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Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), is a devasting disease that leads to significant yield losses. Although QTLs originating from three wild species (Solanum arcanum, S. habrochaites, and S. pimpinellifolium) were identified, none of the QTLs was annotated for candidate gene identification. In the present study, a QTL-based physical map was constructed to reveal the meta-QTLs for Cmm resistance. As a result, seven major QTLs were mapped. Functional annotation of QTLs revealed 48 candidate genes. Additionally, experimentally validated Cmm resistance-related genes based on transcriptomic and proteomic studies were mapped in the genome and 25 genes were found to be located in the QTL regions. The present study is the first report to construct a physical map for Cmm resistance QTLs and identify QTL-specific candidate genes. The candidate genes identified in the present study are valuable targets for fine mapping and developing markers for marker-assisted selection in tomatoes for Cmm resistance breeding.

Bu çalışma, Clavibacter michiganensis subsp. michiganensis (Cmm)’in tohum, toprak ve bitki artıklarındaki yaşam süresini belirlemek amacıyla yapılmıştır. Patojenin tohumdaki yaşam süresi için, rifampicin’e dayanıklı Cmm izolatı ile bulaştırılan tohumlar aylık periyotlarda besi yerlerine ekilerek, enfekteli tohum oranı belirlenmiştir. Ayrıca, tohumlardaki inokulumun hastalığı başlatma yeteneğini belirlemek amacıyla tohumlardan gelişen bitkilerde hastalık gözlemi yapılmıştır. Cmm’in topraktaki yaşam süresi için, Cmm ile bulaştırılan toprak, kutular içerisinde deneme alanına gömülmüş, yaz ve kış ayları boyunca alınan örneklerde bakteri yoğunluğu hesaplanmıştır. Bitki artıklarındaki yaşam süresi için, Cmm ile enfekteli bitki parçaları toprağa gömülmüş ve aylık periyotlarda örneklemeler yapılarak bakteri yoğunluğu hesaplanmıştır. Yapılan çalışma sonuçlarına göre, Cmm ile bulaştırılmış tohumlarda 0. gün %100’lük bir bulaşıklık belirlenirken, bu oran aylık periyotlarda düzenli olarak azalmıştır. En son 370. günde %17’lik bir bulaşıklık tespit edilirken, 400. günde etmene rastlanılmamıştır. Etmenin bulaşık topraklarda, yaz aylarında 15 gün, kış aylarında 30 gün canlı kalabildiği, toprakta bulunan bitki artıklarında ise 30 gün canlı kalabildiği belirlenmiştir. 12 aylık periyotta ilk ay patojen tespit edilirken, diğer aylarda etmen elde edilememiştir. Sonuç olarak, Tokat ilinde etmenin toprak ve bitki artıklarında canlılığını sürdüremediği, bulaşık tohumların birincil inokulum kaynağı oluşturduğu ve tohumlardaki inokulumun hastalığı başlatacak yeteneğe sahip olduğu belirlenmiştir. Bundan dolayı hastalık ile mücadelede başlangıç inokulumunu azaltmak için temiz tohum kullanımı önem arz etmektedir. This study was conducted to determine survival of Clavibacter michiganensis subsp. michiganensis (Cmm) in infested seed, soil, plant residue. Infected seeds rates were determined by plating seeds, which were infected with rifampicin-resistant Cmm isolate, on medium at monthly intervals. Also, seeds were planted and disease observations were made in plants to determine the ability of seed inocula to initiate disease. Infested soil was buried in test area within container and the bacterial density was calculated in samples taken during summer and winter months. Cmm-infected plant parts were buried in the soil and bacterial density was calculated by sampling in monthly periods. Based on the results of study, the survival rate of the pathogen in infected seed were decreased with increase in storage periods. The lowest survival rate of 17% was determined at the end of 370 day, but on the 400th day, Cmm was not recovered from infected seeds. It has been determined that pathogen could survive in infested soil for 15 and 30 days in summer and winter periods, respectively. Also, Cmm could survive for 30 days in plant residues in the soil. As a result, it has been determined that Cmm could not survive in soil and plant residues in Tokat province. However, it has been determined that the infected seeds are primary inoculum source and that inoculum in the seeds has ability to initiate disease. Therefore it is important to use clean seeds to reduce initial inoculum for disease management.

Clavibacter michiganensis subsp. michiganensis (Cmm) strains, collected in greenhouses from 17 farms during tomato bacterial canker outbreaks occurring between 2005 and 2008 in Sicily, were analysed by a multiphasic approach. Population studies were conducted to investigate the possible sources of inocula. Cmm strains were characterized by PCR assays targeting virulence genes, fingerprinting techniques, metabolic profiles and virulence. These strains were comparatively analysed with Cmm strains isolated in other parts of Italy over a period of 15 years. Chromosomal genes encoding virulence determinants tomA, ppaA, chpC, and the plasmid-encoded genes pat-1 and celA were detected by PCR in all tested strains, except for four Sicilian Cmm strains where the pat-1 gene was not amplified. Using BOX-PCR, Cmm strains were differentiated into 13 haplotypes and clonal populations were identified. Cmm strains isolated from different farms in 2008 showed the same BOX-PCR haplotype. A distinct BOX-PCR haplotype was obtained from atypical Cmm strains lacking pat-1 and isolated in 2006/7 from three farms. Cmm strains with two different haplotypes were detected in one farm, whereas the other farms contained strains with only a single haplotype. A new fAFLP protocol based on the amplification of ApaI/MseI fragments was developed and was able to differentiate C. michiganensis subspecies. Different populations were delineated for the multiple outbreaks occurring in Sicily, whereas similar populations were recorded in other Italian regions over a period of 12 years. The results are consistent with previous studies that demonstrate that Cmm outbreaks are associated with propagation material.

Bu çalışmada, E.Ü.Z.F.Tarla Bitkileri Bölümü tarafından klon seleksiyonu yöntemi ile geliştirilen 14 farklı kekik (Origanum onites L.) klonunun bazı kalite özellikleri ve bakteriyel etmenlere karşı antimikrobiyal etkilerinin belirlenmesi amaçlanmıştır. Bu amaç doğrultusunda araziden hasat edilen bitkilerin yapraklarından elde edilen uçucu yağların analizi yapıldıktan sonra bu yaprakların ekstraktları ile uçucu yağların Clavibacter michiganensis subsp. michiganensis patojenine karşı olası in vitro antibakteriyel etkilerinin araştırılması gerçekleştirilmiştir. Böylelikle elde edilen pozitif sonuçlar, özellikle domateste hastalığa yol açan ve tam anlamıyla kimyasal savaşımı mümkün olmayan bu tehlikeli patojene karşı doğal yoldan bir mücadele yöntemini ortaya koymuştur. Ayrıca bu araştırmada, 14 O. onites genotipinin kimıyasal bileşimleri hakkında elde edilen bilgiler ile farklı uçucu yağ içeren bu klonlar arasında seçim yapılmıştır. Çalışmanın sonuçlarına göre tüm klonlar arasında birinci biçimde 5 nolu klon ve ikinci biçimde ise 11 nolu klonun daha iyi bir kaliteye sahip olduğu belirlenmiştir. Üç nolu klonun uçucu yağı birinci biçimde ve 7 nolu klonun uçucu yağı ikinci biçimde en yüksek antibakteriyel etkiyi göstermişlerdir., In this study, quality properties and the antibacterial activity against bacterial factors of 14 different Oregano (Origanum onites L.) clones have been determined. Clones were developed by clonal selection method of Agriculture Faculty of Ege University, Department of Agronomy. For this purpose, at first, the analysis of the essential oils obtained from the leaves of the plants harvested from the field was carried out. Subsequently, possible antibacterial effect of leaves extracts and their essential oils on clavibacter michiganensis subsp. michiganensis pathogens was investigated. In addition, based on the chemical composition conducted in the present study. The opportunity to select clones containing different types of essential oils has been revealed. According to the results, among the 14 clones considered in this study, in the first harvest, clone No. 5 and in the second harvest clone No.11 showed better quality. On the other hand, from antibacterial activity point of view, in the first harvest clone No. 3 and in the second harvest clone No. 7 showed the highest antibacterial activity. As a result, a natural method has been revealed to prevent development of dangerous pathogens which cause disease in tomatoes and have not any non-chemical treatment.

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes wilt and canker disease of tomato (Solanum lycopersicum). Mechanisms of Cmm pathogenicity and tomato response to Cmm infection are not well understood. To explore the interaction between Cmm and tomato, multidimensional protein identification technology (MudPIT) and tandem mass spectrometry were used to analyze in vitro and in planta generated samples. The results show that during infection Cmm senses the plant environment, transmits signals, induces, and then secretes multiple hydrolytic enzymes, including serine proteases of the Pat-1, Ppa, and Sbt familes, the CelA, XysA, and NagA glycosyl hydrolases, and other cell wall-degrading enzymes. Tomato induction of pathogenesis-related (PR) proteins, LOX1, and other defense-related proteins during infection indicates that the plant senses the invading bacterium and mounts a basal defense response, although partial with some suppressed components including class III peroxidases and a secreted serine peptidase. The tomato ethylene-synthesizing enzyme ACC-oxidase was induced during infection with the wild-type Cmm but not during infection with an endophytic Cmm strain, identifying Cmm-triggered host synthesis of ethylene as an important factor in disease symptom development. The proteomic data were also used to improve Cmm genome annotation, and thousands of Cmm gene models were confirmed or expanded.

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