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Brungardt J, Alarcon Y, Shiller J, Young C, Monteros MJ, Randall JJ, Bock CH. Transcriptome profile of pecan scab resistant and susceptible trees from a pecan provenance collection. BMC Genomics 2024; 25:180. [PMID: 38355402 PMCID: PMC10868059 DOI: 10.1186/s12864-024-10010-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management practice for controlling the disease is by application of fungicides at 2-to-3-week intervals throughout the growing season. Besides disease-related yield loss, application of fungicides can result in considerable cost and increases the likelihood of fungicide resistance developing in the pathogen. Resistant cultivars are available for pecan growers; although, in several cases resistance has been overcome as the pathogen adapts to infect resistant hosts. Despite the importance of host resistance in scab management, there is little information regarding the molecular basis of genetic resistance to pecan scab.The purpose of this study was to elucidate mechanisms of natural pecan scab resistance by analyzing transcripts that are differentially expressed in pecan leaf samples from scab resistant and susceptible trees. The leaf samples were collected from trees in a provenance collection orchard that represents the natural range of pecan in the US and Mexico. Trees in the orchard have been exposed to natural scab infections since planting in 1989, and scab ratings were collected over three seasons. Based on this data, ten susceptible trees and ten resistant trees were selected for analysis. RNA-seq data was collected and analyzed for diseased and non-diseased parts of susceptible trees as well as for resistant trees. A total of 313 genes were found to be differentially expressed when comparing resistant and susceptible trees without disease. For susceptible samples showing scab symptoms, 1,454 genes were identified as differentially expressed compared to non-diseased susceptible samples. Many genes involved in pathogen recognition, defense responses, and signal transduction were up-regulated in diseased samples of susceptible trees, whereas differentially expressed genes in pecan scab resistant samples were generally down-regulated compared to non-diseased susceptible samples.Our results provide the first account of candidate genes involved in resistance/susceptibility to pecan scab under natural conditions in a pecan orchard. This information can be used to aid pecan breeding programs and development of biotechnology-based approaches for generating pecan cultivars with more durable scab resistance.
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Affiliation(s)
| | - Yanina Alarcon
- Noble Research Institute, Ardmore, OK, USA
- University of Texas Southwestern, Dallas, TX, USA
| | - Jason Shiller
- Noble Research Institute, Ardmore, OK, USA
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Carolyn Young
- Noble Research Institute, Ardmore, OK, USA.
- Entomology and Plant Pathology, NC State University, Raleigh, NC, USA.
| | - Maria J Monteros
- Noble Research Institute, Ardmore, OK, USA
- Bayer Crop Science, Chesterfield, MO, USA
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Buonaurio R, Almadi L, Famiani F, Moretti C, Agosteo GE, Schena L. Olive leaf spot caused by Venturia oleaginea: An updated review. FRONTIERS IN PLANT SCIENCE 2023; 13:1061136. [PMID: 36699830 PMCID: PMC9868462 DOI: 10.3389/fpls.2022.1061136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/16/2022] [Indexed: 06/01/2023]
Abstract
Olive leaf spot (OLS) caused by Venturia oleaginea is widespread in all olive-growing areas and continents, where can cause severe yield losses. The disease is often underestimated for the difficulty to reveal early leaf symptoms and for the pathogen-induced phylloptosis, which creates the illusion of healthy and restored plants. The present review provide updated information on taxonomy, pathogen life style and cycle, epidemiology, diagnosis, and control. Application of copper-based fungicides is the main method to control OLS. However, the regulation 2009/1107 of the European Commission include these fungicides in the list of substances candidates for substitution. It is therefore urgent to find alternative control strategies especially for organic agriculture. Among new approaches/strategies for controlling OLS, promising results have been obtained using nanotechnology, endophytic microbes, and biostimulants.
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Affiliation(s)
- Roberto Buonaurio
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Leen Almadi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Franco Famiani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Chiaraluce Moretti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | | | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
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Bock CH, Frusso E, Zoppolo R, Ortiz ER, Shiller J, Charlton ND, Young CA, Randall JJ. Population Genetic Characteristics and Mating Type Frequency of Venturia effusa from Pecan in South America. PHYTOPATHOLOGY 2022; 112:2224-2235. [PMID: 35596236 DOI: 10.1094/phyto-01-22-0031-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: 06/15/2023]
Abstract
Scab, caused by the plant-pathogenic fungus Venturia effusa, is a major disease of pecan in South America, resulting in loss of quantity and quality of nut yield. Characteristics of the populations of V. effusa in South America are unknown. We used microsatellites to describe the genetic diversity and population structure of V. effusa in South America, and determined the mating type status of the pathogen. The four hierarchically sampled orchard populations from Argentina (AR), Brazil (BRC and BRS), and Uruguay (UR) had moderate to high genotypic and gene diversity. There was evidence of population differentiation (Fst = 0.196) but the correlation between geographic distance and genetic distance was not statistically significant. Genetic differentiation was minimal between the UR, BRC, and BRS populations, and these populations were more clearly differentiated from the AR population. The MAT1-1 and MAT1-2 mating types occurred in all four orchards and their frequencies did not deviate from the 1:1 ratio expected under random mating; however, multilocus linkage equilibrium was rejected in three of the four populations. The population genetics of South American populations of V. effusa has many similarities to the population genetics of V. effusa previously described in the United States. Characterizing the populations genetics and reproductive systems of V. effusa are important to establish the evolutionary potential of the pathogen and, thus, its adaptability-and can provide a basis for informed approaches to utilizing available host resistance and determining phytosanitary needs.
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Affiliation(s)
- Clive H Bock
- United States Department of Agriculture-Agriculture Research Service, Southeastern Fruit and Tree Nut Research Lab, 21 Dunbar Road, Byron, GA 31008, U.S.A
| | - Enrique Frusso
- Instituto de Recursos Biológicos, INTA Castelar, Las Cabañas y De Los Reseros s.n., (1686) Hurlingham, Buenos Aires, Argentina
| | - Roberto Zoppolo
- Instituto Nacional de Investigación Agropecuaria - INIA Las Brujas, Ruta 48 - km 10, El Colorado, Canelones, Uruguay, CP 90200
| | - Edson R Ortiz
- Divinut Indústria de Nozes Ltda., Rodovia BR-153, km 375, CEP 96504-800 - Cachoeira do Sul/RS, Brazil
| | | | - Nikki D Charlton
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, U.S.A
| | - Carolyn A Young
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, 74078, U.S.A
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Mattupalli C, Cuenca FP, Shiller JB, Watkins T, Hansen K, Garzon CD, Marek SM, Young CA. Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System. PLANT DISEASE 2022; 106:2105-2116. [PMID: 35156845 DOI: 10.1094/pdis-01-22-0013-re] [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
Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.
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Affiliation(s)
- Chakradhar Mattupalli
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant Pathology, Washington State University, Mount Vernon NWREC, Mount Vernon, WA 98273, U.S.A
| | - Fernanda Proaño Cuenca
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Jason B Shiller
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Scion, Rotorua 3046, New Zealand
| | - Tara Watkins
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Karen Hansen
- Department of Botany, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Carla D Garzon
- Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901, U.S.A
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Carolyn A Young
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
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Moore LC, Brenneman TB, Waliullah S, Bock CH, Ali ME. Multiple Mutations and Overexpression in the CYP51A and B Genes Lead to Decreased Sensitivity of Venturia effusa to Tebuconazole. Curr Issues Mol Biol 2022; 44:670-685. [PMID: 35723332 PMCID: PMC8928975 DOI: 10.3390/cimb44020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple demethylation-inhibiting (DMI) fungicides are used to control pecan scab, caused by Venturia effusa. To compare the efficacy of various DMI fungicides on V. effusa, field trials were conducted at multiple locations applying fungicides to individual pecan terminals. In vitro assays were conducted to test the sensitivity of V. effusa isolates from multiple locations to various concentrations of tebuconazole. Both studies confirmed high levels of resistance to tebuconazole. To investigate the mechanism of resistance, two copies of the CYP51 gene, CYP51A and CYP51B, of resistant and sensitive isolates were sequenced and scanned for mutations. In the CYP51A gene, mutation at codon 444 (G444D), and in the CYP51B gene, mutations at codon 357 (G357H) and 177 (I77T/I77L) were found in resistant isolates. Expression analysis of CYP51A and CYP51B revealed enhanced expression in the resistant isolates compared to the sensitive isolates. There were 3.0- and 1.9-fold increases in gene expression in the resistant isolates compared to the sensitive isolates for the CYP51A and CYP51B genes, respectively. Therefore, two potential mechanisms—multiple point mutations and gene over expression in the CYP51 gene of V. effusa isolates—were revealed as likely reasons for the observed resistance in isolates of V. effusa to tebuconazole.
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Affiliation(s)
- Logan C. Moore
- Department of Plant Pathology, Coastal Plain Experiment Station, The University of Georgia, Tifton, GA 31793, USA; (L.C.M.); (T.B.B.); (S.W.)
| | - Timothy B. Brenneman
- Department of Plant Pathology, Coastal Plain Experiment Station, The University of Georgia, Tifton, GA 31793, USA; (L.C.M.); (T.B.B.); (S.W.)
| | - Sumyya Waliullah
- Department of Plant Pathology, Coastal Plain Experiment Station, The University of Georgia, Tifton, GA 31793, USA; (L.C.M.); (T.B.B.); (S.W.)
| | - Clive H. Bock
- United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, USA;
| | - Md Emran Ali
- Department of Plant Pathology, Coastal Plain Experiment Station, The University of Georgia, Tifton, GA 31793, USA; (L.C.M.); (T.B.B.); (S.W.)
- Correspondence:
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Bock CH, Young CA, Zhang M, Chen C, Brannen PM, Adaskaveg J, Charlton ND. Mating Type Idiomorphs, Heterothallism, and High Genetic Diversity in Venturia carpophila, Cause of Peach Scab. PHYTOPATHOLOGY 2021; 111:408-424. [PMID: 32748736 DOI: 10.1094/phyto-12-19-0485-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Scab (caused by Venturia carpophila) is a major disease affecting peach in the eastern United States. The aims of the study were to characterize the mating-type loci in V. carpophila, determine whether they are in equilibrium, and assess the population genetic diversity and structure of the pathogen. The mating-type gene MAT1-1-1 was identified in isolate JP3-5 in an available genome sequence, and the MAT1-2-1 gene was PCR amplified from isolate PS1-1, thus indicating a heterothallic structure. Mating-type loci structures were consistent with those of other Venturia spp. (V. effusa and V. inaequalis): the mating-type gene is positioned between APN2 encoding a DNA lyase and a gene encoding a Pleckstrin homology domain. Primers designed to each of the mating-type genes and a reference gene TUB2 were used as a multiplex PCR to screen a population (n = 81) of V. carpophila from various locations in the eastern United States. Mating types in five of the nine populations studied were in equilibrium. Among the 81 isolates, there were 69 multilocus genotypes. A population genetic analysis of the populations with >10 individuals (four populations) showed them to be genetically diverse. Linkage disequilibrium was found in five of nine populations with ≥4 isolates. A discriminant analysis of principal components indicated three genetic clusters, although extensive admixture was observed. Mating-type identification in V. carpophila provides a basis for understanding reproductive methods of the pathogen and can be a basis for further studies of the genetics of the peach scab pathogen.
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Affiliation(s)
- Clive H Bock
- United States Department of Agriculture-Agricultural Research Service-Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008
| | - Carolyn A Young
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401
| | - Minling Zhang
- United States Department of Agriculture-Agricultural Research Service-Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008
| | - Chunxian Chen
- United States Department of Agriculture-Agricultural Research Service-Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008
| | - Phillip M Brannen
- Department of Plant Pathology, University of Georgia, 2105 Miller Plant Sciences Building, Athens, GA 30602
| | - Jim Adaskaveg
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA 92521
| | - Nikki D Charlton
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401
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Standish JR, Brenneman TB, Bock CH, Stevenson KL. Fungicide Resistance in Venturia effusa, Cause of Pecan Scab: Current Status and Practical Implications. PHYTOPATHOLOGY 2021; 111:244-252. [PMID: 33151825 DOI: 10.1094/phyto-06-20-0221-rvw] [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
Pecan scab, caused by Venturia effusa, is the most economically damaging disease of pecan in the southeastern United States, and annual epidemics are most effectively managed through multiple fungicide applications. The fungicide applications can be the single greatest operating cost for commercial growers and the return on that investment is impacted by fungicide resistance. V. effusa produces multiple generations of conidia per season, exhibits substantial genetic diversity, overwinters as stromata in the tree, and is under immense selection from the applied fungicides, all of which lead to a high risk for developing fungicide resistance. Since the mid-1970s, resistance or reduced sensitivity has been observed in isolates of V. effusa to the methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, organotin compounds, and the guanidines. Over the last 10 years, several studies have been conducted that have improved both scab management and fungicide resistance management in V. effusa. The aim of this review is to summarize recent developments in our understanding of fungicide resistance in V. effusa in the context of scab management in southeastern pecan orchards. The history, modes of action, general use of the labeled fungicides, and mechanisms and stability of fungicide resistance in V. effusa are discussed; conclusions and future research priorities are also presented.
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Affiliation(s)
- J R Standish
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - T B Brenneman
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - C H Bock
- United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008
| | - K L Stevenson
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
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