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Chu HH, Tsao WC, Huang JW, Linda Chang PF, Wang CL. Development of Specific Primers for Fusarium oxysporum Formae Speciales rapae and matthiolae with an Integrated Multiplex PCR for Distinguishing Four Formae Speciales on Brassicaceae. PLANT DISEASE 2024:PDIS08231656RE. [PMID: 38128079 DOI: 10.1094/pdis-08-23-1656-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
There are four formae speciales of Fusarium oxysporum responsible for causing yellows of Brassicaceae. Because of crossbreeding among crops, the host ranges of these formae speciales often overlap, making pathogen identification a challenging task. Among these formae speciales, F. oxysporum f. sp. rapae and F. oxysporum f. sp. matthiolae still lack specific primers for pathogen identification. To address this problem, we targeted the secreted in xylem (SIX) genes, known as specific effectors of pathogenic F. oxysporum, for primer design. Through sequence comparison with other formae speciales, we successfully designed specific primers for F. oxysporum f. sp. rapae and F. oxysporum f. sp. matthiolae on SIX14 and SIX9, respectively. Both primer pairs exhibited high specificity in detecting F. oxysporum f. sp. rapae or F. oxysporum f. sp. matthiolae, distinguishing them from 20 nontarget formae speciales of F. oxysporum, five species of phytopathogenic Fusarium, and four other common pathogenic fungi affecting cruciferous plants. Moreover, the effectiveness of these specific primers was validated by detecting the pathogens in infected plants. To further enhance the identification process of the four formae speciales, we combined the two newly designed specific primer pairs with two previously published primer pairs, enabling the establishment of a multiplex PCR method that can accurately distinguish all four formae speciales of F. oxysporum responsible for causing yellows in cruciferous plants in a single reaction.
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Affiliation(s)
- Huang-Hsi Chu
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Wei-Chin Tsao
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Pi-Fang Linda Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Chih-Li Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
- Master Program for Plant Medicine and Good Agricultural Practice, National Chung Hsing University, Taichung 402, Taiwan
- Plant Health Care Master Degree Program, National Chung Hsing University, Taichung 402, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 402, Taiwan
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Zhong X, Yang Y, Zhao J, Gong B, Li J, Wu X, Gao H, Lü G. Detection and Quantification of Fusarium oxysporum f. sp. niveum Race 1 in Plants and Soil by Real-time PCR. THE PLANT PATHOLOGY JOURNAL 2022; 38:229-238. [PMID: 35678056 PMCID: PMC9343908 DOI: 10.5423/ppj.oa.03.2022.0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) is the most serious soil-borne disease in the world and has become the main limiting factor of watermelon production. Reliable and quick detection and quantification of Fon are essential in the early stages of infection for control of watermelon Fusarium wilt. Traditional detection and identification tests are laborious and cannot efficiently quantify Fon isolates. In this work, a real-time polymerase chain reaction (PCR) assay has been described to accurately identify and quantify Fon in watermelon plants and soil. The FONRT-18 specific primer set which was designed based on identified specific sequence amplified a specific 172 bp band from Fon and no amplification from the other formae speciales of Fusarium oxysporum tested. The detection limits with primers were 1.26 pg/µl genomic DNA of Fon, 0.2 pg/ng total plant DNA in inoculated plant, and 50 conidia/g soil. The PCR assay could also evaluate the relationships between the disease index and Fon DNA quantity in watermelon plants and soil. The assay was further used to estimate the Fon content in soil after disinfection with CaCN2. The real-time PCR method is rapid, accurate and reliable for monitoring and quantification analysis of Fon in watermelon plants and soil. It can be applied to the study of disease diagnosis, plant-pathogen interactions, and effective management.
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Affiliation(s)
- Xin Zhong
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Yang Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Jing Zhao
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Binbin Gong
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Jingrui Li
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Xiaolei Wu
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Hongbo Gao
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
| | - Guiyun Lü
- College of Horticulture, Hebei Agricultural University, Baoding 071001,
China
- Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding 071001,
China
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Baoding 071001,
China
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Overexpression of chitinase in the endophyte Phomopsis liquidambaris enhances wheat resistance to Fusarium graminearum. Fungal Genet Biol 2021; 158:103650. [PMID: 34923123 DOI: 10.1016/j.fgb.2021.103650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/26/2021] [Accepted: 12/04/2021] [Indexed: 11/22/2022]
Abstract
Fusarium head blight (FHB) is a disease that affects wheat crops worldwide and is caused by Fusarium graminearum. Effective and safe strategies for the prevention and treatment of the disease are very limited. Phomopsis liquidambaris, a universal endophyte, can colonize wheat. Two engineered strains, Phomopsis liquidambaris OE-Chi and IN-Chi, were constructed by transformation with a plasmid and integration of a chitinase into the genome, respectively. The OE-Chi and IN-Chi strains could inhibit the expansion of Fusarium sp. in plate confrontation assays in vitro. Colonization of the OE-Chi strain in wheat showed better effects than colonization of the IN-Chi strain and alleviated the inhibition of wheat growth caused by F. graminearum. The shoot length, root length and fresh weight of infected wheat increased by 164.9%, 115.4%, and 190.7%, respectively, when the plants were inoculated with the OE-Chi strain. The peroxidase (POD) activity in the wheat root increased by 38.0%, and it was maintained at a high level in the shoot, which suggested that the OE-Chi strain could enhance the resistance of wheat to F. graminearum. The root and shoot superoxide dismutase (SOD) activities were decreased by 11.8% and 19.0%, respectively, which may be helpful for colonization by the OE-Chi strain. These results suggested that the Phomopsis liquidambaris OE-Chi strain may be a potential endophyte in the biocontrol of FHB.
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Ma Y, Chhapekar SS, Lu L, Yu X, Kim S, Lee SM, Gan TH, Choi GJ, Lim YP, Choi SR. QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3925-3940. [PMID: 34387712 DOI: 10.1007/s00122-021-03937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Two major QTL associated with resistance to Fusarium wilt (FW) were identified using whole-genome resequencing. Sequence variations and gene expression level differences suggest that TIR-NBS and LRR-RLK are candidate genes associated with FW-resistance. Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. raphani is an important disease in radish, leading to severe decrease in yield and quality. YR4 as a novel genetic source to resistant to FW was confirmed through screening with five pathogen isolates. We have generated F2 and F2:3 populations segregated with FW resistance using YR4 and YR18 inbred lines. The disease symptom was evaluated in F2:3 population (n = 180) in three independent studies over two years. We identified 4 QTL including the two major QTL (FoRsR7.159A and FoRsR9.359A). FoRsR7.159A and FoRsR9.359A were detected in three replicated experiments. FoRsR7.159A was delimited to the 2.18-Mb physical interval on chromosome R07, with a high LOD value (5.17-12.84) and explained phenotypic variation (9.34%-27.97%). The FoRsR9.359A represented relatively low LOD value (3.38-4.52) and explained phenotypic variation (6.24%-8.82%). On the basis of the re-sequencing data for the parental lines, we identified five putative resistance-related genes and 13 unknown genes with sequence variations at the gene and protein levels. A semi-quantitative RT-PCR analysis revealed that Rs382940 (TIR-NBS) and Rs382200 (RLK) were expressed only in 'YR4' from 0 to 6 days after the inoculation. Moreover, Rs382950 (TIR-NBS-LRR) was more highly expressed in 'YR4' from 3 to 6 days after the inoculation. These three genes might be important for FW-resistance in radish. We identified several markers based on these potential candidate genes. The marker set should be useful for breeding system to introduce the FW resistance loci from 'YR4' to improve tolerance to FW.
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Affiliation(s)
- Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Shandong Peanut Industry Collaborative Innovation Center, College of Agronomy, Qingdao Agricultural University, Qingdao, 266000, China
| | - Seungho Kim
- Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province, 17565, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Tae Hyoung Gan
- JIREH Seed Co., 104 Dongtansunhwan-daero 20-gil, Hwaseong, Gyeonggi Province, 18484, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
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Penkov NV, Goltyaev MV, Astashev ME, Serov DA, Moskovskiy MN, Khort DO, Gudkov SV. The Application of Terahertz Time-Domain Spectroscopy to Identification of Potato Late Blight and Fusariosis. Pathogens 2021; 10:pathogens10101336. [PMID: 34684285 PMCID: PMC8537707 DOI: 10.3390/pathogens10101336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium and late blight (fungal diseases of cereals and potatoes) are among the main causes of crop loss worldwide. A key element of success in the fight against phytopathogens is the timely identification of infected plants and seeds. That is why the development of new methods for identifying phytopathogens is a priority for agriculture. The terahertz time-domain spectroscopy (THz-TDS) is a promising method for assessing the quality of materials. For the first time, we used THz-TDS for assessing the infection of seeds of cereals (oats, wheat and barley) with fusarium and potato tubers of different varieties (Nadezhda and Meteor) with late blight. We evaluated the refractive index, absorption coefficient and complex dielectric permittivity in healthy and infected plants. The presence of phytopathogens on seeds was confirmed by microscopy and PCR. It is shown, that Late blight significantly affected all the studied spectral characteristics. The nature of the changes depended on the variety of the analyzed plants and the localization of the analyzed tissue relative to the focus of infection. Fusarium also significantly affected all the studied spectral characteristics. It was found that THz-TDS method allows you to clearly establish the presence or absence of a phytopathogens, in the case of late blight, to assess the degree and depth of damage to plant tissues.
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Affiliation(s)
- Nikita V. Penkov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
| | - Mikhail V. Goltyaev
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
| | - Maxim E. Astashev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Dmitry A. Serov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.V.P.); (M.V.G.); (D.A.S.)
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Maxim N. Moskovskiy
- Federal State Budgetary Scientific Institution “Federal Scientific Agroengineering Center VIM”, 109428 Moscow, Russia; (M.N.M.); (D.O.K.)
| | - Dmitriy O. Khort
- Federal State Budgetary Scientific Institution “Federal Scientific Agroengineering Center VIM”, 109428 Moscow, Russia; (M.N.M.); (D.O.K.)
| | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
- Correspondence:
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Dobbs JT, Kim MS, Dudley NS, Klopfenstein NB, Yeh A, Hauff RD, Jones TC, Dumroese RK, Cannon PG, Stewart JE. Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring. BMC Genomics 2020; 21:764. [PMID: 33148175 PMCID: PMC7640661 DOI: 10.1186/s12864-020-07156-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. RESULTS This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. CONCLUSIONS These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.
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Affiliation(s)
- John T. Dobbs
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331 USA
| | - Nicklos S. Dudley
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Ned B. Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Aileen Yeh
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Robert D. Hauff
- Division of Forestry and Wildlife, Department of Land and Natural Resources, 1151 Punchbowl Street, Room 325, Honolulu, HI 96813 USA
| | - Tyler C. Jones
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - R. Kasten Dumroese
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Philip G. Cannon
- USDA Forest Service, Forest Health Protection, 1323 Club Drive, Vallejo, CA 94592 USA
| | - Jane E. Stewart
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
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Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
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Yu X, Lu L, Ma Y, Chhapekar SS, Yi SY, Lim YP, Choi SR. Fine-mapping of a major QTL (Fwr1) for fusarium wilt resistance in radish. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:329-340. [PMID: 31686113 DOI: 10.1007/s00122-019-03461-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
A major radish QTL (Fwr1) for fusarium wilt resistance was fine-mapped. Sequence and expression analyses suggest that a gene encoding a serine/arginine-rich protein kinase is a candidate gene for Fwr1. Fusarium wilt resistance locus 1 (Fwr1) is a major quantitative trait locus (QTL) mediating the resistance of radish inbred line 'B2' to Fusarium oxysporum, which is responsible for fusarium wilt. We previously detected Fwr1 on radish linkage group 3 (i.e., chromosome 5). In this study, a high-resolution genetic map of the Fwr1 locus was constructed by analyzing 354 recombinant F2 plants derived from a cross between 'B2' and '835', the latter of which is susceptible to fusarium wilt. The Fwr1 QTL was fine-mapped to a 139.8-kb region between markers FM82 and FM87 in the middle part of chromosome 5. Fifteen candidate genes were predicted in this region based on a sequence comparison with the 'WK10039' radish reference genome. Additionally, we examined the time-course expression patterns of these predicted genes following an infection by the fusarium wilt pathogen. The ORF4 expression level was significantly higher in the resistant 'B2' plants than in the susceptible '835' plants. The ORF4 sequence was predicted to encode a serine/arginine-rich protein kinase and includes SNPs that result in nonsynonymous mutations, which may have important functional consequences. This study reveals a novel gene responsible for fusarium wilt resistance in radish. Further analyses of this gene may elucidate the molecular mechanisms underlying the fusarium wilt resistance of plants.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
- Agronomy Department, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - So Young Yi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea.
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Liu X, Xing M, Kong C, Fang Z, Yang L, Zhang Y, Wang Y, Ling J, Yang Y, Lv H. Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China. Front Microbiol 2019; 10:1373. [PMID: 31293534 PMCID: PMC6603142 DOI: 10.3389/fmicb.2019.01373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
Cabbage Fusarium wilt (CFW) caused by Fusarium oxysporum f. sp. conglutinans (FOC) is known to significantly affect yield and quality of cabbages worldwide. CFW was first detected in New York, NY, United States, and has now spread to almost all cabbage-planting areas, including a recent outbreak of the disease in China. However, it was unknown whether the FOC strains emerged in China differed from the strains in other areas of the world. From 2009 to 2018, we collected Chinese FOC isolates and compared them to the races 1 and 2 strains in other areas to define their characteristics. Race tests indicated that most of the Chinese FOC strains belonged to race 1 and were more virulent than type strain 52557. To evaluate the genome level diversity, we performed next-generation sequencing and genome assembly for the race 2 strain 58385. Based on the assembled genome, we discovered abundant single-nucleotide polymorphisms and 645 insertion-deletions (InDels) compared with the race 1 strain FGL03-6 by comparative genomic analysis and showed that all FOC race 1 strains have a low genetic variability, with a genomic background distinct from 58385. Furthermore, the internal transcribed spacer, elongation factor-1α, and whole-genome InDel variation studies suggested that the last might be a powerful tool in phylogenetic as well as evolution analysis for F. oxysporum Schlechtend.: Fr. The race, virulence, and genome-based variation profiles could contribute to our knowledge of FOC diversity and support the studies of pathogen characterization in genomic era and also provide clues for CFW-resistance breeding. To our knowledge, this is the first extensive survey conducted for FOC strains.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, China
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Lombard L, Sandoval-Denis M, Lamprecht S, Crous P. Epitypification of Fusarium oxysporum - clearing the taxonomic chaos. PERSOONIA 2018; 43:1-47. [PMID: 32214496 PMCID: PMC7085860 DOI: 10.3767/persoonia.2019.43.01] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/19/2018] [Indexed: 01/06/2023]
Abstract
Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.
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Affiliation(s)
- L. Lombard
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Yamashita S, Nakagawa H, Sakaguchi T, Arima TH, Kikoku Y. Design of a species-specific PCR method for the detection of the heat-resistant fungi Talaromyces macrosporus and Talaromyces trachyspermus. Lett Appl Microbiol 2017; 66:86-92. [PMID: 29108110 DOI: 10.1111/lam.12818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 11/29/2022]
Abstract
Heat-resistant fungi occur sporadically and are a continuing problem for the food and beverage industry. The genus Talaromyces, as a typical fungus, is capable of producing the heat-resistant ascospores responsible for the spoilage of processed food products. Isocitrate lyase, a signature enzyme of the glyoxylate cycle, is required for the metabolism of non-fermentable carbon compounds, like acetate and ethanol. Here, species-specific primer sets for detection and identification of DNA derived from Talaromyces macrosporus and Talaromyces trachyspermus were designed based on the nucleotide sequences of their isocitrate lyase genes. Polymerase chain reaction (PCR) using a species-specific primer set amplified products specific to T. macrosporus and T. trachyspermus. Other fungal species, such as Byssochlamys fulva and Hamigera striata, which cause food spoilage, were not detected using the Talaromyces-specific primer sets. The detection limit for each species-specific primer set was determined as being 50 pg of template DNA, without using a nested PCR method. The specificity of each species-specific primer set was maintained in the presence of 1,000-fold amounts of genomic DNA from other fungi. The method also detected fungal DNA extracted from blueberry inoculated with T. macrosporus. This PCR method provides a quick, simple, powerful and reliable way to detect T. macrosporus and T. trachyspermus. SIGNIFICANCE AND IMPACT OF THE STUDY Polymerase chain reaction (PCR)-based detection is rapid, convenient and sensitive compared with traditional methods of detecting heat-resistant fungi. In this study, a PCR-based method was developed for the detection and identification of amplification products from Talaromyces macrosporus and Talaromyces trachyspermus using primer sets that target the isocitrate lyase gene. This method could be used for the on-site detection of T. macrosporus and T. trachyspermus in the near future, and will be helpful in the safety control of raw materials and in food and beverage production.
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Affiliation(s)
- S Yamashita
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - H Nakagawa
- R & D Center, Aohata Corporation, Takehara, Hiroshima, Japan
| | - T Sakaguchi
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - T-H Arima
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - Y Kikoku
- R & D Center, Aohata Corporation, Takehara, Hiroshima, Japan
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