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Comprehensive Transcriptome Profiling of Root-Knot Nematodes During Plant Infection and Characterisation of Species Specific Trait Chinh Nghia Nguyen
Comprehensive transcriptome profiling of root-knot nematodes during plant infection and characterisation of species specific trait Chinh Nghia Nguyen To cite this version: Chinh Nghia Nguyen. Comprehensive transcriptome profiling of root-knot nematodes during plant infection and characterisation of species specific trait. Agricultural sciences. COMUE Université Côte d’Azur (2015 - 2019), 2016. English. NNT : 2016AZUR4124. tel-01673793 HAL Id: tel-01673793 https://tel.archives-ouvertes.fr/tel-01673793 Submitted on 1 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Ecole Doctorale de Sciences de la Vie et de la Santé Unité de recherche : UMR ISA INRA 1355-UNS-CNRS 7254 Thèse de doctorat Présentée en vue de l’obtention du grade de docteur en Biologie Moléculaire et Cellulaire de L’UNIVERSITE COTE D’AZUR par NGUYEN Chinh Nghia Etude de la régulation du transcriptome de nématodes parasites de plante, les nématodes à galles du genre Meloidogyne Dirigée par Dr. Bruno FAVERY Soutenance le 8 Décembre, 2016 Devant le jury composé de : Pr. Pierre FRENDO Professeur, INRA UNS CNRS Sophia-Antipolis Président Dr. Marc-Henri LEBRUN Directeur de Recherche, INRA AgroParis Tech Grignon Rapporteur Dr. -
Transcriptome Profiling of Resistance Response To
Bali et al. BMC Genomics (2019) 20:907 https://doi.org/10.1186/s12864-019-6257-1 RESEARCH ARTICLE Open Access Transcriptome profiling of resistance response to Meloidogyne chitwoodi introgressed from wild species Solanum bulbocastanum into cultivated potato Sapinder Bali1, Kelly Vining2, Cynthia Gleason1, Hassan Majtahedi3, Charles R. Brown3 and Vidyasagar Sathuvalli4* Abstract Background: Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it infects potato tubers causing internal as well as external defects, thereby reducing the market value of the crop. Commercial potato varieties with CRKN resistance are currently unavailable. Race specific resistance to CRKN has been introgressed from the wild, diploid potato species Solanum bulbocastanum into the tetraploid advanced selection PA99N82–4 but there is limited knowledge about the nature of its resistance mechanism. In the present study, we performed histological and differential gene expression profiling to understand the mode of action of introgressed CRKN resistance in PA99N82–4 in comparison to the CRKN susceptible variety Russet Burbank. Results: Histological studies revealed that the nematode juveniles successfully infect both resistant and susceptible root tissue by 48 h post inoculation, but the host resistance response restricts nematode feeding site formation in PA99N82–4. Differential gene expression analysis shows that 1268, 1261, 1102 and 2753 genes were up-regulated in PA99N82–4 at 48 h, 7 days, 14 days and 21 days post inoculation respectively, of which 61 genes were common across all the time points. -
ABSTRACT WONG, TSZ WAI SAMMI. Management of Root-Knot
ABSTRACT WONG, TSZ WAI SAMMI. Management of Root-knot Nematodes in North Carolina and Sensitivity of Watermelon Pathogens to Succinate Dehydrogenase Inhibitors. (Under the direction of Dr. Lina Quesada-Ocampo). Root-knot nematodes (Meloidogyne spp.) are some of the most economically important and common plant parasitic nematodes in North Carolina cropping systems. These nematodes can be managed using chemical control and cultural methods such as crop rotation. While the southern root-knot nematode, M. incognita, has been a large problem in North Carolina, the guava root-knot nematode, M. enterolobii has become an emerging threat that is impacting many sweetpotato growers. To understand the incidence and distribution of root-knot nematodes (RKN) in the state, soil samples from fields rotated with sweetpotato were collected from 2015 to 2018 across all counties of North Carolina. Amongst these samples, the highest occurrence of RKN-positive were found in Cumberland, Sampson, and Johnston counties. In addition, Sampson and Nash counties had the highest average RKN population density while Wayne and Greene counties had the lowest average RKN population density. Moreover, we analyzed the host susceptibility of 18 plants for a North Carolina population of M. enterolobii by conducting greenhouse trials and measuring the eggs per gram of fresh root (ER) after 45 days. The tomato ‘Rutgers’ was used as a susceptible control. M. enterolobii was able to reproduce on all plants. Two watermelon varieties, cabbage, pepper, one soybean variety, and tobacco were rated as good hosts. Broadleaf signalgrass, corn, one peanut variety, sudangrass, and nutsedge were less susceptible to M. enterolobii and considered poor hosts. -
PM 9/17 (1) Meloidogyne Chitwoodi and Meloidogyne Fallax
Bulletin OEPP/EPPO Bulletin (2013) 43 (3), 527–533 ISSN 0250-8052. DOI: 10.1111/epp.12079 European and Mediterranean Plant Protection Organization Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes PM 9/17 (1) National regulatory control systems Systemes de lutte nationaux reglementaires PM 9/17 (1) Meloidogyne chitwoodi and Meloidogyne fallax Specific scope Specific approval and amendment This standard describes a National regulatory control sys- Approved in 2013-09. tem for Meloidogyne chitwoodi and Meloidogyne fallax. M. fallax, temperature, length of the growing season and Introduction soil texture. These nematodes have mostly been reported Meloidogyne chitwoodi and M. fallax (root-knot nematodes) from sandy and sandy-loam soils. Economic damage are EPPO A2 pests and details about their biology, distribu- increases with the number of generations that occur in one tion and economic importance can be found in EPPO/CABI growing season. Tuber damage in potatoes may occur when (1997) and the Plant Quarantine data Retrieval system soil temperatures exceed 1000 degree days above 5°C but (PQR) on the EPPO website. Recently, pest risk assess- the threshold for significant tuber damage is assessed to be ments for both species have been conducted for the territory about 1500 degree days above 5°C (Macleod et al., 2012). of the EU including extensive datasheets and an evaluation Juveniles of M. chitwoodi and M. fallax can only move of possible risk reduction options. The work has been con- short distances (<1 m) in the soil. Spread therefore mainly ducted within the framework of the EFSA project Prima occurs with the movement of infested planting material Phacie and the reports are available in the EFSA website (e.g. -
ÜRETİM ALANLARINDA KÖK-UR NEMATODLARI (Meloidogyne Spp.)’NIN DURUMU
i EGE ÜNİVERSİTESİ FEN BİLİMLERİ ENSTİTÜSÜ (YÜKSEK LİSANS TEZİ) ÖDEMİŞ VE KİRAZ (İZMİR) İLÇELERİNDE TURŞULUK HIYAR (Cucumis sativus L.) ÜRETİM ALANLARINDA KÖK-UR NEMATODLARI (Meloidogyne spp.)’NIN DURUMU Esmeray CAFARLI Tez Danışmanı : Doç. Dr. Galip KAŞKAVALCI Bitki Koruma Anabilim Dalı Bilim Dalı Kodu : 501.02.01 Sunuş Tarihi: 12.02.2013 Bornova-İZMİR 2013 ii iii Esmeray CAFARLI tarafından Yüksek Lisans tezi olarak sunulan “Ödemiş ve Kiraz (İzmir) İlçelerinde Turşuluk Hıyar (Cucumis sativus L.) Üretim Alanlarında Kök-Ur Nematodları (Meloidogyne spp.)’nın Durumu” baĢlıklı bu çalıĢma E.Ü. Lisansüstü Eğitim ve Öğretim Yönergesi’nin ilgili hükümleri uyarınca tarafımızdan değerlendirilerek savunmaya değer bulunmuĢ ve 12/02/2013 tarihinde yapılan tez savunma sınavında aday oybirliği/oyçokluğu ile baĢarılı bulunmuĢtur. Jüri üyeleri: İmza Jüri Başkanı : Doç. Dr. Galip KAġKAVALCI ……………………. Raportör üye : Doç. Dr. Ferit TURANLI ……………………. Üye : Prof. Dr. Dursun Eġ ĠYOK ……………………. iv v ÖZET ÖDEMİŞ VE KİRAZ (İZMİR) İLÇELERİNDE TURŞULUK HIYAR (Cucumis sativus L.) ÜRETİM ALANLARINDA KÖK-UR NEMATODLARI (Meloidogyne spp.)’NIN DURUMU CAFARLI, Esmeray Yüksek Lisans Tezi, Bitki Koruma Anabilim Dalı Tez Yöneticisi: Doç. Dr. Galip KAġKAVALCI ġubat 2013, 66 sayfa Bu çalıĢmanın amacı, Ġzmir Ġli ÖdemiĢ ve Kiraz ilçeleri turĢuluk hıyar üretimi yapılan tarlalarda bulunan kök-ur nematodlarının yayılıĢ ve bulaĢıklık oranları ile türlerinin saptanmasıdır. AraĢtırmanın materyalini, ÖdemiĢ ve Kiraz ilçeleri tarlarından alınan, kök-ur nematodu ile bulaĢık bitki materyali oluĢturmuĢtur. ÖdemiĢ Ġlçesi’nde 13 köydeki 62 tarladan, Kiraz Ġlçesi’nde ise 11 köydeki 34 tarladan bitki kök örnekleri alınıp, kökler 0-10 bulaĢıklık ıskalasına göre değerlendirilmiĢtir. YayılıĢ ve bulaĢıklık tespiti çalıĢmaları neticesinde; kök-ur nematodları ile bulaĢıklığın ÖdemiĢ Ġlçesi tarlarında % 17,74, Kiraz’da ise % 17,65 oranlarında olduğu saptanmıĢtır. -
Meloidogyne Enterolobii
Bulletin OEPP/EPPO Bulletin (2016) 46 (2), 190–201 ISSN 0250-8052. DOI: 10.1111/epp.12293 European and Mediterranean Plant Protection Organization Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes PM 7/103 (2) Diagnostics Diagnostic PM 7/103 (2) Meloidogyne enterolobii Specific scope Specific approval and amendment This Standard describes a diagnostic protocol for Approved in 2011-09. Meloidogyne enterolobii1. This Standard should be used in Revision approved in 2016-04. conjunction with PM 7/76 Use of EPPO diagnostic Terms used are those in the EPPO Pictorial Glossary of protocols. Morphological Terms in Nematology2. of infested plants and plant products, in soil, adhering to 1. Introduction farm equipment or by irrigation water. Currently, close to 100 species of root-knot nematodes have Infestation by root-knot nematodes affects growth, yield, been described (Hunt & Handoo, 2009). All members are obli- lifespan and tolerance to environmental stresses of affected gate endoparasites on plant roots and they occur worldwide. plants. Typical symptoms include stunted growth, wilting, About 10 species are significant agricultural pests, while four leaf yellowing and deformation of plant organs. Crop dam- are major pests and are distributed worldwide in agricultural age due to root-knot nematodes may consist of reduced areas: Meloidogyne incognita, Meloidogyne javanica, quantity and quality of yield. Meloidogyne arenaria and Meloidogyne hapla. The root-knot Meloidogyne enterolobii was first described from Hainan nematode Meloidogyne enterolobii is polyphagous and has Island, China, in 1983. At present, this species has been many host plants including cultivated plants and weeds. It recorded from Africa (Burkina Faso, Ivory Coast, Malawi, attacks woody as well as herbaceous plants. -
Review on Nematode Molecular Diagnostics: from Bands to Barcodes
Journal of Biology, Agriculture and Healthcare www.iiste.org ISSN 2224-3208 (Paper) ISSN 2225-093X (Online) Vol.4, No.27, 2014 Review on Nematode Molecular Diagnostics: From Bands to Barcodes Alemu Nega Department of Horticulture and Plant Science, Jimma University, P. O. Box 307, Jimma, Ethiopia Email Address: [email protected] Abstract Molecular methods of identification provide accurate, reliable diagnostic approaches for the identification of plant-parasitic nematodes. The promising and attractive results have generated increasing demands for applications in new fields and for better performing techniques. Initially, the techniques were used solely for taxonomic purposes, but increasingly became popular as a component of diagnostic information. Diagnostic procedures are now available to differentiate the plant-pathogenic species from related but non-pathogenic species. The microscopic size of plant parasitic nematodes poses problems and techniques have been developed to enrich samples to obtain qualitative and quantitative information on individual species. In addition, techniques are available to evaluate single nematodes, cysts or eggs of individual species in extracts from soil and plant tissue. DNA or RNA-based techniques are the most widely used approaches for identification, taxonomy and phylogenetic studies, although the development and use of other methods has been, and in some cases still is, important. DNA barcoding and the extraction of DNA from preserved specimens will aid considerably in diagnostic information. In addition, further review is needed to identify all recovered nematode and evaluation of promising treatments for use in integrated disease management strategy to manage not only regulated species such as the potato cyst nematodes Globodera rostochiensis and Globodera pallida, and root-knot nematode Meloidogyne. -
Distribution of Meloidogyne Species in Carrot in Brazil
Ciência Rural, Santa Maria, v.51:5,Distribution e20200552, of Meloidogyne 2021 species in carrot in Brazil. http://doi.org/10.1590/0103-8478cr202005521 ISSNe 1678-4596 CROP PROTECTION Distribution of Meloidogyne species in carrot in Brazil Tiago Garcia da Cunha1 Liliane Evangelista Visôtto1 Letícia Mendes Pinheiro1 Pedro Ivo Vieira Good God1 Juliana Magrinelli Osório Rosa2 Cláudio Marcelo Gonçalves Oliveira2 Everaldo Antônio Lopes1* 1Universidade Federal de Viçosa (UFV), Campus Rio Paranaíba, 38810-000, Rio Paranaíba, MG, Brasil. E-mail: [email protected]. *Corresponding author. 2Instituto Biológico, Campinas, SP, Brasil. ABSTRACT: Root-knot nematodes (RKN – Meloidogyne spp.) are one of the most serious threats to carrot production worldwide. In Brazil, carrots are grown throughout the year, and economic losses due to RKN are reported. Since little is known on the distribution of RKN species in carrot fields in Brazil, we collected plant and soil samples from 35 fields across six states. Based on the morphology of perineal patterns, esterase phenotypes and species-specific PCR, three Meloidogyne species were identified: 60% of the fields were infested with Meloidogyne incognita, M. javanica was reported in 42.9% of the areas, whereas M. hapla was detected in 17.1% of carrot fields. Mixed populations were reported in 20% of the areas with a predominance of M. incognita + M. javanica. The combination of morphological, biochemical, and molecular techniques is a useful approach to identify RKN species. Key words: Daucus carota, integrative taxonomy, isozyme phenotypes, species-specific PCR. Distribuição de espécies de Meloidogyne em cenoura no Brasil RESUMO: Os nematoides-das-galhas (RKN - Meloidogyne spp.) são uma das mais sérias ameaças à produção de cenoura no mundo. -
Meloidogyne Chitwoodi
EPPO quarantine pest Data Sheets on Quarantine Pests Meloidogyne chitwoodi IDENTITY Name:Meloidogyne chitwoodi Golden, O'Bannon, Santo & Finley Taxonomic position: Nematoda: Meloidogynidae Common names: Columbia root-knot nematode (English) Nématode cécidogène du Columbia (French) Bayer computer code: MELGCH EPPO A2 list: No. 227 HOSTS M. chitwoodi has a wide host range among several plant families (Santo et al., 1980; O'Bannon et al., 1982), including crop plants and common weed species. Potatoes (Solanum tuberosum) and tomatoes (Lycopersicon esculentum) are good hosts, while barley (Hordeum vulgare), maize (Zea mays), oats (Avena sativa), sugarbeet (Beta vulgaris var. saccharifera), wheat (Triticum aestivum) and various Poaceae (grasses and weeds) will maintain the nematode. Moderate to poor hosts occur in the Brassicaceae, Cucurbitaceae, Fabaceae, Lamiaceae, Liliaceae, Umbelliferae and Vitaceae. Capsicum annuum and tobacco (Nicotiana tabacum and N. rustica) are not hosts of M. chitwoodi. Lucerne (Medicago sativa) is a good host for race 2 but not for race 1, whereas carrots (Daucus carota) are a non-host for race 2 but a good host for race 1. Ferris et al. (1994), investigating suitable crops for rotation with potato in the presence of race 1 in USA, recommend Amaranthus, lucerne, rape (Brassica napus var. oleifera), Raphanus sativus var. oleifera and safflower (Carthamus tinctorius). In the Netherlands, host crops recorded to be attacked by M. chitwoodi are carrots, cereals, maize, peas (Pisum sativum), Phaseolus vulgaris, potatoes, Scorzonera hispanica, sugarbeet and tomatoes (OEPP/EPPO, 1991). GEOGRAPHICAL DISTRIBUTION M. chitwoodi was first described from the Pacific Northwest of the USA in 1980, its common name deriving from the Columbia River between Oregon and Washington states. -
Diagnostic Methods for Identification of Root-Knot Nematodes Species from Brazil
Ciência Rural, Santa Maria,Diagnostic v.48: methods 02, e20170449, for identification 2018 of root-knot nematodes specieshttp://dx.doi.org/10.1590/0103-8478cr20170449 from Brazil. 1 ISSNe 1678-4596 CROP PROTECTION Diagnostic methods for identification of root-knot nematodes species from Brazil Tiago Garcia da Cunha1 Liliane Evangelista Visôtto2* Everaldo Antônio Lopes1 Claúdio Marcelo Gonçalves Oliveira3 Pedro Ivo Vieira Good God1 1Instituto de Ciências Agrárias, Universidade Federal de Viçosa (UFV), Campus Rio Paranaíba, Rio Paranaíba, MG, Brasil. 2Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa (UFV), Campus Rio Paranaíba, 38810-000, Rio Paranaíba, MG, Brasil. E-mail: [email protected]. *Corresponding author. 3Instituto Biológico, Campinas, SP, Brasil. ABSTRACT: The accurate identification of root-knot nematode (RKN) species (Meloidogyne spp.) is essential for implementing management strategies. Methods based on the morphology of adults, isozymes phenotypes and DNA analysis can be used for the diagnosis of RKN. Traditionally, RKN species are identified by the analysis of the perineal patterns and esterase phenotypes. For both procedures, mature females are required. Over the last few decades, accurate and rapid molecular techniques have been validated for RKN diagnosis, including eggs, juveniles and adults as DNA sources. Here, we emphasized the methods used for diagnosis of RKN, including emerging molecular techniques, focusing on the major species reported in Brazil. Key words: DNA, esterase, Meloidogyne, molecular biology, morphological pattern. Métodos diagnósticos usados na identificação de espécies do nematoide das galhas do Brasil RESUMO: A identificação acurada de espécies do nematoide das galhas (NG) (Meloidogyne spp.) é essencial para a implementação de estratégias de manejo. -
Prioritising Plant-Parasitic Nematode Species Biosecurity Risks Using Self Organising Maps
Prioritising plant-parasitic nematode species biosecurity risks using self organising maps Sunil K. Singh, Dean R. Paini, Gavin J. Ash & Mike Hodda Biological Invasions ISSN 1387-3547 Volume 16 Number 7 Biol Invasions (2014) 16:1515-1530 DOI 10.1007/s10530-013-0588-7 1 23 Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media Dordrecht. This e-offprint is for personal use only and shall not be self- archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Biol Invasions (2014) 16:1515–1530 DOI 10.1007/s10530-013-0588-7 ORIGINAL PAPER Prioritising plant-parasitic nematode species biosecurity risks using self organising maps Sunil K. Singh • Dean R. Paini • Gavin J. Ash • Mike Hodda Received: 25 June 2013 / Accepted: 12 November 2013 / Published online: 17 November 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract The biosecurity risks from many plant- North and Central America, Europe and the Pacific parasitic nematode (PPN) species are poorly known with very similar PPN assemblages to Australia as a and remain a major challenge for identifying poten- whole. -
ABSTRACT SCHWARZ, TANNER. Distribution
ABSTRACT SCHWARZ, TANNER. Distribution, Virulence, and Sweetpotato Resistance to Meloidogyne enterolobii in North Carolina. (Under the direction of Dr. Eric Davis). Meloidogyne enterolobii is an aggressive root-knot nematode (RKN) species that has been detected in North Carolina (NC) within the last decade. Its ability to infect a wide range of host plants and overcome root-knot nematode resistance genes has threatened economic crop production. In collaboration with the North Carolina Department of Agriculture (NCDA) Nematode Assay Lab, DNA from RKN samples from economic crops grown in the eastern-half of North Carolina were analyzed by polymerase chain reaction (PCR) to assay for the presence of M. enterolobii. This species was detected in Columbus, Sampson, Harnett, Johnston, Wayne, Greene, Wilson, and Nash counties in this survey. Three populations of M. enterolobii from NC sweetpotato farms, and one population from a NC soybean farm have been cultured on roots of greenhouse tomato plants (Lycopersicon lycopersicum L.). A study to assess potential differences in virulence among the four cultured North Carolina populations of M. enterolobii on six selected sweetpotato [Ipomoea batatas (L.) Lam.] genotypes found no difference in virulence among the four populations of M. enterolobii that were tested. Potential resistance to M. enterolobii in 91 selected sweetpotato genotypes was evaluated in greenhouse experiments. Genotype susceptibility to M. enterolobii was assessed as the number of nematode eggs per gram of root. Sweetpotato genotype was significantly different (P ˂ 0.001) for gall rating, total eggs, and eggs per gram of root based on mean separations, and based upon Fisher’s LSD t test (alpha=.05), sweetpotato genotypes that supported 500 eggs/gram root or less were classified as resistant to M.