive interaction with Psa AvrPto5 as both prey and bait. Electronic supplementary material The online version of this article (10.1186/s13104-019-4102-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karthikeyan Dharmaraj
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.,The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,Plant Health and Environment Laboratory, Ministry for Primary Industries, 231 Morrin Road, Auckland, 1072, New Zealand
| | - Wei Cui
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Erik H A Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Matthew D Templeton
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. .,The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
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Omrani M, Roth M, Roch G, Blanc A, Morris CE, Audergon JM. Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker. BMC Plant Biol 2019; 19:31. [PMID: 30665361 PMCID: PMC6341767 DOI: 10.1186/s12870-019-1631-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/04/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard. In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models. Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals. RESULTS We detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions. CONCLUSIONS Our study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy.
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Affiliation(s)
- Mariem Omrani
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- INRA, UR407 Pathologie Végétale, Centre de Recherche PACA, Montfavet, France
- ENGREF, AgroParisTech, Paris, France
| | - Morgane Roth
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- Present Address: Agroscope, Research Division Plant Breeding, Wädenswil, Switzerland
| | - Guillaume Roch
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
- CEP Innovation, Lyon, France
| | - Alain Blanc
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
| | - Cindy E. Morris
- INRA, UR407 Pathologie Végétale, Centre de Recherche PACA, Montfavet, France
| | - Jean-Marc Audergon
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Montfavet, France
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