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Demiwal P, Mir JI, Sircar D. A non-invasive method for phenotyping scab-tolerant apple plants using volatile organic compounds. PHYSIOLOGIA PLANTARUM 2024; 176:e14377. [PMID: 38837251 DOI: 10.1111/ppl.14377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 06/07/2024]
Abstract
One of the most devastating diseases of apples is scab, caused by the fungus Venturia inaequalis. Most commercial apple varieties are susceptible to this disease; only a few are resistant. Breeding approaches are being used to develop better apple varieties that are resistant to scab. Volatile organic compounds (VOCs) contribute greatly to a plant's phenotype, and their emission profile largely depends on the genotype. In the non-destructive phenotyping of plants, VOCs can be used as biomarkers. In this study, we assessed non-destructively the scab tolerance potential of resistant (cv. 'Prima') and susceptible (cv. 'Oregon Spur') apple cultivars by comparing their major leaf VOC compositions and relative proportions. A comparison of the leaf VOC profiles of the two cultivars revealed 16 different VOCs, with cis-3-hexenyl acetate (3HA) emerging as a biomarker of cultivar differences. V. inaequalis growth was significantly inhibited in vitro by 3HA treatment. 3HA was significantly effective in reducing scab symptoms on V. inaequalis-inoculated leaves of 'Oregon Spur.' The resistant cultivar 'Prima' also exhibited higher lipoxygenase (LOX) activity and α-linolenic acid (ALA) levels, suggesting that V. inaequalis resistance is linked to LOX activity and 3HA biosynthesis. This study proposes 3HA as a potential biomarker for rapid non-destructive screening of scab-resistant apple germplasm of 'Prima' based on leaf VOCs.
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Affiliation(s)
- Pratibha Demiwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Javid Iqbal Mir
- Central Institute of Temperate Horticulture (ICAR-CITH), Srinagar, J&K, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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2
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Švara A, De Storme N, Carpentier S, Keulemans W, De Coninck B. Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab ( Venturia inaequalis) in apple cultivars ( Malus × domestica). HORTICULTURE RESEARCH 2024; 11:uhae002. [PMID: 38371632 PMCID: PMC10873587 DOI: 10.1093/hr/uhae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024]
Abstract
Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
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Affiliation(s)
- Anže Švara
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Genetic resources, Bioversity International, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Barbara De Coninck
- Laboratory of Plant Health and Protection, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
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Švara A, Sun H, Fei Z, Khan A. Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3 (BETHESDA, MD.) 2023; 14:jkad253. [PMID: 37936323 PMCID: PMC10755186 DOI: 10.1093/g3journal/jkad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in "Honeycrisp" and Rvi17 in "Antonovka," were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95 and 81-95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.
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Affiliation(s)
- Anže Švara
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
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Peil A, Howard NP, Bühlmann-Schütz S, Hiller I, Schouten H, Flachowsky H, Patocchi A. Rvi4 and Rvi15 are the same apple scab resistance genes. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:74. [PMID: 37830083 PMCID: PMC10564682 DOI: 10.1007/s11032-023-01421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
The apple (Malus x domestica) scab (Venturia inaequalis) resistance genes Rvi4 and Rvi15 were mapped to a similar region on the top of linkage group 2 and both resistance genes elicit the same type of resistance reaction, i.e., a hypersensitive response; hence, it is suspected that the two genes may be the same. As the two resistance genes Rvi4 and Rvi15 are currently used in apple breeding, it is important to clarify whether the two resistance genes are the same or not. Several approaches were used to make this determination. First, the pedigree of the genotype GMAL 2473, the source of Rvi15, was reconstructed. GMAL 2473 was found to be an F1 of 'Russian seedling', the genotype, which is known to also be the source of Rvi4. Next, it was further demonstrated that 'Regia', a cultivar known to carry Rvi4 (and Rvi2), carries the same gene (Vr2-C), which was demonstrated to be the gene inducing Rvi15 resistance. Finally, it was shown that transgenic lines carrying Vr2-C are compatible with race 4 apple scab isolates. Taken all together, these results definitively demonstrate that Rvi4 and Rvi15 are the same resistance gene. For future studies, we suggest referring to this resistance with the first name that was assigned to this gene, namely Rvi4. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01421-0.
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Affiliation(s)
- Andreas Peil
- Julius Kühn Institut (JKI)—Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Pillnitz Germany
| | - Nicholas P Howard
- Fresh Forward Breeding and Marketing B.V., Hogewoerd 1C, 6851 ET Huissen, The Netherlands
| | - Simone Bühlmann-Schütz
- Research Division Plant Breeding, Agroscope, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Ines Hiller
- Julius Kühn Institut (JKI)—Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Pillnitz Germany
| | - Henk Schouten
- Department of Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Henryk Flachowsky
- Julius Kühn Institut (JKI)—Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Pillnitz Germany
| | - Andrea Patocchi
- Research Division Plant Breeding, Agroscope, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
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Dar MS, Ahmad M, Yetoo NUN, Bhatt B, Bhat SN, Altaf H, Rafiqee S, Nabi A, Mohiddin FA, Gaafar ARZ, Mansoor S, Shah MD, Mushtaq M. Genetic footprint of population diversity and genetic structure of Venturia inaequalis infecting apple (Malus × domestica Borkh.). 3 Biotech 2023; 13:273. [PMID: 37449250 PMCID: PMC10335993 DOI: 10.1007/s13205-023-03672-2] [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: 02/18/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Apple scab instigated by Venturia inaequalis impels remarkable losses to apple fruit production. In an effort to comprehend the key mechanisms of evolutionary potential defining V. inaequalis population, 132 isolates of V. inaequalis from five commercial apple orchards were collected and assayed using 14 microsatellite markers. The average diversity was observed within the individuals of populations based on the Shannon-Wieners index (I) and observed heterozygosity (Ho) was average but considerably lower than expected heterozygosity (He). The genetic differentiation based on FST values was revealed as an average measure of divergence between populations and had varying proportions of gene flow and migration among themselves. Analysis of Molecular Variance (AMOVA) revealed that variance (94%) was dispersed across individuals with a significant (6%) variation between populations from different regions. To examine host specialization within the V. inaequalis population, the assignment approach based on K-means of clustering (an unsupervised machine learning approach), revealed that the clustering method supported three clusters at (K = 3) and three major clusters were also observed in Principle Component Analysis (PCA). Additionally, Nei's genetic distance values, pairwise estimates of genetic differentiation, dendrogram using the neighbor-joining and PCoA revealed the random distribution of V. Inaequalis isolates that depicted a high proportion of genotypic diversity within populations and population genetic structure. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03672-2.
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Affiliation(s)
- Mohammad Saleem Dar
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Mushtaq Ahmad
- Division of Plant Pathology, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Nakeeb-Un-Nisa Yetoo
- Division of Genetics and Plant Breeding, FoA, SKUAST-K, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Bhagyshree Bhatt
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
| | - Suhail Nazir Bhat
- Division of Fruit Science, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Heena Altaf
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Sumira Rafiqee
- Division of Genetics and Plant Breeding, FoA, SKUAST-K, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Asha Nabi
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - F. A. Mohiddin
- Mountain Research Centre for Field Crops, SKUAST-Kashmir, Khudwani, Kulgam, Jammu and Kashmir 192101 India
| | - Abdel-Rhman Z. Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
| | - Mehraj D. Shah
- Division of Plant Pathology, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
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Awan SI, Thapa R, Svara A, Feulner H, Streb N, Khan A. Evaluation of Malus Germplasm Identifies Genetic Sources of Powdery Mildew and Frogeye Leaf Spot Resistance for Apple Breeding. PHYTOPATHOLOGY 2023; 113:1289-1300. [PMID: 36802874 DOI: 10.1094/phyto-11-22-0417-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Apple is an important fruit crop of temperate regions. The narrow genetic base of commercially cultivated apples has resulted in its vulnerability to a large number of fungal, bacterial, and viral pathogens. Apple breeders are always seeking new sources of resistance within the cross-compatible Malus species that can be deployed into elite genetic backgrounds. We have evaluated resistance to two major fungal diseases of apples: powdery mildew and frogeye leaf spot, using a germplasm collection of 174 Malus accessions to identify novel sources of genetic resistance. In 2020 and 2021, we evaluated these accessions for the incidence and severity of powdery mildew and frogeye leaf spot diseases at Cornell AgriTech, Geneva, New York, in a partially managed orchard. The severity and incidence of powdery mildew and frogeye leaf spot, as well as weather parameters were recorded in June, July, and August. Total incidence of powdery mildew and frogeye leaf spot infections increased from 33 to 38%, and 56 to 97% in 2020 and 2021, respectively. Our analysis showed that relative humidity and precipitation correlate with powdery mildew and frogeye leaf spot susceptibility. The predictor variables with highest impact to the variability of powdery mildew were accessions and relative humidity in May. A total of 65 Malus accessions were found to be resistant to powdery mildew, and only one accession showed moderate resistance to frogeye leaf spot. Several of these accessions belong to Malus hybrid species and domesticated apples and can therefore be potential sources of novel resistance alleles for apple breeding.
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Affiliation(s)
- Shahid Iqbal Awan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Ranjita Thapa
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Anze Svara
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Hana Feulner
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Nicholas Streb
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
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Moureu S, Jacquin J, Samaillie J, Deweer C, Rivière C, Muchembled J. Antifungal Activity of Hop Leaf Extracts and Xanthohumol on Two Strains of Venturia inaequalis with Different Sensitivities to Triazoles. Microorganisms 2023; 11:1605. [PMID: 37375106 DOI: 10.3390/microorganisms11061605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Hop cones are well-known for their antimicrobial properties, attributed to their specialized metabolites. Thus, this study aimed to determine the in vitro antifungal activity of different hop parts, including by-products such as leaves and stems, and some metabolites against Venturia inaequalis, the causal agent of apple scab. For each plant part, two types of extracts, a crude hydro-ethanolic extract and a dichloromethane sub-extract, were tested on spore germination of two strains with different sensitivities to triazole fungicides. Both extracts of cones, leaves and stems were able to inhibit the two strains, whereas rhizomes did not show activity. The apolar sub-extract of leaves appeared as the most active modality tested with half maximal inhibitory concentrations (IC50) of 5 and 10.5 mg·L-1 on the sensitive strain and the strain with reduced sensitivity, respectively. Differences in activity level between strains were noticed for all active modalities tested. Sub-extracts of leaves were then separated into seven fractions by preparative HPLC and tested on V. inaequalis. One fraction, containing xanthohumol, was especially active on both strains. This prenylated chalcone was then purified by preparative HPLC and showed significant activity against both strains, with IC50 of 1.6 and 5.1 mg·L-1. Therefore, xanthohumol seems to be a promising compound to control V. inaequalis.
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Affiliation(s)
- Sophie Moureu
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
| | - Justine Jacquin
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
| | - Jennifer Samaillie
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
| | - Caroline Deweer
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
| | - Céline Rivière
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
| | - Jérôme Muchembled
- Joint Research Unit 1158 BioEcoAgro, INRAE, University of Lille, JUNIA, University of Liège, UPJV, University of Artois, ULCO, 59000 Lille, France
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Sestras RE, Sestras AF. Quantitative Traits of Interest in Apple Breeding and Their Implications for Selection. PLANTS (BASEL, SWITZERLAND) 2023; 12:903. [PMID: 36840249 PMCID: PMC9964287 DOI: 10.3390/plants12040903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Apple breeding is a laborious and long-lasting process that requires qualified resources, land, time, and funds. In this study, more than 5000 F1 apple hybrids from direct and testcrosses were analyzed. The results revealed how the phenotypic expression of the main quantitative traits of interest assessed in five half-sib families was controlled by the additive genetic effects and by non-additive effects of dominance and epistasis. The statistical number of hybrids required to ensure efficient selection increased exponentially with the number of desirable traits. The minimum number of progenies required to obtain a hybrid with associated quantitative traits of agronomic interest was highly variable. For two independent traits essential in selection (fruit size and quality), but incorporated together in the same hybrid, the statistical number was between about 30 and 300. If three more cumulative traits were added (a large number of fruits per tree, resistance/tolerance to apple scab, and powdery mildew attack), the limits increased to between 1500 and 18,000. The study highlighted the need for new apple varieties due to the narrowing of the genetic diversity of the cultivated species and how the choice of parents used in hybridizations (as well as the objectives pursued in the selection) can increase the efficiency of apple breeding.
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Affiliation(s)
- Radu E. Sestras
- Department of Horticulture and Landscape, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 3–5 Manastur Street, 400372 Cluj-Napoca, Romania
| | - Adriana F. Sestras
- Department of Forestry, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 3–5 Manastur Street, 400372 Cluj-Napoca, Romania
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Secretomic Insights into the Pathophysiology of Venturia inaequalis: The Causative Agent of Scab, a Devastating Apple Tree Disease. Pathogens 2022; 12:pathogens12010066. [PMID: 36678413 PMCID: PMC9860705 DOI: 10.3390/pathogens12010066] [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: 10/22/2022] [Revised: 12/10/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Apple scab, caused by Venturia inaequalis, is one of the world's most commercially significant apple diseases. The fungi have a catastrophic impact on apples, causing considerable losses in fruit quality and productivity in many apple-growing locations despite numerous control agents. Fungi secrete various effectors and other virulence-associated proteins that suppress or alter the host's immune system, and several such proteins were discovered in this work. Using state-of-the-art bioinformatics techniques, we examined the V. inaequalis reference genome (EU-B04), resulting in the identification of 647 secreted proteins, of which 328 were classified as small secreted proteins (SSPs), with 76.52% of SSPs identified as anticipated effector proteins. The more prevalent CAZyme proteins were the enzymes engaged in plant cell wall disintegration (targeting pectin and xylanase), adhesion and penetration (Cutinases/acetyl xylan esterase), and reactive oxygen species formation (multicopper oxidases). Furthermore, members of the S9 prolyl oligopeptidase family were identified as the most abundant host defense peptidases. Several known effector proteins were discovered to be expressed during the V. inaequalis infection process on apple leaves. The present study provides valuable data that can be used to develop new strategies for controlling apple scab.
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10
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Li Q, Hou Z, Zhou D, Jia M, Lu S, Yu J. Antifungal Activity and Possible Mechanism of Bacillus amyloliquefaciens FX2 Against the Postharvest Apple Ring Rot Pathogen. PHYTOPATHOLOGY 2022; 112:2486-2494. [PMID: 35793153 DOI: 10.1094/phyto-02-22-0047-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Botryosphaeria dothidea-induced apple ring rot is one of the most serious postharvest diseases in apple production. In our preliminary work, we isolated a bacterial strain (FX2) from an infested apple orchard. Here, we confirmed the strong antifungal activity of FX2 on B. dothidea. Through phylogenetic analysis and morphological observations, we identified FX2 as a Bacillus amyloliquefaciens strain. We also found that 10% cell-free supernatant (CFS) of FX2 significantly affected mycelial growth and morphology and almost completely inhibited spore germination and germ tube elongation in B. dothidea. Furthermore, 10% CFS damaged the cell ultrastructure, resulting in a remarkable increase in cellular leakage in B. dothidea mycelia. Thus, CFS has the potential to effectively reduce in vivo B. dothidea infection, reduced lesion diameters to 64.7% compared with the control group, and reduced disease incidence by 15%. Finally, ultrafiltration, desalting chromatography, and anion exchange chromatography showed that the antifungal constituents in CFS are composed mainly of antifungal proteins. We further characterized these potential antifungal proteins via liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Herein, we provide novel insights into the antifungal mechanisms of B. amyloliquefaciens FX2, and we highlight its potential as a novel biocontrol agent for controlling postharvest apple ring rot.
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Affiliation(s)
- Qi Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhaoqi Hou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Dongqin Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Mingyun Jia
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Shipeng Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jinping Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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11
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Strong Genetic Differentiation between Generalist Populations of Venturia inaequalis and Populations from Partially Resistant Apple Cultivars Carrying Rvi3 or Rvi5. DIVERSITY 2022. [DOI: 10.3390/d14121050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The ascomycete fungus Venturia inaequalis causes scab disease, a major problem in apple production. The utilization of resistant cultivars is hindered by emerging new pathogen races, which erode their resistance. Increasing our knowledge on the population genetic processes of the fungus can contribute to the development of resistance gene deployment strategies and more durable resistance. We investigated the effect of four scab race indicator cultivars, ‘Gala’ (no R-gene), ‘Golden Delicious’ (Rvi1), ‘Geneva’ (Rvi3, complex), and OR45t132 (Rvi5), on the V. inaequalis population genetic structure and diversity. Sixty-six monosporic fungal isolates from the four cultivars were genotyped with seven simple sequence repeat primers. Furthermore, the partial resistance of the indicators and the pathogenicity profile of the conidia from each host were assessed. The genetic diversity and structure of the investigated V. inaequalis subpopulations correspond to the partial resistance of the original hosts as well as the subpopulations’ pathogenicity profiles. Indicators carrying Rvi3 and Rvi5 had strongly diverged and specialized V. inaequalis populations on them and fewer symptoms on the field. In line with the complete breakdown of the Rvi1 gene, the population from ‘Golden Delicious’ did not segregate from the susceptible ‘Gala’, and virulence towards Rvi1 was present in all subpopulations.
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Bazzicalupo A. Local adaptation in fungi. FEMS Microbiol Rev 2022; 46:6604384. [PMID: 35675293 DOI: 10.1093/femsre/fuac026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host-pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
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Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver V6T 1Z4, Canada
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Khan A, Korban SS. Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3961-3985. [PMID: 35441862 DOI: 10.1007/s00122-022-04093-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.
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Affiliation(s)
- Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
| | - Schuyler S Korban
- Department of Natural Sciences and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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14
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Sokolova O, Moročko-Bičevska I, Lācis G. Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers. Pathogens 2022; 11:pathogens11101165. [PMID: 36297222 PMCID: PMC9611756 DOI: 10.3390/pathogens11101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
Apple scab caused by the ascomycete Venturia inaequalis is an economically significant disease worldwide. The annual sexual reproduction of V. inaequalis leads to high variation, changes in the population's genetic structure and adaptations to the changing environment, including overcoming the host's resistance. The objective of this study is to characterise and assess the genetic diversity of V. inaequalis populations in two main apple-growing regions in Latvia. In total, 143 V. inaequalis isolates were collected from Latvia, six reference strains with known virulence were obtained from other countries, and all strains were genotyped by 12 SSR markers. The SSR markers were highly variable and informative, identifying 158 alleles that ranged from two to 29 per locus. The Bayesian clustering identified three genetic lineages among the Latvian isolates that did not correlate to the geographic origin, host genotype, organ (leaves or fruits) from which the pathogen was isolated, time of collection, and type of isolation (single conidium or ascospore). The possible relatedness to virulence was detected when reference strains with known virulence were included in the analysis. Our findings correspond with previous studies demonstrating that V. inaequalis in Europe has a high genetic diversity within populations, but low diversity among the populations.
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Affiliation(s)
- Olga Sokolova
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
- Institute of Soil and Plant Sciences, Latvia University of Life Sciences and Technologies, Lielā str. 2, LV-3001 Jelgava, Latvia
- Correspondence:
| | - Inga Moročko-Bičevska
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
| | - Gunārs Lācis
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
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Comparative transcriptomics unravels new genes imparting scab resistance in apple (Malus x domestica Borkh.). Funct Integr Genomics 2022; 22:1315-1330. [PMID: 35931837 DOI: 10.1007/s10142-022-00889-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022]
Abstract
Apple scab is caused by an ascomycete fungus, Venturia inaequalis (Cke.) Wint., which is one of the most severe disease of apple (Malus × Domestica Borkh.) worldwide. The disease results in 30-40% fruit loss annually and even complete loss in some places. Owing to the evolving susceptibility of resistant apple genotypes harboring R-genes to new variants of V. inaequalis, a comparative transcriptome analysis using Illumina (HiSeq) platform of three scab-resistant (Florina, Prima, and White Dotted Red) and three susceptible (Ambri, Vista Bella, and Red Delicious) apple genotypes was carried out to mine new scab resistance genes. The study led to the identification of 822 differentially expressed genes in the tested scab-resistant and scab-susceptible apple genotypes. The most upregulated genes uniformly expressed in resistant varieties compared to susceptible ones were those coding for 17.3 kDa class II heat shock protein-like, chaperone protein ClpB1, glutathione S-transferase L3-like protein, B3 domain-containing protein At3g18960-like, transcription factor bHLH7, zinc finger MYM-type protein 1-like, and nine uncharacterized proteins, besides three lncRNAs. The genes that were downregulated in susceptible and upregulated in resistant cultivars were those coding for non-specific lipid transfer protein GPI-anchored 1, rust resistance kinase Lr10-like, disease resistance protein RPS6-like, and many uncharacterized proteins. DESeq2 analysis too revealed 20 DEGs that were upregulated in scab-resistant cultivars. Furthermore, a total of 361 genes were significantly upregulated in scab-susceptible variety, while 461 were found downregulated (P value < 0.05 and Log2 (FC) > 1). The differentially expressed genes (DEGs) were related to various pathways, i.e., metabolic, protein processing, biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, ubiquitin-mediated proteolysis, plant-pathogen interaction, lipid metabolism, and protein modification pathways. Real-time expression of a set of selected twelve DEGs further validated the results obtained from RNA-seq. Overall, these findings lay the foundation for investigating the genetic basis of apple scab resistance and defense pathways that might have a plausible role in governing scab resistance in apple against V. inaequalis.
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Caffier V, Shiller J, Bellanger MN, Collemare J, Expert P, Gladieux P, Pascouau C, Sannier M, Le Cam B. Hybridizations Between formae speciales of Venturia inaequalis Pave the Way for a New Biocontrol Strategy to Manage Fungal Plant Pathogens. PHYTOPATHOLOGY 2022; 112:1401-1405. [PMID: 35080437 DOI: 10.1094/phyto-05-21-0222-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hybridization and adaptation to new hosts are important mechanisms of fungal disease emergence. Evaluating the risk of emergence of hybrids with enhanced virulence is then key to develop sustainable crop disease management. We evaluated this risk in Venturia inaequalis, the fungus responsible for the common and serious scab disease on Rosaceae hosts, including apple, pyracantha, and loquat. Field isolates from these three hosts and progenies obtained from five crosses between formae speciales isolates collected from pyracantha (f. sp. pyracantha) and apple (f. sp. pomi) were tested for their pathogenicity on the three hosts. We confirmed a strict host specificity between isolates from apple and pyracantha and showed that most isolates were able to cause disease on loquat. None of the 251 progeny obtained from five crosses between V. inaequalis f. sp. pyracantha and V. inaequalis f. sp. pomi could infect apple. If confirmed on more crosses, the inability of the hybrids to infect apple could lead to a novel biocontrol strategy based on a sexual hijacking of V. inaequalis f. sp. pomi by a massive introduction of V. inaequalis f. sp. pyracantha in apple orchards. This strategy, analogous to the sterile insect approach, could lead to the collapse of the population size of V. inaequalis and dramatically reduce the use of chemicals in orchards.
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Affiliation(s)
- Valérie Caffier
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Jason Shiller
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | | | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Pascale Expert
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Université Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Claire Pascouau
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Mélanie Sannier
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
| | - Bruno Le Cam
- Univ Angers, Institut Agro, INRAE IRHS, SFR QUASAV, F-49000 Angers, France
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Wang Z, Jiang X, Zhang Y, Du Z, Feng J, Quan W, Ren J, Che M, Zhang Z. Identification and Validation of a Major Quantitative Trait Locus for Adult Plant Resistance Against Leaf Rust From the Chinese Wheat Landrace Bai Qimai. FRONTIERS IN PLANT SCIENCE 2022; 13:812002. [PMID: 35665144 PMCID: PMC9158542 DOI: 10.3389/fpls.2022.812002] [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: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust caused by Puccinia triticina Eriks. (Pt) is a common disease of wheat worldwide. The Chinese wheat landrace Bai Qimai (BQM) has shown high resistance to leaf rust for a prolonged period of time; the infected leaves of BQM displayed high infection types (ITs), but they showed low disease severities at the adult plant stage. To find quantitative trait loci (QTL) for resistance to leaf rust, 186 recombinant inbred lines from the cross Nugaines × BQM were phenotyped for leaf rust response in multiple field environments under natural Pt infections and genotyped using the 90K wheat single nucleotide polymorphism (SNP) chip and simple sequence repeat (SSR) markers. A total of 2,397 polymorphic markers were used for QTL mapping, and a novel major QTL (QLr.cau-6DL) was detected on chromosome 6DL from BQM. The effectiveness of QLr.cau-6DL was validated using the three additional wheat populations (RL6058 × BQM, Aikang58 × BQM, and Jimai22 × BQM). QLr.cau-6DL could significantly reduce leaf rust severities across all tested environments and different genetic backgrounds, and its resistance was more effective than that of Lr34. Moreover, QLr.cau-6DL acted synergistically with Lr34 to confer strong resistance to leaf rust. We believe that QLr.cau-6DL should have high potential value in the breeding of wheat cultivars with leaf rust resistance.
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Affiliation(s)
- Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Yuzhu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Ziyi Du
- School of Agroforestry & Medicine, Open University of China, Beijing, China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
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Wang T, Balla B, Kovács S, Kereszt A. Varietas Delectat: Exploring Natural Variations in Nitrogen-Fixing Symbiosis Research. FRONTIERS IN PLANT SCIENCE 2022; 13:856187. [PMID: 35481136 PMCID: PMC9037385 DOI: 10.3389/fpls.2022.856187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The nitrogen-fixing symbiosis between leguminous plants and soil bacteria collectively called rhizobia plays an important role in the global nitrogen cycle and is an essential component of sustainable agriculture. Genetic determinants directing the development and functioning of the interaction have been identified with the help of a very limited number of model plants and bacterial strains. Most of the information obtained from the study of model systems could be validated on crop plants and their partners. The investigation of soybean cultivars and different rhizobia, however, has revealed the existence of ineffective interactions between otherwise effective partners that resemble gene-for-gene interactions described for pathogenic systems. Since then, incompatible interactions between natural isolates of model plants, called ecotypes, and different bacterial partner strains have been reported. Moreover, diverse phenotypes of both bacterial mutants on different host plants and plant mutants with different bacterial strains have been described. Identification of the genetic factors behind the phenotypic differences did already and will reveal novel functions of known genes/proteins, the role of certain proteins in some interactions, and the fine regulation of the steps during nodule development.
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Affiliation(s)
- Ting Wang
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Benedikta Balla
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Szilárd Kovács
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
| | - Attila Kereszt
- Eötvös Loránd Research Network, Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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Oh S, Han H, Kim D. A Novel Pear Scab (Venturia nashicola) Resistance Gene, Rvn3, from Interspecific Hybrid Pear (Pyrus pyrifolia × P. communis). PLANTS 2021; 10:plants10122632. [PMID: 34961103 PMCID: PMC8705610 DOI: 10.3390/plants10122632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022]
Abstract
Asian pear scab is a fungal disease caused by Venturia nashicola. The identification of genes conferring scab resistance could facilitate the breeding of disease-resistant cultivars. Therefore, the present study aimed to identify a scab-resistance gene using an interspecific hybrid population ((Pyrus pyrifolia × P. communis) × P. pyrifolia). Artificial inoculation of V. nashicola was carried out for two years. The segregation ratio (1:1) of resistant to susceptible individuals indicated that resistance to V. nashicola was inherited from P. communis and controlled by a single dominant gene. Based on two years phenotypic data with the Kruskal–Wallis test and interval mapping, 12 common markers were significantly associated with scab resistance. A novel scab resistance gene, Rvn3, was mapped in linkage group 6 of the interspecific hybrid pear, and co-linearity between Rvn3 and one of the apple scab resistance genes, Rvi14, was confirmed. Notably, an insertion in pseudo-chromosome 6 of the interspecific hybrid cultivar showed homology with apple scab resistance genes. Hence, the newly discovered Rvn3 was considered an ortholog of the apple scab resistance gene. Since the mapping population used in the present study is a pseudo-BC1 population, pyramiding of multiple resistance genes to pseudo-BC1 could facilitate the breeding of pear cultivars with durable resistance.
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Affiliation(s)
| | | | - Daeil Kim
- Correspondence: ; Tel.: +82-43-261-2527
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Perchepied L, Chevreau E, Ravon E, Gaillard S, Pelletier S, Bahut M, Berthelot P, Cournol R, Schouten HJ, Vergne E. Successful intergeneric transfer of a major apple scab resistance gene (Rvi6) from apple to pear and precise comparison of the downstream molecular mechanisms of this resistance in both species. BMC Genomics 2021; 22:843. [PMID: 34802418 PMCID: PMC8607633 DOI: 10.1186/s12864-021-08157-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Scab is the most important fungal disease of apple and pear. Apple (Malus x domestica Borkh.) and European pear (Pyrus communis L.) are genetically related but they are hosts of two different fungal species: Venturia inaequalis for apple and V. pyrina for European pear. The apple/V. inaequalis pathosystem is quite well known, whereas knowledge about the pear/V. pyrina pathosystem is still limited. The aim of our study was to analyse the mode of action of a major resistance gene of apple (Rvi6) in transgenic apple and pear plants interacting with the two scab species (V. inaequalis and V. pyrina), in order to determine the degree of functional transferability between the two pathosystems. Results Transgenic pear clones constitutively expressing the Rvi6 gene from apple were compared to a scab transgenic apple clone carrying the same construct. After inoculation in greenhouse with V. pyrina, strong defense reactions and very limited sporulation were observed on all transgenic pear clones tested. Microscopic observations revealed frequent aborted conidiophores in the Rvi6 transgenic pear / V. pyrina interaction. The macro- and microscopic observations were very comparable to the Rvi6 apple / V. inaequalis interaction. However, this resistance in pear proved variable according to the strain of V. pyrina, and one of the strains tested overcame the resistance of most of the transgenic pear clones. Comparative transcriptomic analyses of apple and pear resistant interactions with V. inaequalis and V. pyrina, respectively, revealed different cascades of molecular mechanisms downstream of the pathogen recognition by Rvi6 in the two species. Signal transduction was triggered in both species with calcium (and G-proteins in pear) and interconnected hormonal signaling (jasmonic acid in pear, auxins in apple and brassinosteroids in both species), without involvement of salicylic acid. This led to the induction of defense responses such as a remodeling of primary and secondary cell wall, lipids biosynthesis (galactolipids in apple and cutin and cuticular waxes in pear), systemic acquired resistance signal generation (in apple) or perception in distal tissues (in pear), and the biosynthesis of phenylpropanoids (flavonoids in apple but also lignin in pear). Conclusion This study is the first example of a successful intergeneric transfer of a resistance gene among Rosaceae, with a resistance gene functioning towards another species of pathogen. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08157-1.
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Affiliation(s)
- L Perchepied
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - E Chevreau
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - E Ravon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - S Gaillard
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - S Pelletier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - M Bahut
- Univ Angers, SFR QUASAV, F-49000, Angers, France
| | - P Berthelot
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - R Cournol
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
| | - H J Schouten
- Wageningen Univ & Res, Plant Breeding, NL-6700, Wageningen, AJ, Netherlands
| | - E Vergne
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France.
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Ishii H, Nishimura K, Tanabe K, Yamaoka Y. Pathogenic Specialization of Venturia nashicola, Causal Agent of Asian Pear Scab, and Resistance of Pear Cultivars Kinchaku and Xiangli. PHYTOPATHOLOGY 2021; 111:990-1000. [PMID: 32910743 DOI: 10.1094/phyto-06-20-0220-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Scab caused by Venturia nashicola is one of the most serious diseases of Asian pears, including Japanese pear (Pyrus pyrifolia var. culta) and Chinese pears (P. bretschneideri and P. ussuriensis). Breeding scab-resistant pear cultivars is essential to minimize fungicide use and development of fungicide resistance. A survey of pathogenic specialization in V. nashicola is needed to ensure durable scab resistance in cultivated pears. V. nashicola race 1, 2, and 3 isolates, each differing in pathogenicity to Japanese pear cultivar Kousui and Asian pear strain Mamenashi 12, have been reported in Japan. In this study, isolates collected from scabbed pears in China and Taiwan were classified as V. nashicola based on conidial size and mating ability. However, various isolates had pathogenicity distinct from races 1, 2, and 3 according to tests on seven differential host genotypes of pear cultivars from Japan (Kousui and strain Mamenashi 12), China (Jingbaili, Yali, Linyuli, and Nanguoli), and Taiwan (Hengshanli). These new races were designated as races 4 to 7. Progenies characteristic of race 3 isolates were produced using a cross between race 1 and race 2 isolates, suggesting the possible role of sexual recombination in the emergence of novel races. Japanese pear cultivar Kinchaku and Chinese P. sinkiangensis 'Xiangli' (a Korla fragrant pear grown in China) did not show visible symptoms after inoculation with any of the seven races. Broad scab resistance in Kinchaku and Xiangli makes them a promising genetic resource for resistance breeding programs.
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Affiliation(s)
- Hideo Ishii
- National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki 305-8604, Japan
- University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kumiko Nishimura
- National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki 305-8604, Japan
| | - Kenji Tanabe
- Tottori University, Tottori, Tottori 680-8550, Japan
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Multilocus Sequence Analysis of Selected Housekeeping- and Pathogenicity-Related Genes in Venturia inaequalis. Pathogens 2021; 10:pathogens10040447. [PMID: 33918069 PMCID: PMC8068995 DOI: 10.3390/pathogens10040447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
The relationship between housekeeping and pathogenicity-related genes and virulence or avirulence towards the primary Malus resistance genes (R) has not been previously studied for Venturia inaequalis fungus, the causal agent of apple scab. In this study, the sequences of two housekeeping genes encoding elongation factor alpha (EF-1α) and β-tubulin and two previously unstudied effector genes of V. inaequalis from mannosidase and glucosidase families of 100 strains collected from apple cultivars with Rvi6, Rvi1, and Rvi17 and without known scab resistance genes were submitted to the analyses. Based on the phylogenetic and diversity data, as well as recombination analyses of the sequenced regions, we assessed the phylogenetic relationships and genetic structure of the pathogen within the species and the evolutionary forces that are currently acting upon this microorganism. The topology of the obtained phylograms demonstrates the lack of a relationship between the phylogenetic position of the strain and the host cultivar and the geographical origin or race of the strain. The isolates from different hosts were differentiated but did not form diagnosable, distinct phylogenetic groups. These results suggest that the analyzed genes may be too conserved to reflect the adaptation of pathogens to apple genotypes with different R genes; thus, they do not adequately reflect race discrimination. In contrast, based on variation and gene flow estimation, genetic divergence was observed among strains virulent to apple trees containing Rvi6. The results of this study confirmed a lack of free recombination between strains and demonstrated that the analyzed regions are in linkage disequilibrium and contain non-random polymorphisms associated with the strain.
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Henry PM, Pincot DD, Jenner BN, Borrero C, Aviles M, Nam M, Epstein L, Knapp SJ, Gordon TR. Horizontal chromosome transfer and independent evolution drive diversification in Fusarium oxysporum f. sp. fragariae. THE NEW PHYTOLOGIST 2021; 230:327-340. [PMID: 33616938 PMCID: PMC7986148 DOI: 10.1111/nph.17141] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/02/2020] [Indexed: 05/13/2023]
Abstract
The genes required for host-specific pathogenicity in Fusarium oxysporum can be acquired through horizontal chromosome transfer (HCT). However, it is unknown if HCT commonly contributes to the diversification of pathotypes. Using comparative genomics and pathogenicity phenotyping, we explored the role of HCT in the evolution of F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry, with isolates from four continents. We observed two distinct syndromes: one included chlorosis ('yellows-fragariae') and the other did not ('wilt-fragariae'). All yellows-fragariae isolates carried a predicted pathogenicity chromosome, 'chrY-frag ', that was horizontally transferred at least four times. chrY-frag was associated with virulence on specific cultivars and encoded predicted effectors that were highly upregulated during infection. chrY-frag was not present in wilt-fragariae; isolates causing this syndrome evolved pathogenicity independently. All origins of F. oxysporum f. sp. fragariae occurred outside of the host's native range. Our data support the conclusion that HCT is widespread in F. oxysporum, but pathogenicity can also evolve independently. The absence of chrY-frag in wilt-fragariae suggests that multiple, distinct pathogenicity chromosomes can confer the same host specificity. The wild progenitors of cultivated strawberry (Fragaria × ananassa) did not co-evolve with this pathogen, yet we discovered several sources of genetic resistance.
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Affiliation(s)
- Peter M. Henry
- United States Department of AgricultureAgricultural Research Service1636 E. Alisal St.SalinasCA93905USA
| | - Dominique D.A. Pincot
- Department of Plant SciencesUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Bradley N. Jenner
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Celia Borrero
- Department of Ciencias AgroforestalesEscuela Técnica Superior de Ingeniería AgronómicaUniversidad de SevillaCtra. Utrera km 1Sevilla41013Spain
| | - Manuel Aviles
- Department of Ciencias AgroforestalesEscuela Técnica Superior de Ingeniería AgronómicaUniversidad de SevillaCtra. Utrera km 1Sevilla41013Spain
| | - Myeong‐Hyeon Nam
- Strawberry Research InstituteChungcheongnam‐do Agricultural Research & Extension ServicesNonsan32914Korea
| | - Lynn Epstein
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Steven J. Knapp
- Department of Plant SciencesUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Thomas R. Gordon
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
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Apple Autotetraploids with Enhanced Resistance to Apple Scab ( Venturia inaequalis) Due to Genome Duplication-Phenotypic and Genetic Evaluation. Int J Mol Sci 2021; 22:ijms22020527. [PMID: 33430246 PMCID: PMC7825683 DOI: 10.3390/ijms22020527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Among the fungal diseases of apple trees, serious yield losses are due to an apple scab caused by Venturia inaequalis. Protection against this disease is based mainly on chemical treatments, which are currently very limited. Therefore, it is extremely important to introduce cultivars with reduced susceptibility to this pathogen. One of the important sources of variability for breeding is the process of polyploidization. Newly obtained polyploids may acquire new features, including increased resistance to diseases. In our earlier studies, numerous tetraploids have been obtained for several apple cultivars with 'Free Redstar' tetraploids manifesting enhanced resistance to apple scab. In the present study, tetraploids of 'Free Redstar' were assessed in terms of phenotype and genotype with particular emphasis on the genetic background of their increased resistance to apple scab. Compared to diploid plants, tetraploids (own-rooted plants) were characterized with poor growth, especially during first growing season. They had considerably shorter shoots, fewer branches, smaller stem diameter, and reshaped leaves. In contrast to own-rooted plants, in M9-grafted three-year old trees, no significant differences between diplo- and tetraploids were observed, either in morphological or physiological parameters, with the exceptions of the increased leaf thickness and chlorophyll content recorded in tetraploids. Significant differences between sibling tetraploid clones were recorded, particularly in leaf shape and some physiological parameters. The amplified fragment length polymorphism (AFLP) analysis confirmed genetic polymorphism of tetraploid clones. Methylation-sensitive amplification polymorphism (MSAP) analysis showed that the level of DNA methylation was twice as high in young tetraploid plants as in a diploid donor tree, which may explain the weaker vigour of neotetraploids in the early period of their growth in the juvenile phase. Molecular analysis showed that 'Free Redstar' cultivar and their tetraploids bear six Rvi genes (Rvi5, Rvi6, Rvi8, Rvi11, Rvi14 and Rvi17). Transcriptome analysis confirmed enhanced resistance to apple scab of 'Free Redstar' tetraploids since the expression levels of genes related to resistance were strongly enhanced in tetraploids compared to their diploid counterparts.
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Ulyanovskaya E, Stcheglov S, Belenko E, Balapanov I. Mobilization of genetic diversity of the genus Malus on the basis of information technologies for the breeding of varieties with complex resistance to fungal pathogens. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213402003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Breeding renewal of the southern assortment of apple trees for the Russian fruit growing industry based on the accelerated process of creating domestic genotypes with a complex increased resistance to the main fungal pathogens of the culture (Venturia inaequalis (Cooke) Wint., Podosphaera leucotricha (Ell. & Ev.) E.S. Salmon, Phyllosticta mali Pr. et. Del., Phyllosticta briardi Sacc.) is due to the systematic use of modern methods, innovative breeding techniques and improved techniques. The purpose of the study is to develop and create a database of representatives of the genus Malus Mill., which is promising for use in the production and accelerated breeding of new domestic genetic resources for the southern region of Russia. During the research work, Russian modern and generally accepted programs and methods of breeding, variety study for fruit plants were used. The formed database “Main economically valuable, morphological and molecular-genetic characters of representatives of the genus Malus Mill. with resistance to the main fungal pathogens in the south of Russia”; filed an application for its patent. Using the data of the obtained information system will significantly speed up the solution of practical selection problems and reduce the costs of organizing the breeding process.
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Balykina E, Ivanova O, Yagodinskaya L, Kovalenko L, Romanov G. Susceptibility of collection pear cultivars to the agent of scab pathogen Venturia pirina Aderh. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213404014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The objective of the research is to study the biology of the pathogen of the scab Venturia pirina Aderh depending on the agrometeorological conditions of the pear vegetation and to assess the collection cultivars for susceptibility to the disease. The biological features of the pear scab in the western foothill agro-climatic region of the Crimea are studied. The influence of climatic conditions on the occurrence of various epidemiological types of scab manifestations on pears is estimated. As a result of the research, highly resistant cultivars were found: Zhukovka, Zaporozhskaya, Triumph of Jodoin, Vodyanistaya, Dorodnaya, Bere Shibasso, Martin Sekl, which showed moderate levels of infection spread in all years of research, with the development of the disease in the range of 0.2-1.3%. Immune cultivars of pears with absolute resistance to the pathogen agent V. pirina, which was not affected by changes in weather conditions, were identified. These cultivars are the following: Zimovka, Trapezitsa, Chervona, Shara Bera, Seyanets Kolossa, Populyarnaya, Kurzemskaya Maslyanaya, Wonderful Italy, which can be used in breeding and ecologized protection systems when supplying with cuttings horticultural industries in the Crimea and the south of Russia.
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Prencipe S, Sillo F, Garibaldi A, Gullino ML, Spadaro D. Development of a Sensitive TaqMan qPCR Assay for Detection and Quantification of Venturia inaequalis in Apple Leaves and Fruit and in Air Samples. PLANT DISEASE 2020; 104:2851-2859. [PMID: 32902358 DOI: 10.1094/pdis-10-19-2160-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A TaqMan quantitative PCR (qPCR) assay based on the translation elongation factor 1-α gene was developed for the quantification of Venturia inaequalis in leaves and fruits of Malus × domestica and in spore trap samples. The designed primers and hydrolysis probe amplified a specific 86-bp fragment for V. inaequalis. The specificity of the assay was tested using 35 strains of V. inaequalis and 20 different fungal species, including common pathogens of apple and other species of Venturia. The limit of detection was 20 fg, which is lower than a single genome of V. inaequalis. The selectivity of the assay was tested using DNA from three cultivars of Malus × domestica, and no influence on pathogen amplification was found. The assay was also validated for repeatability and reproducibility. With this assay, it was possible to detect and quantify V. inaequalis in four cultivars (Ambrosia, Florina, Golden Delicious, and Mondial Gala) in both symptomatic and asymptomatic leaves and in symptomatic Golden Delicious apple fruit stored for 2 months. Furthermore, the assay was successfully tested on spore trap samples originating from apple orchards. The quantification of the molecular assay when compared with the estimated number of V. inaequalis cells, using an optical microscope, showed a correlation coefficient of 0.8186. The developed technique could be used to detect V. inaequalis in asymptomatic samples without any cross-reaction with other fungal species. Furthermore, to improve the efficacy of disease management with a timely application of fungicides, this assay could be used for the analysis of spore trap samples by using an implemented extraction method.
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Affiliation(s)
- Simona Prencipe
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, via Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Fabiano Sillo
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, via Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Angelo Garibaldi
- Centre of Competence for the Innovation in the Agro-environmental Sector-AGROINNOVA, University of Turin, via Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Maria Lodovica Gullino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, via Paolo Braccini 2, 10095, Grugliasco, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector-AGROINNOVA, University of Turin, via Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, via Paolo Braccini 2, 10095, Grugliasco, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector-AGROINNOVA, University of Turin, via Paolo Braccini 2, 10095, Grugliasco, Italy
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Sweet Immunity: The Effect of Exogenous Fructans on the Susceptibility of Apple ( Malus × domestica Borkh.) to Venturia inaequalis. Int J Mol Sci 2020; 21:ijms21165885. [PMID: 32824325 PMCID: PMC7461573 DOI: 10.3390/ijms21165885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
There is an urgent need for novel, efficient and environmentally friendly strategies to control apple scab (Venturia inaequalis), for the purpose of reducing overall pesticide use. Fructans are recently emerging as promising “priming” compounds, standing out for their safety and low production costs. The objective of this work was to test a fructan-triggered defense in the leaves of apple seedlings. It was demonstrated that exogenous leaf spraying can reduce the development of apple scab disease symptoms. When evaluated macroscopically and by V. inaequalis-specific qPCR, levan-treated leaves showed a significant reduction of sporulation and V. inaequalis DNA in comparison to mock- and inulin-treated leaves, comparable to the levels in fosetyl-aluminum-treated leaves. Furthermore, we observed a significant reduction of in vitro mycelial growth of V. inaequalis on plates supplemented with levans when compared to controls, indicating a direct inhibition of fungal growth. Variations in endogenous sugar contents in the leaves were followed during priming and subsequent infection, revealing complex dynamics as a function of time and leaf ontogeny. Our data are discussed in view of the present theories on sugar signaling and fructan-based immunity, identifying areas for future research and highlighting the potential use of fructans in apple scab management in orchards.
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29
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Patocchi A, Wehrli A, Dubuis PH, Auwerkerken A, Leida C, Cipriani G, Passey T, Staples M, Didelot F, Philion V, Peil A, Laszakovits H, Rühmer T, Boeck K, Baniulis D, Strasser K, Vávra R, Guerra W, Masny S, Ruess F, Le Berre F, Nybom H, Tartarini S, Spornberger A, Pikunova A, Bus VGM. Ten Years of VINQUEST: First Insight for Breeding New Apple Cultivars With Durable Apple Scab Resistance. PLANT DISEASE 2020; 104:2074-2081. [PMID: 32525450 DOI: 10.1094/pdis-11-19-2473-sr] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Apple scab, caused by Venturia inaequalis, is a major fungal disease worldwide. Cultivation of scab-resistant cultivars would reduce the chemical footprint of apple production. However, new apple cultivars carrying durable resistances should be developed to prevent or at least slow the breakdown of resistance against races of V. inaequalis. One way to achieve durable resistance is to pyramid multiple scab resistance genes in a cultivar. The choice of the resistance genes to be combined in the pyramids should take into account the frequency of resistance breakdown and the geographical distribution of apple scab isolates able to cause such breakdowns. In order to acquire this information and to make it available to apple breeders, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after launching this project, 24 partners from 14 countries regularly contribute data. From 2009 to 2018, nearly 9,000 data points have been collected. This information has been used to identify the most promising apple scab resistance genes for developing cultivars with durable resistance, which to date are: Rvi5, Rvi11, Rvi12, Rvi14, and Rvi15. As expected, Rvi1, together with Rvi3 and Rvi8, were often overcome, and have little value for scab resistance breeding. Rvi10 may also belong to this group. On the other hand, Rvi2, Rvi4, Rvi6, Rvi7, Rvi9, and Rvi13 are still useful for breeding, but their use is recommended only in extended pyramids of ≥3 resistance genes.
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Affiliation(s)
| | - Andreas Wehrli
- Agroscope, Breeding Research, 8820 Wädenswil, Switzerland
| | | | | | - Carmen Leida
- Consorzio Italiano Vivaisti CIV, 44022 San Giuseppe di Comacchio, Italy
| | - Guido Cipriani
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, 33100 Udine, Italy
| | - Tom Passey
- NIAB EMR, East Malling, West Malling ME19 6BJ, United Kingdom
| | - Martina Staples
- Höhere Bundeslehranstalt und Bundesamt für Wein- und Obstbau Klosterneuburg, 3400 Klosterneuburg, Austria
| | - Frédérique Didelot
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, 49071 Beaucouzé, France
| | - Vincent Philion
- Institut de Recherche et de Développement en Agroenvironnement, Saint-Bruno-de-Montarville, QC J3V 0G7, Canada
| | - Andreas Peil
- Julius Kühn-Institut (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Züchtungsforschung an Obst, 01326 Dresden, Germany
| | | | - Thomas Rühmer
- Versuchsstation Obst- und Weinbau Haidegg, 8047 Graz, Austria
| | - Klemens Boeck
- Landwirtschaftskammer Tirol, 6020 Innsbruck, Austria
| | - Danas Baniulis
- Lithuanian Research Centre for Agriculture and Forestry, 54333 Babtai, Lithuania
| | | | - Radek Vávra
- Research and Breeding Institute of Pomology, Holovousy 129, 508 01 Horice, Czech Republic
| | - Walter Guerra
- Laimburg Research Centre, Laimburg 6, 39040 Ora, Italy
| | | | - Franz Ruess
- Staatliche Lehr- und Versuchsanstalt für Wein und Obstbau Weinsberg, 74189 Weinsberg, Germany
| | - Fanny Le Berre
- Station d'études et d'expérimentations fruitières de La Morinière, La Morinière, 37800 Saint Epain, France
| | - Hilde Nybom
- Swedish University of Agricultural Sciences, Balsgård, 29194 Kristianstad, Sweden
| | - Stefano Tartarini
- Department of Agricultural and Food Sciences, University of Bologna, 40126 Bologna, Italy
| | | | - Anna Pikunova
- VNIISPK - Russian Research Institute of Fruit Crop Breeding, 302530 Zilina, Russia
| | - Vincent G M Bus
- The New Zealand Institute for Plant and Food Research Limited, 4157 Havelock North, New Zealand
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Dar MS, Padder BA, Ahmad M, Sofi TA, Mir AA, Nabi A, Shah MD. Population structure of Venturia inaequalis, a hemibiotrophic fungus, under different host resistance specificities in the Kashmir valley. Arch Microbiol 2020; 202:2245-2253. [PMID: 32533207 DOI: 10.1007/s00203-020-01950-8] [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: 02/17/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/25/2022]
Abstract
Venturia inaequalis is a notorious fungal pathogen and show classical gene for gene interaction with its apple host. Neutral markers provide clues about history, evolutionary potential, genetic diversity and population structure of V. inaequalis. The genetic diversity and population structure of fungus indicates that the pathogen is highly diverse with the capacity to breach the scab resistance genes. In the present study, we collected 108 V. inaequalis isolates from three apple cultivars differing in Rvi1 resistance gene. Based on the AMOVA, the variation was mostly distributed among the isolates, providing evidence of non-existence of subpopulation in orchards thus founder population is difficult to arise in Kashmir apple orchards. Pair wise genetic differentiation is less due to regular occurrence of gene flow between the populations residing on different orchard as infected material is transported without stringent quarantine measures. Based on principal coordinate analysis and clustering algorithm as implemented in STRUCTURE, we observed admixture between the two subpopulations, which is quite low, suggesting the existence of pre-zygotic and post-zygotic barriers to gene flow and we cannot rule out the existence of other structures shared by accessions belonging to different varieties. Due to the continuous increase in introduction and monoculture of apple varieties, mixed orchard with different host resistance specificities are more suitable for managing the apple scab in Kashmir valley.
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Affiliation(s)
- M S Dar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - T A Sofi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - A A Mir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Asha Nabi
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-K, Sopore, Wadura, 193201, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
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31
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Wu JQ, Dong C, Song L, Park RF. Long-Read-Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes. Front Genet 2020; 11:521. [PMID: 32582280 PMCID: PMC7287177 DOI: 10.3389/fgene.2020.00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 11/18/2022] Open
Abstract
Leaf rust, caused by Puccinia triticina (Pt), is one of the most devastating diseases of wheat, affecting production in nearly all wheat-growing regions worldwide. Despite its economic importance, genomic resources for Pt are very limited. In the present study, we have used long-read sequencing (LRS) and the pipeline of FALCON and FALCON-Unzip (v4.1.0) to carry out the first LRS-based de novo genome assembly for Pt. Using 22.4-Gb data with an average read length of 11.6 kb and average coverage of 150-fold, we generated a genome assembly for Pt104 [strain 104-2,3,(6),(7),11; isolate S423], considered to be the founding isolate of a clonal lineage of Pt in Australia. The Pt104 genome contains 162 contigs with a total length of 140.5 Mb and N50 of 2 Mb, with the associated haplotigs providing haplotype information for 91% of the genome. This represents the best quality of Pt genome assembly to date, which reduces the contig number by 91-fold and improves the N50 by 4-fold as compared to the previous Pt race1 assembly. An annotation pipeline that combined multiple lines of evidence including the transcriptome assemblies derived from RNA-Seq, previously identified expressed sequence tags and Pt race 1 protein sequences predicted 29,043 genes for Pt104 genome. Based on the presence of a signal peptide, no transmembrane segment, and no target location to mitochondria, 2,178 genes were identified as secreted proteins (SPs). Whole-genome sequencing (Illumina paired-end) was performed for Pt104 and six additional strains with differential virulence profile on the wheat leaf rust resistance genes Lr26, Lr2a, and Lr3ka. To identify candidates for the corresponding avirulence genes AvrLr26, AvrLr2a, and AvrLr3ka, genetic variation within each strain was first identified by mapping to the Pt104 genome. Variants within predicted SP genes between the strains were then correlated to the virulence profiles, identifying 38, 31, and 37 candidates for AvrLr26, AvrLr2a, and AvrLr3ka, respectively. The identification of these candidate genes lays a good foundation for future studies on isolating these avirulence genes, investigating the molecular mechanisms underlying host-pathogen interactions, and the development of new diagnostic tools for pathogen monitoring.
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Affiliation(s)
| | | | | | - Robert F. Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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Gruner P, Schmitt AK, Flath K, Schmiedchen B, Eifler J, Gordillo A, Schmidt M, Korzun V, Fromme FJ, Siekmann D, Tratwal A, Danielewicz J, Korbas M, Marciniak K, Krysztofik R, Niewińska M, Koch S, Piepho HP, Miedaner T. Mapping Stem Rust ( Puccinia graminis f. sp. secalis) Resistance in Self-Fertile Winter Rye Populations. FRONTIERS IN PLANT SCIENCE 2020; 11:667. [PMID: 32528509 PMCID: PMC7265987 DOI: 10.3389/fpls.2020.00667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 06/03/2023]
Abstract
Rye stem rust caused by Puccinia graminis f. sp. secalis can be found in all European rye growing regions. When the summers are warm and dry, the disease can cause severe yield losses over large areas. To date only little research was done in Europe to trigger resistance breeding. To our knowledge, all varieties currently registered in Germany are susceptible. In this study, three biparental populations of inbred lines and one testcross population developed for mapping resistance were investigated. Over 2 years, 68-70 genotypes per population were tested, each in three locations. Combining the phenotypic data with genotyping results of a custom 10k Infinium iSelect single nucleotide polymorphism (SNP) array, we identified both quantitatively inherited adult plant resistance and monogenic all-stage resistance. A single resistance gene, tentatively named Pgs1, located at the distal end of chromosome 7R, could be identified in two independently developed populations. With high probability, it is closely linked to a nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene homolog. A marker for a competitive allele-specific polymerase chain reaction (KASP) genotyping assay was designed that could explain 73 and 97% of the genetic variance in each of both populations, respectively. Additional investigation of naturally occurring rye leaf rust (caused by Puccinia recondita ROEBERGE) revealed a gene complex on chromosome 7R. The gene Pgs1 and further identified quantitative trait loci (QTL) have high potential to be used for breeding stem rust resistant rye.
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Affiliation(s)
- Paul Gruner
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Anne-Kristin Schmitt
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Kleinmachnow, Germany
| | - Kerstin Flath
- Institute for Plant Protection in Field Crops and Grassland, Julius-Kuehn Institute, Kleinmachnow, Germany
| | | | | | | | | | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, Kazan, Russia
| | | | | | - Anna Tratwal
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | - Jakub Danielewicz
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | - Marek Korbas
- Institute of Plant Protection – National Research Institute, Poznań, Poland
| | | | | | | | - Silvia Koch
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
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Zhang J, Zhang P, Dodds P, Lagudah E. How Target-Sequence Enrichment and Sequencing (TEnSeq) Pipelines Have Catalyzed Resistance Gene Cloning in the Wheat-Rust Pathosystem. FRONTIERS IN PLANT SCIENCE 2020; 11:678. [PMID: 32528511 PMCID: PMC7264398 DOI: 10.3389/fpls.2020.00678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 05/02/2023]
Abstract
The wheat-rust pathosystem has been well-studied among host-pathogen interactions since last century due to its economic importance. Intensified efforts toward cloning of wheat rust resistance genes commenced in the late 1990s with the first successful isolation published in 2003. Currently, a total of 24 genes have been cloned from wheat that provides resistance to stem rust, leaf rust, and stripe rust. Among them, more than half (15) were cloned over the last 4 years. This rapid cloning of resistance genes from wheat can be largely credited to the development of approaches for reducing the genome complexity as 10 out of the 15 genes cloned recently were achieved by approaches that are summarized as TEnSeq (Target-sequence Enrichment and Sequencing) pipelines in this review. The growing repertoire of cloned rust resistance genes provides new tools to support deployment strategies aimed at achieving durable resistance. This will be supported by the identification of genetic variation in corresponding Avr genes from rust pathogens, which has recently begun. Although developed with wheat resistance genes as the primary targets, TEnSeq approaches are also applicable to other classes of genes as well as for other crops with complex genomes.
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Affiliation(s)
| | - Peng Zhang
- Plant Breeding Institute Cobbitty, The University of Sydney, Sydney, NSW, Australia
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Evans Lagudah
- CSIRO Agriculture & Food, Canberra, ACT, Australia
- Plant Breeding Institute Cobbitty, The University of Sydney, Sydney, NSW, Australia
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Bueno de Mesquita CP, Sartwell SA, Schmidt SK, Suding KN. Growing-season length and soil microbes influence the performance of a generalist bunchgrass beyond its current range. Ecology 2020; 101:e03095. [PMID: 32380574 DOI: 10.1002/ecy.3095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/14/2019] [Accepted: 04/03/2020] [Indexed: 11/10/2022]
Abstract
As organisms shift their geographic distributions in response to climate change, biotic interactions have emerged as an important factor driving the rate and success of range expansions. Plant-microbe interactions are an understudied but potentially important factor governing plant range shifts. We studied the distribution and function of microbes present in high-elevation unvegetated soils, areas that plants are colonizing as climate warms, snow melts earlier, and the summer growing season lengthens. Using a manipulative snowpack and microbial inoculation transplant experiment, we tested the hypothesis that growing-season length and microbial community composition interact to control plant elevational range shifts. We predicted that a lengthening growing season combined with dispersal to patches of soils with more mutualistic microbes and fewer pathogenic microbes would facilitate plant survival and growth in previously unvegetated areas. We identified negative effects on survival of the common alpine bunchgrass Deschampsia cespitosa in both short and long growing seasons, suggesting an optimal growing-season length for plant survival in this system that balances time for growth with soil moisture levels. Importantly, growing-season length and microbes interacted to affect plant survival and growth, such that microbial community composition increased in importance in suboptimal growing-season lengths. Further, plants grown with microbes from unvegetated soils grew as well or better than plants grown with microbes from vegetated soils. These results suggest that the rate and spatial extent of plant colonization of unvegetated soils in mountainous areas experiencing climate change could depend on both growing-season length and soil microbial community composition, with microbes potentially playing more important roles as growing seasons lengthen.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
| | - Samuel A Sartwell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA
| | - Katharine N Suding
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80309-0450, USA
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Papp D, Singh J, Gadoury D, Khan A. New North American Isolates of Venturia inaequalis Can Overcome Apple Scab Resistance of Malus floribunda 821. PLANT DISEASE 2020; 104:649-655. [PMID: 31961770 DOI: 10.1094/pdis-10-19-2082-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Apple scab, caused by Venturia inaequalis, is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, NY, U.S.A., where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. We observed both chlorosis, typical to Rvi6, and pinpoint pitting symptoms typical to failed infections by V. inaequalis on hosts bearing the Rvi7 gene. We assessed genetic diversity and population genetic structure of 11 V. inaequalis isolates in total, of North American and European origin, isolated from M. floribunda 821, 'Nova Easygro', 'Golden Delicious', TSR33T239, 'Schone van Boskoop', and 'Prima', using 16,321 genome-wide SNPs. Population genetic structure and PCA separated the isolates into distinct European and U.S. groups. The forgoing suggests that the new Rvi6 virulent isolates emerged within U.S. populations, rather than being transported from Europe. The complete resistance breakdown in M. floribunda 821 but not in descendant cultivars, which kept their field resistance, suggests that durable resistance to apple scab will require a more comprehensive understanding of Rvi6 mediated resistance in diverse genetic backgrounds.
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Affiliation(s)
- David Papp
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
| | - Jugpreet Singh
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, U.S.A
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Winter DJ, Charlton ND, Krom N, Shiller J, Bock CH, Cox MP, Young CA. Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:149-152. [PMID: 31631770 DOI: 10.1094/mpmi-08-19-0236-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pecan scab, caused by Venturia effusa, is a devastating disease of pecan (Carya illinoinensis), which results in economic losses on susceptible cultivars throughout the southeastern United States. To enhance our understanding of pathogenicity in V. effusa, we have generated a complete telomere-to-telomere reference genome of V. effusa isolate FRT5LL7-Albino. By combining Illumina MiSeq and Oxford Nanopore MinION data, we assembled a 45.2-Mb genome represented by 20 chromosomes and containing 10,820 putative genes, of which 7,619 have at least one functional annotation. The likely causative mutation of the albino phenotype was identified as a single base insertion and a resulting frameshift in the gene encoding the polyketide synthase ALM1. This genome represents the first full chromosome-level assembly of any Venturia sp.
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Affiliation(s)
- David J Winter
- School of Fundamental Sciences and the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Jason Shiller
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Clive H Bock
- United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008, U.S.A
| | - Murray P Cox
- School of Fundamental Sciences and the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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Prokchorchik M, Won K, Lee Y, Segonzac C, Sohn KH. Whole Genome Enabled Phylogenetic and Secretome Analyses of Two Venturia nashicola Isolates. THE PLANT PATHOLOGY JOURNAL 2020; 36:98-105. [PMID: 32089665 PMCID: PMC7012575 DOI: 10.5423/ppj.nt.10.2019.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 05/19/2023]
Abstract
Venturia nashicola is a fungal pathogen causing scab disease in Asian pears. It is particularly important in the Northeast Asia region where Asian pears are intensively grown. Venturia nashicola causes disease in Asian pear but not in European pear. Due to the highly restricted host range of Venturia nashicola, it is hypothesized that the small secreted proteins deployed by the pathogen are responsible for the host determination. Here we report the whole genome based phylogenetic analysis and predicted secretomes for V. nashicola isolates. We believe that our data will provide a valuable information for further validation and functional characterization of host determinants in V. nashicola.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju 58216,
Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673,
Korea
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Ulyanovskaya E, Belenko E. Using the genetic diversity of the Malus genus to solve the priority areas of breeding. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202502001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The breeding use of the most valuable species and interspecies forms of fruit plants remains currently the most important biological resource for creating the varieties with increased adaptability to the complex of abioand biotic stressors of the environment, improved biochemical composition of fruits and with other important features for breeding. The results of a long-term study (2005-2019) of interspecific hybrid forms of apple-tree-representatives of the Malus genus, growing in the North Caucasus Region of Russia are presented. The aim of the study is to identify the most rapid and productive interspecific hybrid forms of apple-tree with polygenic and oligogenic types of scab resistance (Venturia inaequalis (Cook) G. Winter). Modern breeding programs and methods were used. We have identified the early-fruiting interspecies apple forms created with the participation of the summer Melba variety, the species of M. purpurea. It is allocated the elite and selected apple forms resistant to scab with a high average yield (29.03-40.03 t/ha), high indicators of total yield (377.27-520.33 t/he) from hybrid families with the participation of species: M. atrosanguinea 804/240-57, M. floribunda 821, M. purpurea and the large-fruited form No. 62 (created with the participation of Golden Delicious 4x, Wolf River, M. atrosanguinea 804/240-57) with fruits of 202.3 g an average weight.
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Chatzidimopoulos M, Ganopoulos I, Moraitou-Daponta E, Lioliopoulou F, Ntantali O, Panagiotaki P, Vellios EK. High-Resolution Melting (HRM) Analysis Reveals Genotypic Differentiation of Venturia inaequalis Populations in Greece. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Elucidating genetic variability and population structure in Venturia inaequalis associated with apple scab diseaseusing SSR markers. PLoS One 2019; 14:e0224300. [PMID: 31693681 PMCID: PMC6834240 DOI: 10.1371/journal.pone.0224300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/09/2019] [Indexed: 01/20/2023] Open
Abstract
Apple scab caused by Venturia inaequalis Cooke (Wint.) is one the important diseases of trade and industrial significance in apple. In present study variability studies in pathogen isolates were studied, which is one of the most important factors for devising management studies of scab disease in apple. Genetic diversity of 30 Venturia inaequalis isolates from 12 districts of two geographical distinct regions of Jammu and Kashmir was calculated based on the allele frequencies of 28 SSR markers and the internal transcribed spacer (ITS) region of the ribosomal DNA. The ITS based characterized sequences were submitted to NCBI GenBank and accession numbers were sanctioned. Dendrogram showed that all the accessions formed 2 main clusters with various degree of sub clustering within the clusters. Analysis based on SSR study reveals that the heterozygosity ranged from 0.0 and 0.5, with an average value of 0.39. The expected heterozygosis or gene diversity (He) ranged from 0.0 to 0.50 with an average of 0.40. The Fst value ranges from 0 to 0.6 with an average of 0.194. Diversity within each population (HS) values ranging from 0.26 to 0.33. Average differentiation among populations (GST) was 0.11 and populations were isolated by significant distance (r 2 = 0.50, P < 0.01). From the AMOVA analysis, 25% of variation was observed among population, 9% among individuals and 66% within individuals observed in the population. Structure analysis grouped isolates into two populations. Principle coordinate analysis explained variation of 36.6% in population 1, 14.30% in population 2 and 13.10% in population 3(Admixture) with 64.07% as overall cumulative percentage of variation. This indicates that extensive short-distance gene flow occurs in Kashmir region that dispersal over longer distances also appears to occur frequently enough to prevent differentiation due to genetic drift. Also it is evident that Jammu and Kashmir most likely has V. inaequalis subpopulations linked to diverse climatic conditions of the Jammu region compared to the mountainous inland Kashmir region. The results of present study would help to understand the genetic diversity of V. inaequalis from Jammu and Kashmir that would lead in the development of more effective management strategies and development of new resistant cultivars through marker-assisted selection.
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Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. A Multifaceted Overview of Apple Tree Domestication. TRENDS IN PLANT SCIENCE 2019; 24:770-782. [PMID: 31296442 DOI: 10.1016/j.tplants.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.
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Affiliation(s)
- Amandine Cornille
- Génétique Quantitative et Evolution- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Ferran Antolín
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Elena Garcia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, USA
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Alice Fietta
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Otto Brinkkemper
- Cultural Heritage Agency, PO Box 1600, 3800 BP Amersfoort, The Netherlands
| | - Wiebke Kirleis
- Institute for Prehistoric and Protohistoric Archeology/Graduate School Human Development in Landscapes, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angela Schlumbaum
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
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Singh PK, Mahato AK, Jain P, Rathour R, Sharma V, Sharma TR. Comparative Genomics Reveals the High Copy Number Variation of a Retro Transposon in Different Magnaporthe Isolates. Front Microbiol 2019; 10:966. [PMID: 31134015 PMCID: PMC6512758 DOI: 10.3389/fmicb.2019.00966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/16/2019] [Indexed: 01/02/2023] Open
Abstract
Magnaporthe oryzae is one of the fungal pathogens of rice which results in heavy yield losses worldwide. Understanding the genomic structure of M. oryzae is essential for appropriate deployment of the blast resistance in rice crop improvement programs. In this study we sequenced two M. oryzae isolates, RML-29 (avirulent) and RP-2421 (highly virulent) and performed comparative study along with three publically available genomes of 70-15, P131, and Y34. We identified several candidate effectors (>600) and isolate specific sequences from RML-29 and RP-2421, while a core set of 10013 single copy orthologs were found among the isolates. Pan-genome analysis showed extensive presence and absence variations (PAVs). We identified isolate-specific genes across 12 isolates using the pan-genome information. Repeat analysis was separately performed for each of the 15 isolates. This analysis revealed ∼25 times higher copy number of short interspersed nuclear elements (SINE) in virulent than avirulent isolate. We conclude that the extensive PAVs and occurrence of SINE throughout the genome could be one of the major mechanisms by which pathogenic variability is emerging in M. oryzae isolates. The knowledge gained in this comparative genome study can provide understandings about the fungal genome variations in different hosts and environmental conditions, and it will provide resources to effectively manage this important disease of rice.
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Affiliation(s)
- Pankaj Kumar Singh
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Ajay Kumar Mahato
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Priyanka Jain
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya (CSK HPKV), Palampur, India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Tilak Raj Sharma
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, India
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Sarkate A, Saini SS, Teotia D, Gaid M, Mir JI, Roy P, Agrawal PK, Sircar D. Comparative metabolomics of scab-resistant and susceptible apple cell cultures in response to scab fungus elicitor treatment. Sci Rep 2018; 8:17844. [PMID: 30552373 PMCID: PMC6294756 DOI: 10.1038/s41598-018-36237-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/16/2018] [Indexed: 01/13/2023] Open
Abstract
Apple scab disease caused by the fungus Venturia inaequalis is a devastating disease that seriously affects quality and yield of apples. In order to understand the mechanisms involved in scab resistance, we performed gas chromatography-mass spectrometry based metabolomics analysis of the cell culture of scab resistant cultivar 'Florina' and scab susceptible cultivar 'Vista Bella' both prior -to and -following treatment with V. inaequalis elicitor (VIE). A total 21 metabolites were identified to be altered significantly in 'Florina' cell cultures upon VIE-treatment. Among 21 metabolites, formation of three new specialized metabolites aucuparin, noraucuparin and eriobofuran were observed only in resistant cultivar 'Florina' after the elicitor treatment. The score plots of principal component analysis (PCA) exhibited clear discrimination between untreated and VIE-treated samples. The alteration in metabolite levels correlated well with the changes in the transcript levels of selected secondary metabolite biosynthesis genes. Aucuparin, noraucuparin and eriobofuran isolated from the 'Florina' cultures showed significant inhibitory effect on the conidial germination of V. inaequalis. The results expand our understanding of the metabolic basis of scab-resistance in apple and therefore are of interest in apple breeding programs to fortify scab resistance potential of commercially grown apple cultivars.
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Affiliation(s)
- Amol Sarkate
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shashank Sagar Saini
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Deepa Teotia
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Mariam Gaid
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, D-38106, Braunschweig, Germany
| | - Javid Iqbal Mir
- Plant Biotechnology Department, Central Institute of Temperate Horticulture (ICAR-CITH) Srinagar, 190 005, J&K, India
| | - Partha Roy
- Molecular Endocrinology Laboratory, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | | | - Debabrata Sircar
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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Lasserre-Zuber P, Caffier V, Stievenard R, Lemarquand A, Le Cam B, Durel CE. Pyramiding Quantitative Resistance with a Major Resistance Gene in Apple: From Ephemeral to Enduring Effectiveness in Controlling Scab. PLANT DISEASE 2018; 102:2220-2223. [PMID: 30145950 DOI: 10.1094/pdis-11-17-1759-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genetic resistance is a useful strategy to control plant disease, but its effectiveness may be reduced over time due to the emergence of pathogens able to circumvent the defenses of the plant. However, the pyramiding of different resistance factors in the same plant can improve the effectiveness and durability of the resistance. To investigate the potential for this approach in apple to control scab disease we surveyed scab incidence in two experimental orchards located at a distance of more than 300 km planted with apple genotypes carrying quantitative resistance and major gene resistance alone or in combination. Our results showed that the effectiveness of pyramiding in controlling scab was dependent on the site and could not be completely explained by the effectiveness level of the resistances alone.
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Affiliation(s)
- Pauline Lasserre-Zuber
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France; present address: INRA, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Valérie Caffier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - René Stievenard
- CRRG, Centre Régional de Ressources Génétiques, Ferme du Héron, Chemin de la ferme de Lenglet, 59650, Villeneuve d'Ascq, France
| | - Arnaud Lemarquand
- UE0449 Unité Expérimentale Horticole, INRA, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Bruno Le Cam
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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Choi S, Lee JH, Kang WH, Kim J, Huy HN, Park SW, Son EH, Kwon JK, Kang BC. Identification of Cucumber mosaic resistance 2 ( cmr2) That Confers Resistance to a New Cucumber mosaic virus Isolate P1 (CMV-P1) in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2018; 9:1106. [PMID: 30186289 PMCID: PMC6110927 DOI: 10.3389/fpls.2018.01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/09/2018] [Indexed: 05/09/2023]
Abstract
Cucumber mosaic virus (CMV) is one of the most devastating phytopathogens of Capsicum. The single dominant resistance gene, Cucumber mosaic resistant 1 (Cmr1), that confers resistance to the CMV isolate P0 has been overcome by a new isolate (CMV-P1) after being deployed in pepper (Capsicum annuum) breeding for over 20 years. A recently identified Indian C. annuum cultivar, "Lam32," displays resistance to CMV-P1. In this study, we show that the resistance in "Lam32" is controlled by a single recessive gene, CMV resistance gene 2 (cmr2). We found that cmr2 conferred resistance to CMV strains including CMV-Korean, CMV-Fny, and CMV-P1, indicating that cmr2 provides a broad-spectrum type of resistance. We utilized two molecular mapping approaches to determine the chromosomal location of cmr2. Bulked segregant analysis (BSA) using amplified fragment-length polymorphism (AFLP) (BSA-AFLP) revealed one marker, cmvAFLP, located 16 cM from cmr2. BSA using the Affymetrix pepper array (BSA-Affy) identified a single-nucleotide polymorphism (SNP) marker (Affy4) located 2.3 cM from cmr2 on chromosome 8. We further screened a pepper germplasm collection of 4,197 accessions for additional CMV-P1 resistance sources and found that some accessions contained equivalent levels of resistance to that of "Lam32." Inheritance and allelism tests demonstrated that all the resistance sources examined contained cmr2. Our result thus provide genetic and molecular evidence that cmr2 is a single recessive gene that confers to pepper an unprecedented resistance to the dangerous new isolate CMV-P1 that had overcome Cmr1.
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Affiliation(s)
- Seula Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Won-Hee Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joonyup Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hoang N. Huy
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sung-Woo Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Eun-Ho Son
- RDA-Genebank Information Center, Jeonju, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Yoo Y, Park JC, Cho MH, Yang J, Kim CY, Jung KH, Jeon JS, An G, Lee SW. Lack of a Cytoplasmic RLK, Required for ROS Homeostasis, Induces Strong Resistance to Bacterial Leaf Blight in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:577. [PMID: 29868050 PMCID: PMC5968223 DOI: 10.3389/fpls.2018.00577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/13/2018] [Indexed: 05/02/2023]
Abstract
Many scientific findings have been reported on the beneficial function of reactive oxygen species (ROS) in various cellular processes, showing that they are not just toxic byproducts. The double-edged role of ROS shows the importance of the regulation of ROS level. We report a gene, rrsRLK (required for ROS-scavenging receptor-like kinase), that encodes a cytoplasmic RLK belonging to the non-RD kinase family. The gene was identified by screening rice RLK mutant lines infected with Xanthomonas oryzae pv. oryzae (Xoo), an agent of bacterial leaf blight of rice. The mutant (ΔrrsRLK) lacking the Os01g02290 gene was strongly resistant to many Xoo strains, but not to the fungal pathogen Magnaporthe grisea. ΔrrsRLK showed significantly higher expression of OsPR1a, OsPR1b, OsLOX, RBBTI4, and jasmonic acid-related genes than wild type. We showed that rrsRLK protein interacts with OsVOZ1 (vascular one zinc-finger 1) and OsPEX11 (peroxisomal biogenesis factor 11). In the further experiments, abnormal biogenesis of peroxisomes, hydrogen peroxide (H2O2) accumulation, and reduction of activity of ROS-scavenging enzymes were investigated in ΔrrsRLK. These results suggest that the enhanced resistance in ΔrrsRLK is due to H2O2 accumulation caused by irregular ROS-scavenging mechanism, and rrsRLK is most likely a key regulator required for ROS homeostasis in rice.
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Affiliation(s)
- Youngchul Yoo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Chan Park
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Man-Ho Cho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jungil Yang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
- Institute for Molecular Physiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chi-Yeol Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Sang-Won Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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Barchenger DW, Lamour KH, Bosland PW. Challenges and Strategies for Breeding Resistance in Capsicum annuum to the Multifarious Pathogen, Phytophthora capsici. FRONTIERS IN PLANT SCIENCE 2018; 9:628. [PMID: 29868083 PMCID: PMC5962783 DOI: 10.3389/fpls.2018.00628] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Phytophthora capsici is the most devastating pathogen for chile pepper production worldwide and current management strategies are not effective. The population structure of the pathogen is highly variable and few sources of widely applicable host resistance have been identified. Recent genomic advancements in the host and the pathogen provide important insights into the difficulties reported by epidemiological and physiological studies published over the past century. This review highlights important challenges unique to this complex pathosystem and suggests strategies for resistance breeding to help limit losses associated with P. capsici.
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Affiliation(s)
- Derek W. Barchenger
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Kurt H. Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
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Chen H, Zuo X, Shao H, Fan S, Ma J, Zhang D, Zhao C, Yan X, Liu X, Han M. Genome-wide analysis of carotenoid cleavage oxygenase genes and their responses to various phytohormones and abiotic stresses in apple (Malus domestica). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:81-93. [PMID: 29223850 DOI: 10.1016/j.plaphy.2017.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 05/25/2023]
Abstract
Carotenoid cleavage oxygenases (CCOs) are able to cleave carotenoids to produce apocarotenoids and their derivatives, which are important for plant growth and development. In this study, 21 apple CCO genes were identified and divided into six groups based on their phylogenetic relationships. We further characterized the apple CCO genes in terms of chromosomal distribution, structure and the presence of cis-elements in the promoter. We also predicted the cellular localization of the encoded proteins. An analysis of the synteny within the apple genome revealed that tandem, segmental, and whole-genome duplication events likely contributed to the expansion of the apple carotenoid oxygenase gene family. An additional integrated synteny analysis identified orthologous carotenoid oxygenase genes between apple and Arabidopsis thaliana, which served as references for the functional analysis of the apple CCO genes. The net photosynthetic rate, transpiration rate, and stomatal conductance of leaves decreased, while leaf stomatal density increased under drought and saline conditions. Tissue-specific gene expression analyses revealed diverse spatiotemporal expression patterns. Finally, hormone and abiotic stress treatments indicated that many apple CCO genes are responsive to various phytohormones as well as drought and salinity stresses. The genome-wide identification of apple CCO genes and the analyses of their expression patterns described herein may provide a solid foundation for future studies examining the regulation and functions of this gene family.
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Affiliation(s)
- Hongfei Chen
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiya Zuo
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Hongxia Shao
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Sheng Fan
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Juanjuan Ma
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Dong Zhang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Caiping Zhao
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiangyan Yan
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Liu
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Mingyu Han
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, China.
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Michalecka M, Masny S, Leroy T, Puławska J. Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation. BMC Evol Biol 2018; 18:5. [PMID: 29351730 PMCID: PMC5775622 DOI: 10.1186/s12862-018-1122-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 10 orchards composed of various host cultivars. RESULTS Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. CONCLUSIONS Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.
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Affiliation(s)
- Monika Michalecka
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Sylwester Masny
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
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Lamm CE, Kraner ME, Hofmann J, Börnke F, Mock HP, Sonnewald U. Hop/Sti1 - A Two-Faced Cochaperone Involved in Pattern Recognition Receptor Maturation and Viral Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:1754. [PMID: 29075278 PMCID: PMC5641557 DOI: 10.3389/fpls.2017.01754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 05/03/2023]
Abstract
Perception of pathogens by host pattern recognition receptors (PRRs) or R proteins is a prerequisite to promote successful immune responses. The Hsp70/Hsp90 organizing protein Hop/Sti1, a multifunctional cochaperone, has been implicated in the maturation of a receptor-like kinase (RLK) necessary for chitin sensing. However, it remains unknown whether Hop/Sti1 is generally participating in PRR genesis. Using RNA-interference (RNAi), we silenced Hop/Sti1 expression in Nicotiana tabacum to gain further insight into the role of the cochaperone in plant defense responses. As expected, transgenic plants do not respond to chitin treatment anymore. In contrast to this, trafficking and functionality of the flagellin PRR FLS2 were unaltered, suggesting a selective involvement of Hop/Sti1 during PRR maturation. Furthermore, Hop/Sti1 was identified as a cellular determinant of Potato virus Y (PVY) symptom development in tobacco, since PVY was able to accumulate to near wild-type level without provoking the usual veinal necrosis phenotype. In addition, typical antiviral host defense responses were suppressed in the transgenic plants. These data suggest that perception of PVY is dependent on Hop/Sti1-mediated receptor maturation, while viral symptoms represent a failing attempt to restrict PVY spread. In addition, Hop/Sti1 colocalized with virus-induced membrane aggregates in wild-type plants. The retention of Hop/Sti1 in potential viral replication complexes suggests a role during viral translation/replication, explaining why RNAi-lines do not exhibit increased susceptibility to PVY. This study provides evidence for a dual role of Hop/Sti1 in PRR maturation and pathogen perception as well as in promoting viral proliferation.
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Affiliation(s)
- Christian E. Lamm
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Max. E. Kraner
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jörg Hofmann
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Frederik Börnke
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Uwe Sonnewald
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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