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Key message: Whole-genome QTL mining and meta-analysis in tomato for resistance to bacterial and fungal diseases identified 73 meta-QTL regions with significantly refined/reduced confidence intervals. Tomato production is affected by a range of biotic stressors, causing yield losses and quality reductions. While sources of genetic resistance to many tomato diseases have been identified and characterized, stability of the resistance genes or quantitative trait loci (QTLs) across the resources has not been determined. Here, we examined 491 QTLs previously reported for resistance to tomato diseases in 40 independent studies and 54 unique mapping populations. We identified 29 meta-QTLs (MQTLs) for resistance to bacterial pathogens and 44 MQTLs for resistance to fungal pathogens, and were able to reduce the average confidence interval (CI) of the QTLs by 4.1-fold and 6.7-fold, respectively, compared to the average CI of the original QTLs. The corresponding physical length of the CIs of MQTLs ranged from 56 kb to 6.37 Mb, with a median of 921 kb, of which 27% had a CI lower than 500 kb and 53% had a CI lower than 1 Mb. Comparison of defense responses between tomato and Arabidopsis highlighted 73 orthologous genes in the MQTL regions, which were putatively determined to be involved in defense against bacterial and fungal diseases. Intriguingly, multiple genes were identified in some MQTL regions that are implicated in plant defense responses, including PR-P2, NDR1, PDF1.2, Pip1, SNI1, PTI5, NSL1, DND1, CAD1, SlACO, DAD1, SlPAL, Ph-3, EDS5/SID1, CHI-B/PR-3, Ph-5, ETR1, WRKY29, and WRKY25. Further, we identified a number of candidate resistance genes in the MQTL regions that can be useful for both marker/gene-assisted breeding as well as cloning and genetic transformation. [ABSTRACT FROM AUTHOR]

Soft rot‐inducing bacterial pathogens are considered among the main biotic constraints on vegetables and annual crops. Most of the bacterial soft rot pathogens are members of Pectobacterium spp. and Dickeya, with the former genus encompassing a continuously increasing number of species varying in geographic distribution and host of isolation. In Iran, Pectobacterium species have rarely been investigated using high‐throughput nucleotide sequence‐based techniques, leaving the genetic diversity of these pathogens mostly undetermined. During 2021, vegetables and annual crops with symptoms of soft rot and maceration were collected from Fars, Hamedan, Isfahan, Khuzestan and Kohgiluyeh‐Boyer‐Ahmad provinces of Iran. Forty‐four pectinolytic bacterial strains were isolated from symptomatic tissues of bell pepper, cabbage, carrot, lettuce, potato and zucchini. The bacterial strains were subjected to pathogenicity and host range assays, specific PCR tests and phylogenetic analysis of three housekeeping genes (dnaX, gapA and leuS). All strains were pathogenic on their host of isolation. Among the 44 pectinolytic strains, 26 strains were identified as members of Pectobacterium based on PCR using the primer pair Y1/Y2. Multilocus sequence analysis confirmed the latter bacterial strains belonging to the genus Pectobacterium and revealed that the strains scattered into four species: P. brasiliense (five strains), P. carotovorum (eight strains), P. polaris (five strains) and P. versatile (eight strains). P. polaris and P. versatile have not previously been reported in the country. Host range assays showed that P. brasiliense and P. carotovorum have a broader host range than the other two species. [ABSTRACT FROM AUTHOR]

Root-knot nematodes (Meloidogyne spp.) are dangerous parasites of many crops worldwide. The threat of chemical nematicides has led to increasing interest in studying the inhibitory effects of organic amendments and bacteria on plant-parasitic nematodes, but their combination has been less studied. One laboratory and four glasshouse experiments were conducted to study the effect on M. javanica of animal manure, common vermicompost, shrimp shells, chitosan, compost and vermicompost from castor bean, chinaberry and arugula, and the combination of arugula vermicompost with some bacteria, isolated from vermicompost or earthworms. The extract of arugula compost and vermicompost, common vermicompost and composts from castor bean and chinaberry reduced nematode egg hatch by 12–32% and caused 13–40% mortality of second-stage juveniles in vitro. Soil amendments with the combination vermicompost of arugula + Pseudomonas. resinovorans + Sphingobacterium daejeonense + chitosan significantly increased the yield of infected tomato plants and reduced nematode reproduction factor by 63.1–76.6%. Comparison of chemical properties showed that arugula vermicompost had lower pH, EC, and C/N ratio than arugula compost. Metagenomics analysis showed that Bacillus, Geodermatophilus, Thermomonas, Lewinella, Pseudolabrys and Erythrobacter were the major bacterial genera in the vermicompost of arugula. Metagenomics analysis confirmed the presence of chitinolytic, detoxifying and PGPR bacteria in the vermicompost of arugula. The combination of arugula vermicompost + chitosan + P. resinovorans + S. daejeonense could be an environmentally friendly approach to control M. javanica. [ABSTRACT FROM AUTHOR]

Bacterial canker and spot of stone fruits and bacterial blight of walnut, caused by different pathovars of Xanthomonas arboricola, namely X. arboricola pv. pruni and X. arboricola pv. juglandis, respectively, are considered among quarantine or regulated (nonquarantine) agents in different countries. The two pathogens were initially reported in Iran in 2005 and 1977, respectively. However, the precise identity, pathogenicity status and geographic distribution of these pathogens have been questioned. In this study, we have employed a series of comprehensive field surveys and samplings over a course of 5 years (2015–2019) across 16 provinces to reassess and clarify the occurrence and distribution of X. arboricola on fruit and nut trees in Iran. Besides dozens of non‐Xanthomonas and nonpathogenic bacterial strains, 27 X. arboricola strains were isolated from stone fruits (n = 13) and walnut (n = 14). Except for the strains Peh35, Peh78 and Peh79, the stone fruit strains were nonpathogenic on their host of isolation as well as several other plant species, while the walnut strains were pathogenic on their host of isolation. Multilocus sequence analysis (MLSA) of four housekeeping genes, atpD, dnaK, gyrB and rpoD, revealed that among the stone fruit strains only Peh78 and Peh79 could be assigned into X. arboricola pv. pruni, while the walnut strains were identified as X. arboricola pv. juglandis. Based on the results of pathogenicity assays and phylogenetic analyses, we confirm the occurrence of X. arboricola pv. juglandis in Iran, while X. arboricola pv. pruni was absent in the plant samples evaluated in this study. [ABSTRACT FROM AUTHOR]

Background: Common bean (Phaseolus vulgaris) is considered a staple food in a number of developing countries. Several diseases attack the crop leading to substantial economic losses around the globe. However, the crop has rarely been investigated for multiple disease resistance traits using Meta-analysis approach. Results and conclusions: In this study, in order to identify the most reliable and stable quantitative trait loci (QTL) conveying disease resistance in common bean, we carried out a meta-QTL (MQTL) analysis using 152 QTLs belonging to 44 populations reported in 33 publications within the past 20 years. These QTLs were decreased into nine MQTLs and the average of confidence interval (CI) was reduced by 2.64 folds with an average of 5.12 cM in MQTLs. Uneven distribution of MQTLs across common bean genome was noted where sub-telomeric regions carry most of the corresponding genes and MQTLs. One MQTL was identified to be specifically associated with resistance to halo blight disease caused by the bacterial pathogen Pseudomonas savastanoi pv. phaseolicola, while three and one MQTLs were specifically associated with resistance to white mold and anthracnose caused by the fungal pathogens Sclerotinia sclerotiorum and Colletotrichum lindemuthianum, respectively. Furthermore, two MQTLs were detected governing resistance to halo blight and anthracnose, while two MQTLs were detected for resistance against anthracnose and white mold, suggesting putative genes governing resistance against these diseases at a shared locus. Comparative genomics and synteny analyses provide a valuable strategy to identify a number of well‑known functionally described genes as well as numerous putative novels candidate genes in common bean, Arabidopsis and soybean genomes. [ABSTRACT FROM AUTHOR]

The Gram-negative bacterium Xanthomonas translucens infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven X. translucens strains representing an entire set of genetic diversity of two pathovars X. translucens pv. undulosa and X. translucens pv. translucens is provided and compared with those of seven publicly available complete genomes of the pathogen. Organization of the 25 type III secretion system genes in all the 14 X. translucens strains was exactly the same, while TAL effector genes localized singly or in clusters across four loci in X. translucens pv. translucens and five to six loci in X. translucens pv. undulosa. Beside two previously unreported endogenous plasmids in X. translucens pv. undulosa , and variations in repeat variable diresidue (RVD) of the 14 strains, tal1a of X. translucens pv. translucens strain XtKm8 encode the new RVDs HE and YI which have not previously been reported in xanthomonads. Further, a number of truncated tal genes were predicted among the 14 genomes lacking conserved Bam HI site at N-terminus and Sph I site at C-terminus. Our data have doubled the number of complete genomes of X. translucens clarifying the population structure and genomics of the pathogen to pave the way in the small grain cereals industry for disease resistance breeding in the 21st century's agriculture. [ABSTRACT FROM AUTHOR]

During July 2015 to June 2017, 63 walnut and 94 stone fruit orchards were surveyed in Iran to identify and characterize the causal agent of a disease inducing leaf spot and fruit canker symptoms. Altogether, 189 Prunus spp. and 141 walnut samples (i.e. leaves, branches and fruits) were collected from 10 Provinces in northern, northwestern, central and southern Iran. Forty-three yellow-pigmented Gram-negative bacterial isolates were recovered from symptomatic plants. Only seven bacterial strains isolated from walnut in Mazandaran and Golestan Provinces were identified as X. arboricola pv. juglandis based on pathogenicity assays, specific PCRs, and multilocus sequence analysis. Based on the phenotypic features and phylogenetic analysis of gyrB gene sequences, strains isolated from stone fruit trees were identified as multiple Pantoea species (i.e. P. agglomerans, P. ananatis, P. vagans and P. pleuroti). None of these strains caused symptoms on Prunus spp. plantlets tested under greenhouse conditions. Although the occurrence of bacterial blight of walnut in Iran was ascertained using molecular-phylogenetic analysis, no evidence was obtained that the observed disease was the same as the bacterial spot and canker of stone fruits caused by X. arboricola pv. pruni in the country. [ABSTRACT FROM AUTHOR]

Xanthomonas perforans is the causal agent of bacterial spot, one of the most devastating diseases of tomato that results in considerable yield losses worldwide. Rutin, as a polyphenolic substance, was used to induce resistance in tomato against X. perforans. Rutin at concentration of 2 mM had ability to reduce the disease severity of bacterial spot. On the other hand, 2 mM rutin had no antibacterial activity in vitro. Expression profiling of pathogenesis-related gene 5 (PR-5), Phenylalanine ammonia-lyase (PAL) and lipoxygenase (LOX) was probed during the enhanced resistance by rutin. Pretreatment with rutin (rutin/ X. perforans) led to induction of PR-5, PAL and LOX compared to controls (water/ X. perforans). Our results suggest that rutin-induced resistance against X. perforans in tomato might be mediated through stimulation of some defense genes such as PR-5, PAL and LOX. [ABSTRACT FROM AUTHOR]

In autumn 2011, a survey was conducted for the identification of plant pathogenic bacteria affecting Cucurbitaceae grown in southwestern Iran. Squash (Cucurbita pepo var. styriaca) plants with suspected bacterial symptoms, i.e. necrotic spots surrounded by chlorotic haloes, were collected and brought to the laboratory for further analysis. Two Gram-negative, red-pigmented bacterial strains were isolated from squash leaves in Shushtar county, Khuzestan province. The isolates induced hypersensitive reaction (HR) on tobacco plants 24 h post-inoculation. A pathogenicity test on 25-day-old squash plants yielded symptoms consisting of necrotic spots surrounded by chlorotic haloes that appeared 5-10 days post-inoculation. The causal agent was identified as Serratia marcescens based on biochemical and phylogenetic analyses. Phylogenetic analysis of 16S rRNA, gyrB and groE genes sequences showed that the isolates have 99-100% similarity with S. marcescens strains previously described as pathogenic to bell pepper and corn plants. Although non-pigmented strains of S. marcescens have previously been described as the causal agents of cucurbit yellow vine disease, this is the first report of a HR-inducing red-pigmented strain of the bacterium associated with squash leaf chlorosis and necrosis. [ABSTRACT FROM AUTHOR]

The goal of this study was to investigate the role of lipopolysaccharides (LPS) in induction of resistance in tomato against the causal agent of bacterial spot,Xanthomonas perforans. The results showed that pre-treatment with LPS leads to enhancing resistance of tomato againstX. perforans. In addition, expression profiling of β-1,3-glucanase (BGL), Phenylalanine ammonia-lyase (PAL) and catalase (CAT) was examined during the induced resistance by LPS. The effect of LPS on induction ofBGL,PALandCATwas demonstrated in the present study. The data suggest that the effect of LPS on resistance of tomato againstX. perforanscould be through activation of some defence genes such as ofBGL,PALandCATwhich afford defence responses against the pathogen. Our findings might help to better understanding the molecular bases of the induced resistance by LPS. [ABSTRACT FROM PUBLISHER]

We report in this study for the first time the occurrence of bacterial spot of pepper in Iran and both phenotypic and genetic characterization of its causal agent, Xanthomonas euvesicatoria. Pepper plants grown in 15 of 30 surveyed private gardens and commercial fields were infected by the pathogen in Marand County, East Azerbaijan Province, north-western Iran. The obtained strains of X. euvesicatoria had different amylolytic and pectolytic activities compared with those reported for this species elsewhere. Pathogenicity tests showed that strains isolated from diseased pepper are able to infect tomato, in addition to pepper. Host range of the pathogen was assessed on eight annual plant species including crops and weeds by measuring the population dynamics. The host range assessment showed that in addition to pepper and tomato, known hosts of X. euvesicatoria, the Iranian strains were able to colonize a number of new hosts such as nightshade and common bean. In contrast, none of them were able to build up their population on cowpea, eggplant, bindweed and zucchini. All X. euvesicatoria strains obtained in this study were sensitive to copper sulphate and streptomycin at concentrations higher than 20 and 50 mg/l, respectively. Phylogenetic analyses of the strains using the sequences of gyrB and hrpB genes confirmed their species as X. euvesicatoria. Given a direct commercial trade of fresh solanaceous vegetables between Iran and Turkey, it is hypothesized that the pathogen entered north-western Iran from eastern parts of Turkey through infected plant materials. Finally, the role of prevention - based on the use of healthy planting materials and resistant and/or tolerant plant varieties - to contain the potential disease epidemics is discussed. [ABSTRACT FROM AUTHOR]

Pectobacteria are one of the most important groups of plant pathogenic bacteria which occur world-wide. The bacteria have a wide host range and infect plants with fleshy organs. Thirty five bacterial isolates were collected from potato, cabbage, sugar beet, pepper, carrot, onion, cucumber, turnip, and tomato host plants cultivated in Fars province. The bacteria were identified using biochemical and physiological tests. The genetic diversity among the isolates was evaluated using RAPD assay. The isolates were rod-shape, gram-negative, facultative anaerobes, oxidase-negative, catalase-positive, and had ability to rot the potato, while they could not induce hypersensitive reaction on tobacco leaf. All of isolates were identified as soft-rot bacteria. Based on phenotypic criteria, the isolated strains were categorized into three groups. The strains of first, second and third groups were related to Pectobacterium carotovorum subsp. carotovorum, Pectobacterium betavascularum and Dickeya chrysanthemi, respectively. According to RAPD assay and using six primers including 19300, 91200, OPB07, OPB08, OPB11, OPB18, isolates categorized in three groups. The used primers showed significant diversity among the strains and the specific primers GTGC4, GAGC4 and GTG5 confirmed the classification. The diversity among the isolates has been confirmed based on the molecular works and clustering based on RAPD. This is the first RAPD assay to investigate the genetic diversity of soft-rot bacteria. [ABSTRACT FROM AUTHOR]

Stem rot of tomato caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) results in economic yield loss worldwide. Previous studies have demonstrated the role of β-aminobutyric acid (BABA) in control of numerous plant diseases. To extend our understanding for the efficacy of BABA as an inducer agent against plant diseases, we evaluated the effect of BABA on disease severity of stem rot during infection of tomato by Pcc. BABA at concentration of 200 µM reduced the disease severity and offered protection against Pcc. On the other hand, BABA did not have direct antibacterial effect in vitro. Furthermore, we examined the effects of BABA on expression of pathogenesis-related gene 1 (PR-1), pathogenesis-related gene 2 (PR-2), phenylalanine ammonia-lyase (PAL) and catalase (CAT). Pretreatment with BABA led to more expression of PR-1 and PR-2 after Pcc infection when compared with their counterparts pretreated with water (control). PR-1 expression in BABA/Pcc treatment increased 2.83-, 4.31-, 2.46- and 1.88-fold at 24, 48, 72 and 96 h postpathogen inoculation (hpi), respectively, compared to water/Pcc treatment. Moreover, PR-2 expression in BABA/Pcc treatment increased 2.66-, 3.43-, 2.19- and 1.91-fold at 24, 48, 72 and 96 hpi, respectively, compared to water/Pcc treatment. On the other hand, PAL expression was transient during enhanced resistance by BABA. In comparison with water/Pcc treatment, PAL expression enhanced 2.42-fold at 24 hpi in BABA/Pcc treatment, whereas PAL expression was remained unchanged at 48, 72 and 96 hpi. CAT expression increased in early stages of the resistance induced by BABA. In BABA/Pcc treatment, CAT expression enhanced 4.6- and 3.1-fold at 24 and 48 hpi, respectively, compared to water/Pcc treatment. Our data confirmed the role of BABA as an effective resistance inducer against Pcc that might be considered in integrated diseases management programs. [ABSTRACT FROM AUTHOR]

Bacterial blight of common bean caused by Xanthomonas axonopodis pv. phaseoli (Xap) is one of the most devastating diseases and causes serious yield losses worldwide. To extend our understanding for the efficacy of salicylic acid (SA) as a therapeutic agent against bacterial diseases, we have studied the impact of exogenous SA treatment on disease incidence and development during the course of Xap infection. In this study, an enhanced resistance response induced by SA was detected in common bean infected with Xap. On the other hand, SA did not have direct antibacterial effect in vitro. Additionally, we examined the effects of SA on expression of superoxide dismutase (SOD), malate dehydrogenase (MDH) and phenylalanine ammonia-lyase (PAL). SA-pretreated leaves had higher expression of MDH after Xap infection when compared with their counterparts pretreated with water (control). SA/Xap treatments showed more expression of SOD at 24, 48 and 72 h post-pathogen inoculation (hpi) compared to water/Xap samples, whereas PAL expression was significantly different only at 24 hpi. The results showed the contribution of SA as an effective resistance activator and may provide an additional approach in bacterial blight integrated diseases management programs. [ABSTRACT FROM AUTHOR]

Members of the genus Pseudomonas bacterium are of great interest because of their importance in plant disease. In this study, DNA fingerprints of 60 strains of Pseudomonas bacteria including three species of Pseudomonas syringae ( Pseudomonas syringae pv. syringae ( Pss) and Pseudomonas syringae pv. Lachrymans ( Psl)), Pseudomonas savastanoi ( Psa) and Pseudomonas tolaasii ( Pt) were used for developing a robust predictive classification model. The DNA fingerprints were obtained by repetitive polymerase chain reaction (Rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindromes (REP), and BOXAIR primers. The classification results of counter propagation artificial neural network (CP-ANN) modeling indicated that a combination of Rep-PCR fingerprinting and chemometrics analysis can be used as an effective and powerful methodology to differentiate species of Pseudomonas and pathovars of P. syringae strains based on a predictive model. • A robust classification model was introduced for classification of Pseudomonas species • Genetic diversity of the Iranian Pseudomonas strains was evaluated by cluster analysis • Combinatorial use of Rep-PCR with classification algorithms was successful [ABSTRACT FROM AUTHOR]

Pseudomonas syringaepv.syringae(Pss) strains were isolated from almond, apricot, peach, pear, sweet cheery and wheat in Kohgiluye and Boyer-Ahmad, Kordestan, Fras and Chaharmahal and Bakhtiari provinces of Iran. The strains were examined for host specificity, the presence of virulence genes and pathogenicity on different hosts. After inoculation of isolates, in compatible reactions bacterial populations increased within six days of inoculation and final cell numbers increased several-fold over initial inoculum levels, but in incompatible reactions, bacterial populations declined within four days of inoculation. Almond, sweet cherry and wheat isolates induced progressive necrotic symptoms on almond leaves and stems. Apricot, peach and sweet cherry isolates induced necrotic lesions when inoculated on apricot leaves. On pear leaves and stems, only the pear isolate incited pathogenic reaction and isolates from other hosts did not. ThesyrBgene was detected in all of the tested isolates. Almond and pear isolates did not have thesyrDgene. ThesypAgene was detected in the almond, peach, pear and sweet cherry isolates while thesypBgene was detected in the apricot, peach, sweet cherry and wheat isolates. Almond, apricot, pear and wheat isolates gave negative results for the detection ofnitgene. The geneAch, was detected only in the peach isolate and genehrmA, was detected only in the wheat isolate. This study indicates that host specificity exists among differentPssstrains, and genes responsible for syringomycin and syringopeptin production contribute to the virulence ofPssstrains. [ABSTRACT FROM AUTHOR]

During 2007-2009, 170 bacterial isolates were obtained from wilting potato and tomato plants from Iran. Specific polymerase chain reaction (PCR) analyses identified all the isolates as Ralstonia solanacearum. Diversity among the Iranian isolates was determined by a study based on biovar determination, pathogenicity, repetitive sequence PCR and phylotype classification. On the basis of genotypic, phenotypic and pathogenic characteristics two distinct clusters obtained. Cluster I comprised all biovar 2 isolates and cluster II comprised all biovar N2 (2T) isolates. Phylotype-specific multiplex PCR (pmx-PCR) indicated that all biovar 2 and N2 belong to phylotype II. This is the first report of phylotype determination of biovars of R. solanacearum with pmx-PCR in Iran. [ABSTRACT FROM AUTHOR]

During 2005-2006, 42 soft rot bacterial strains were isolated from the infected tubers of potato, roots of carrot, sugar beet and turnip, and the leaves of lettuce and cabbage with soft rot symptoms in Iran. The isolates were rod-shaped, motile with peritrichous flagella, gram negative, facultative anaerobe, oxidase and urease negative and they rotted potato tuber slices. Of the 42 isolates, 20 were identified as Pectobacterium carotovorum subsp. carotovorum (Pcc), 6 as P. carotovorum subsp. odoriferum (Pco), 4 as P. betavasculorum (Pb) and 12 strains as Dickeya dadantii (Dda). PCR amplification of fingerprints of repetitive bacterial DNA elements using the REP, ERIC and BOX primers differentiated the soft rot bacteria to the species and sub-species level. Strains of Pcc and Dda were phenotypically and genotypically highly variable, but Pb and Pco strains had low variability. REP-PCR was found to be a promising genotypic tool for the rapid and reliable speciation and typing of soft rot bacteria.. [ABSTRACT FROM AUTHOR]

We compared lipoxygenase (LOX) expression in cucumber in response to host and non-host pathogens. Our results displayed significant difference in expression of LOX between compatible and incompatible interaction at 12, 24 and 48 h after inoculation. Moreover, LOX expression at 72 h after inoculation was similar in both compatible and incompatible interaction. It seems that early induction of LOX plays a crucial role in plant defense against pathogens. [ABSTRACT FROM AUTHOR]