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Lin F, Salman M, Zhang Z, McCoy AG, Li W, Magar RT, Mitchell D, Zhao M, Gu C, Chilvers MI, Wang D. Identification and molecular mapping of a major gene conferring resistance to Phytophthora sansomeana in soybean 'Colfax'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:55. [PMID: 38386094 DOI: 10.1007/s00122-024-04556-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
KEY MESSAGE The first single dominant resistance gene contributing major resistance to the oomycete pathogen Phytophthora sansomeana was identified and mapped from soybean 'Colfax'. Phytophthora root rot (PRR) is one of the most important diseases in soybean (Glycine max). PRR is well known to be caused by Phytophthora sojae, but recent studies showed that P. sansomeana also causes extensive root rot of soybean. Depending upon the isolate, it might produce aggressive symptoms, especially in seeds and seedlings. Unlike P. sojae which can be effectively managed by Rps genes, no known major resistance genes have yet been reported for P. sansomeana. Our previous study screened 470 soybean germplasm lines for resistance to P. sansomeana and found that soybean 'Colfax' (PI 573008) carries major resistance to the pathogen. In this study, we crossed 'Colfax' with a susceptible parent, 'Senaki', and developed three mapping populations with a total of 234 F2:3 families. Inheritance pattern analysis indicated a 1:2:1 ratio for resistant: segregating: susceptible lines among all the three populations, indicating a single dominant gene conferring the resistance in 'Colfax' (designated as Rpsan1). Linkage analysis using extreme phenotypes anchored Rpsan1 to a 30 Mb region on chromosome 3. By selecting nine polymorphic SNP markers within the region, Rpsan1 was genetically delimited into a 21.3 cM region between Gm03_4487138_A_C and Gm03_5451606_A_C, which corresponds to a 1.06 Mb genomic region containing nine NBS-LRR genes based on Gmax2.0 assembly. The mapping results were then validated using two breeding populations derived from 'E12076T-03' × 'Colfax' and 'E16099' × 'Colfax'. Marker-assisted resistance spectrum analyses with 9 additional isolates of P. sansomeana indicated that Rpsan1 may be effective towards a broader range of P. sansomeana isolates and has strong merit in protecting soybean to this pathogen in the future.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA.
| | - Muhammad Salman
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Punjab, 38000, Pakistan
| | - Zhanguo Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
- Northeast Agricultural University, National Soybean Engineering Research Center, Harbin, 150030, Heilongjiang Province, China
| | - Austin G McCoy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
| | - Wenlong Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Lekai South Street 2596, Baoding, 071001, Hebei Province, China
| | - Raju Thada Magar
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
| | - Drew Mitchell
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Cuihua Gu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824-1325, USA.
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Hosseini B, Voegele RT, Link TI. Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments. J Fungi (Basel) 2023; 9:jof9050587. [PMID: 37233298 DOI: 10.3390/jof9050587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/03/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.
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Affiliation(s)
- Behnoush Hosseini
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
| | - Ralf Thomas Voegele
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
| | - Tobias Immanuel Link
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Str. 5, 70599 Stuttgart, Germany
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New Reports of Phytophthora Species in Plant Nurseries in Spain. Pathogens 2022; 11:pathogens11080826. [PMID: 35894049 PMCID: PMC9394253 DOI: 10.3390/pathogens11080826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
The plant nursery industry has become an ideal reservoir for Phytophthora species and other soilborne pathogens. In this context, isolation from tissues and soil of ornamental and forest plants from nurseries in four regions of Spain was carried out. A high diversity of Phytophthora species was confirmed. Fourteen Phytophthora phylotypes (P. cactorum, P. cambivora, P. cinnamomi, P. citrophthora, P. crassamura, P. gonapodyides, P. hedraiandra, P. nicotianae, P. niederhauserii, P. palmivora, P. plurivora, P. pseudocryptogea, P. sansomeana, and Phytophthora sp. tropicalis-like 2) were isolated from over 500 plant samples of 22 species in 19 plant genera. Nine species were detected in water sources, two of them (P. bilorbang and P. lacustris) exclusively from water samples. P. crassamura was detected for the first time in Spain. This is the first time P. pseudocryptogea is isolated from Chamaecyparis lawsoniana and Yucca rostrata in Spain.
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Lin F, Li W, McCoy AG, Gao X, Collins PJ, Zhang N, Wen Z, Cao S, Wani SH, Gu C, Chilvers MI, Wang D. Molecular mapping of quantitative disease resistance loci for soybean partial resistance to Phytophthora sansomeana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1977-1987. [PMID: 33721030 DOI: 10.1007/s00122-021-03799-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Two soybean QDRL were identified with additive interaction to P. sansomeana isolate MPS17-22. Further analyses uncovered four interaction patterns between the two QDRL and seven additional P. sansomeana isolates. Phytophthora sansomeana is a recently recognized species that contributes to root rot in soybean. Previous studies indicated that P. sansomeana is widely distributed among soybean growing regions and has a much wider host range than P. sojae, a well-known pathogen of soybean. Unlike P. sojae, no known disease resistance genes have been documented that can effectively control P. sansomeana. Therefore, it is important to identify resistance that can be quickly integrated into future soybean varieties. E13901 is an improved soybean line that confers partial resistance to P. sansomeana. A mapping population of 228 F4:5 families was developed from a cross between E13901 and a susceptible improved soybean variety E13390. Using a composite interval mapping method, two quantitative disease resistance loci (QDRL) were identified on Chromosomes 5 (designated qPsan5.1) and 16 (designated qPsan16.1), respectively. qPsan5.1 was mapped at 54.71 cM between Gm05_32565157_T_C and Gm05_32327497_T_C. qPsan5.1 was contributed by E13390 and explained about 6% of the disease resistance variation. qPsan16.1 was located at 39.01 cM between Gm16_35700223_G_T and Gm16_35933600/ Gm16_35816475. qPsan16.1 was from E13901 and could explain 5.5% of partial disease resistance. Further analysis indicated an additive interaction of qPsan5.1 and qPsan16.1 against P. sansomeana isolate MPS17-22. Marker assisted resistance spectrum analysis and progeny tests verified the two QDRL and their interaction patterns with other P. sansomeana isolates. Both QDRL can be quickly integrated into soybean varieties using marker assisted selection.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Wenlong Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
- Hebei Agricultural University, Baoding, 071001, Hebei Province, China
| | - Austin G McCoy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Xuan Gao
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, China
| | - Paul J Collins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Na Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Sizhe Cao
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Shabir H Wani
- Mountain Research Centre for Field Crops, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India
| | - Cuihua Gu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824-1325, USA.
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Cai G, Scofield SR. Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes. PLoS One 2020; 15:e0231296. [PMID: 32407378 PMCID: PMC7224479 DOI: 10.1371/journal.pone.0231296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Phytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3' truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.
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Affiliation(s)
- Guohong Cai
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Steven R. Scofield
- Crop Production and Pest Control Research Unit, Agricultural Research Service, USDA, and College of Agriculture, Purdue University, West Lafayette, Indiana, United States of America
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Jung T, Jung MH, Cacciola SO, Cech T, Bakonyi J, Seress D, Mosca S, Schena L, Seddaiu S, Pane A, di San Lio GM, Maia C, Cravador A, Franceschini A, Scanu B. Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal. IMA Fungus 2017; 8:219-244. [PMID: 29242773 PMCID: PMC5729710 DOI: 10.5598/imafungus.2017.08.02.02] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/20/2017] [Indexed: 12/02/2022] Open
Abstract
During surveys of Phytophthora diversity in natural and semi-natural Fagaceae forests in Austria, Italy and Portugal, four new cryptic species were isolated from rhizosphere soil samples. Multigene phylogeny based on nuclear ITS, ß-tubulin and HSP90 and mitochondrial cox1 and NADH1 gene sequences demonstrated that two species, P. tyrrhenica and P. vulcanica spp. nov., belong to phylogenetic Clade 7a, while the other two species, P. castanetorum and P. tubulina spp. nov., clustered together with P. quercina forming a new clade, named here as Clade 12. All four new species are homothallic and have low optimum and maximum temperatures for growth and very slow growth rates at their respective optimum temperature. They differed from each other and from related species by a unique combination of morphological characters, cardinal temperatures, and growth rates. Pathogenicity of all Phytophthora species to the root system of their respective host species was demonstrated in soil infestation trials.
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Affiliation(s)
- Thomas Jung
- Phytophthora Research Centre, Mendel University, 613 00 Brno, Czech Republic
- Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, University of Algarve, 8005–130 Faro, Portugal
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
| | - Marília Horta Jung
- Phytophthora Research Centre, Mendel University, 613 00 Brno, Czech Republic
- Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, University of Algarve, 8005–130 Faro, Portugal
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - Thomas Cech
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, A-1131 Vienna, Austria
| | - József Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Diána Seress
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Saveria Mosca
- Dipartimento di Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy
| | - Leonardo Schena
- Dipartimento di Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy
| | - Salvatore Seddaiu
- Dipartimento della ricerca per il sughero e la silvicoltura, Agris Sardegna, Via Limbara 9, 07029 Tempio Pausania, Italy
| | - Antonella Pane
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | | | - Cristiana Maia
- Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, University of Algarve, 8005–130 Faro, Portugal
| | - Alfredo Cravador
- Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, University of Algarve, 8005–130 Faro, Portugal
| | - Antonio Franceschini
- Dipartimento di Agraria, Sezione di Patologia vegetale ed Entomologia, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Bruno Scanu
- Dipartimento di Agraria, Sezione di Patologia vegetale ed Entomologia, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
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Bienapfl JC, Malvick DK, Percich JA. Specific molecular detection of Phytophthora sojae using conventional and real-time PCR. Fungal Biol 2011; 115:733-40. [PMID: 21802053 DOI: 10.1016/j.funbio.2011.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 04/28/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
Abstract
Phytophthora rot, caused by Phytophthora sojae, is one of the most damaging diseases of soybean (Glycine max) worldwide. This disease can be difficult to diagnose and other Phytophthora species can infect soybean. Accurate diagnosis is important for management of Phytophthora rot. The objective of this study was to evaluate polymerase chain reaction (PCR) methods for rapid and specific detection of P. sojae and diagnosis of Phytophthora rot. PCR assays using two sets of primers (PS and PSOJ) that target the ITS region were evaluated for specificity and sensitivity to P. sojae. Genomic DNA extracted from 11 species of Phytophthora and 19 other species of fungal and oomycete pathogens were used to test the specificity of each primer set. The previously published PS primers amplified DNA from P. sojae and from four other Phytophthora species using conventional PCR, indicating they are not specific for P. sojae. The new PSOJ primers amplified DNA only from P. sojae using conventional and real-time PCR and not from Phytophthora sansomeana, which has been found in soybean production areas, indicating that they are specific for P. sojae. The PSOJ primers were also used to detect P. sojae in diseased soybean tissue and infested soil. The PCR assays based on the PSOJ primers are specific, rapid, and sensitive tools for the detection of P. sojae.
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Affiliation(s)
- John C Bienapfl
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.
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Érsek T, Ribeiro O. Mini Review Article: An annotated list of newPhytophthoraspecies described post 1996. ACTA ACUST UNITED AC 2010. [DOI: 10.1556/aphyt.45.2010.2.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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