Black rot, a disease of significance affecting vegetable Brassica crops, is primarily caused by the bacterium Xanthomonas campestris pv. campestris (Xcc). When the disease spreads extensively in the field, it can lead to substantial yield losses, particularly under favorable environmental conditions. Controlling the spread of this disease is challenging, and the primary approach involves utilizing resistant cultivars or disease-free seeds. Among the various methods available for identifying different Xcc races, Polymerase Chain Reaction (PCR)-based molecular markers have proven to be highly reliable. To date, the PCR method has successfully identified Xcc races 1 to 7. In this study, molecular markers were developed for races 4 and 9 through the sequencing and alignment of the whole genome sequences of Xcc races, closely related Xanthomonas campestris (Xc) pathovars, and two Xanthomonas species. These designed markers were subsequently validated by PCR with bacterial genomic DNA samples from Xcc races and 7 other bacteria. The results indicated successful amplification only for race 4 and race 9, yielding amplicon sizes of 1080 bp and 830 bp, respectively, while the other strains failed to amplify. Furthermore, the amplicons from races 4 and 9 were cloned and sequenced, confirming that both races exhibited matching sequences after alignment. Consequently, the molecular marker method offers a rapid and efficient means of differentiating between Xcc races 4 and 9 within a few hours, presenting itself as a viable alternative to conventional methods that rely on the use of differential cultivars of Brassicaceae for identifying Xcc races.

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• Development of molecular markers for the detection of Paracidovorax citrulli strains causing bacterial fruit blotch in watermelon
  San Ha Choe, Nihar Sahu, Ijaz Yaseen, Se Hyeon Jeong, Gyoung Hee Kim, Jong In Park, Hoy Taek Kim
  Canadian Journal of Plant Pathology.2026; 48(3): 220.     CrossRef
• An update to the molecular identification of Xanthomonas campestris disease causing pathogens in crucifers – A mini review
  Nihar Sahu, Masao Watanabe, Jong-In Park
  Physiological and Molecular Plant Pathology.2026; 142: 103102.     CrossRef
• Molecular marker development for specific amplification of Xanthomonas campestris pv. campestris race 8 causing black rot disease in Brassica crops
  Sopheap Mao, Yeo-Hyeon Kim, Nihar Sahu, Su-Won Kim, Hoy-Taek Kim, Masao Watanabe, Jong-In Park
  Journal of General Plant Pathology.2025; 91(1): 31.     CrossRef

Xanthomonas campestris pv. incanae (Xci) is the causal agent of bacterial blight disease in ornamental crucifers. We compared the whole genomes of closely related Xanthomonas campestris pv. campestris, incanae, raphani and four other species of Xanthomonas following comparative genomics approach. We found 82 singletons out of 4024 Xci genes upon comparison. Out of 82 singletons, top 10 were selected for designing Xci specific marker. Five primers; XCI_1F/R, XCI_2F/R, XCI_3F/R, XCI_5F/R and XCI_6F/R produced amplicons of 495 bp, 503 bp, 612 bp, 665 bp and 468 bp, respectively expected to detect Xanthomonas campestris pv. incanae (Xci). In conclusion, five effective markers were developed for the detection of Xci pathogen by whole genome alignment, which could be served as effective tools in seed quarantine.

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• An update to the molecular identification of Xanthomonas campestris disease causing pathogens in crucifers – A mini review
  Nihar Sahu, Masao Watanabe, Jong-In Park
  Physiological and Molecular Plant Pathology.2026; 142: 103102.     CrossRef

Cherry tomatoes are highly nutritious, flavory with a pleasant taste and are becoming increasingly popular to the consumers. The cherry tomato cv. ‘Minichal’ produced some dwarf plants along with normal plants. Lignin, a phenolic biopolymer is the key component of cell walls in plants. Here, we analyzed lignin biosynthesis-related genes in leaves, inflorescences and fruits of dwarf and normal cherry tomato plants by reverse-transcription quantitative PCR (RT-qPCR). Among analyzed genes, SlCCOAOMT1, SlCCOAOMT2, SlCCOAOMT3, SlF5H, and SlCOMT showed significantly higher expressions, in leaf and inflorescence of dwarf plants compared with the normal plants, while SlPAL1 showed a significantly higher expression only in the leaves. On the contrary, SlHCT and SlC3H showed significantly lower expression levels in the leaves and inflorescences of dwarf plants compared with normal ones. The results suggest that SlHCT and SlC3H might have an impact on the dwarf cherry tomato plants.

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• Joint Impacts of Meloidogyne incognita and Soil Nutrition on Solanum lycopersicum var. cerasiforme
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• Nutrients Regulate the Effects of Arbuscular Mycorrhizal Fungi on the Growth and Reproduction of Cherry Tomato
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Clubroot, caused by the obligate biotrophic protist Plasmodiophora brassicae is a devastating disease of crucifers that causes substantial economic loss worldwide. The disease is characterized by the formation of galls in the root and hypocotyl of infected plants which restricts host vascular cambium development inhibiting efficient water and nutrient uptake by the plant. The pathogen-driven interference of hormonal homeostasis, particularly of cytokinin, in the root tissue is intricately linked with induction of hypertrophy and cell divisions leading to formation of galls. Levels of cytokinins and cell division generally increase at the onset of the disease which declines at the later stages of gall formation. The genes involved cytokinin biosynthesis such as cytokinin oxidase/dehydrogenases and isopentenyl transferases shows differential expressions during clubroot infection and gall expansion in root tissues. Wider understanding of the roles of cytokinins and associated genes along the development of the disease will be helpful in unravelling plants defense mechanism against clubroot disease.

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  Haohui Yang, Xiaochun Wei, Weiwei Lei, Henan Su, Yanyan Zhao, Yuxiang Yuan, Xiaowei Zhang, Xixiang Li
  International Journal of Molecular Sciences.2024; 25(16): 8974.     CrossRef
• Bioinformatics and functional analysis of EDS1 genes in Brassica napus in response to Plasmodiophora brassicae infection
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• Genome-wide identification and analysis of cytokinin dehydrogenase/oxidase (CKX) family genes in Brassica oleracea L. reveals their involvement in response to Plasmodiophora brassicae infections
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• Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus
  Dinesh Adhikary, Anna Kisiala, Ananya Sarkar, Urmila Basu, Habibur Rahman, Neil Emery, Nat N V Kav
  Molecular Omics.2022; 18(10): 991.     CrossRef
• A Novel Target (Oxidation Resistant 2) in Arabidopsis thaliana to Reduce Clubroot Disease Symptoms via the Salicylic Acid Pathway without Growth Penalties
  Regina Mencia, Elina Welchen, Susann Auer, Jutta Ludwig-Müller
  Horticulturae.2021; 8(1): 9.     CrossRef
• Comparative transcriptome analysis of canola carrying clubroot resistance from ‘Mendel’ or Rutabaga and the development of molecular markers
  Aarohi Summanwar, Mehdi Farid, Urmila Basu, Nat Kav, Habibur Rahman
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• Expression and Role of Biosynthetic, Transporter, Receptor, and Responsive Genes for Auxin Signaling during Clubroot Disease Development
  Arif Hasan Khan Robin, Gopal Saha, Rawnak Laila, Jong-In Park, Hoy-Taek Kim, Ill-Sup Nou
  International Journal of Molecular Sciences.2020; 21(15): 5554.     CrossRef
• Demystifying biotrophs: FISHing for mRNAs to decipher plant and algal pathogen–host interaction at the single cell level
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• Expression and Role of Response Regulating, Biosynthetic and Degrading Genes for Cytokinin Signaling during Clubroot Disease Development
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  International Journal of Molecular Sciences.2020; 21(11): 3896.     CrossRef
• Biocontrol arsenals of bacterial endophyte: An imminent triumph against clubroot disease
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Black rot of Brassica crops is the most devastating disease which causes substantial yield reduction of cabbage throughout the world. The use of resistant cabbage cultivars could be inexpensive and effective measure to combat this destructive disease. We screened cabbage inbred lines for black rot disease resistance through bioassay and identified some novel lines that showed race-specific resistance to Xanthomonas campestris pv. campestris (Xcc) races. The pathogenicity test revealed that out of 27 cabbage lines, one (SCNU-C-4074), six (SCNU-C-3631, SCNU-C-3637, SCNU-C-3639, SCNU-C-4072, SCNU-C-4073 and SCNU-C-3273), two (SCNU-C-3273 and SCNU-C-4118), two (SCNU-C-3270 and SCNU-C-4118), two (SCNU-C-3470 and SCNU-C-41148) and four (SCNU-C-107, SCNU-C-3270, SCNU-C-3470 and SCNU-C-4059) were shown to be resistant to Xcc races 1, 2, 3, 5, 6 and 7, respectively while none of these showed resistance against race 4. Furthermore, these resistant and susceptible lines were evaluated by previously reported molecular markers for black rot resistance. The molecular screening results were also revealed the existence of race-specific resistance in these cabbage lines. This result will help Brassica breeder to develop race-specific black rot resistant cabbage cultivars.

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• Integrating Hybrid and Molecular Breeding as Approaches in Vegetable Breeding Strategies
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Powdery mildew disease caused by an obligatory parasitic fungus Podosphaera xanthii is a serious problem of melon (Cucumis melo L.) production worldwide. Severity of problem is further associated with emergence of new races over the years. In this study a new race of powdery mildew fungus was discovered from Ibaraki, Japan. The race was different from all other existing races of P. xanthii occurring in Japan. Phenotypic and genetic analysis established the new fungus type as a new race, N5. Ten melon lines were infected with a total of eight fungal races including the new N5 race and it was found that all melon lines had different disease reactions against the new race compared to other seven races. Only four melon genotypes were found resistant out of 42 commercial cultivars and lines were tested. Disease reactions of two sets of F₂ populations and one set of backcross population revealed that two separate epistatic gene loci located in two different linkage groups (LG), LG II and LG XII, interact together for the resistant or susceptible reaction of melon lines. A total of six simple sequence repeat (SSR) markers were found polymorphic in melon lines out of 16 tested in response to N5 race. Two different sets of F₂ populations between resistant and susceptible melon lines were assessed with two polymorphic SSR markers located in two different groups, LG II and LG XII. SSR genotyping yielded 78% and 94% expected polymerase chain reaction fragments in favor of resistance or susceptibility of F₂ populations of CM17187×PMR5 and PMR45×PMR5 of melon lines, respectively.

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• A survey of Podosphaera xanthii races in melon-producing regions in Rio Grande do Norte State, Brazil
  Anânkia de Oliveira Ricarte Marinho, Adriano Ferreira Martins, Francisco Linco de Souza Tomaz, Elaíne Welk Lopes Pereira Nunes, Denilson Eduardo Silva Dantas, Geovanna Alicia Dantas Gomes, Edicleide Macedo da Silva, Glauber Henrique de Sousa Nunes
  Journal of Plant Pathology.2025; 108(1): 777.     CrossRef
• Status, Gaps and Perspectives of Powdery Mildew Resistance Research and Breeding in Cucurbits
  Aleš Lebeda, Eva Křístková, Barbora Mieslerová, Narinder P. S. Dhillon, James D. McCreight
  Critical Reviews in Plant Sciences.2024; 43(4): 211.     CrossRef
• Identification of powdery mildew resistance quantitative trait loci in melon and development of resistant near-isogenic lines through marker-assisted backcrossing
  Chun-San Wang, Ssu-Yu Lin, Jin-Hsing Huang, Hsin-Yi Chang, Di-Kuan Lew, Yu-Hua Wang, Kae-Kang Hwu, Yung-Fen Huang
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• Identification of Gene Responsible for Conferring Resistance against Race KN2 of Podosphaera xanthii in Melon
  Sopheak Kheng, San-Ha Choe, Nihar Sahu, Jong-In Park, Hoy-Taek Kim
  International Journal of Molecular Sciences.2024; 25(2): 1134.     CrossRef
• Fine mapping and identification of candidate genes associated with powdery mildew resistance in melon (Cucumis melo L.)
  Xiaoyu Duan, Yue Yuan, Núria Real, Mi Tang, Jian Ren, Jiaqi Wei, Bin Liu, Xuejun Zhang
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• Inheritance of Resistance to Race 5 of Powdery Mildew Fungus Podosphaera xanthii in Melon and Development of Race 5-Specific High Resolution Melting Markers
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• Development of powdery mildew race 5-specific SNP markers in Cucumis melo L. using whole-genome resequencing
  Jewel Howlader, Yeji Hong, Sathishkumar Natarajan, Kanij Rukshana Sumi, Hoy-Taek Kim, Jong-In Park, Ill-Sup Nou
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• Genetic Mapping and Nucleotide Diversity of Two Powdery Mildew Resistance Loci in Melon (Cucumis melo)
  Cui Haonan, Ding Zhuo, Fan Chao, Zhu Zicheng, Zhang Hao, Gao Peng, Luan Feishi
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• PCR-Based InDel Marker Associated with Powdery Mildew-Resistant MR-1
  Yu-Ri Choi, Jae Yong Lee, Seongbin Hwang, Hyun Uk Kim
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• Identification of Two New Races of Podosphaera xanthii Causing Powdery Mildew in Melon in South Korea
  Ye-Ji Hong, Mohammad Rashed Hossain, Hoy-Taek Kim, Jong-In Park, Ill-Sup Nou
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Powdery mildew (PM) is a severe fungal disease for melon cultivation worldwide. Stress resistance related genes could be important tools to address this problem. In this study, we retrieved defense related peroxidase and glucan synthase genes from Melon Genome Database ‘Melonomics’. Thereafter, we analyzed the genes in silico. We conducted protein blast in the NCBI database and found a high degree of homology among them. Based on the highest protein homology we named two isoforms of Cucumis melo peroxidase 2-like genes (CmPrx2-1 and CmPrx2-2) and one glucan synthase1-like gene (CmGLS1). In reverse transcription- polymerase chain reaction (PCR), all 3 genes showed organ specific expression in a C. melo line, SCNU1154. Real-time quantitative PCR expression of these 3 genes was conducted in the infected leaf samples by PM fungus Podosphaera xanthii and also treated leaf samples by exogenous phytohormones (salicylic acid and methyl jasmonate). The CmPrx2-2 gene was up-regulated in response to all seven races of PM fungus whereas up-regulation or down-regulation of CmPrx2-1 gene was race-specific. The CmGLS1 gene was down-regulated in response to all races except one race. The CmPrx2-1, CmPrx2-2, and CmGLS1 genes were up-regulated under both salicylic acid and methyl jasmonate treatments but their level of expression was higher in salicylic acid treated plants compared to methyl jasmonate. Therefore, we speculate that defense response of the three tested genes is largely mediated by the salicylic acid signaling pathway under PM infection. Taken together, the data presented herein may be useful resources in the development of PM stress resistant in C. melo L.

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• Induction of defense related enzymatic and non-enzymatic antioxidants and their gene expression imparts resistance to muskmelon against Fusarium oxysporum f. sp. melonis infection
  Chahak Jain, Shilpa Gupta, Sat Pal Sharma, Manjeet Kaur Sangha, Navraj Kaur Sarao, Anu Kalia, Shabda Verma
  Journal of Plant Biochemistry and Biotechnology.2025; 34(4): 941.     CrossRef
• Magnaporthe grisea infection modifies expression of anti-oxidant genes in finger millet [Eleusine coracana (L.) Gaertn.]
  Jinu Jacob, Madhu Pusuluri, Balakrishna Domathoti, Indra Kanta Das
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Global population is increasing day-by-day, simultaneously, crop production need to increase proportionately. Whereas, increase crop production being restricted due to abiotic and biotic stresses. Abiotic stresses are adversely affected crop growth and development, leading to crop loss globally and thereby causing huge amount of economic loss as well. Contrary, pathogens are attacked the plants imposing biotic stress and severely hampers the yield. Therefore, it is prime need to understand the molecular mechanism and genes involved to minimize the biotic and abiotic stresses for mitigating the Brassica vegetable crop losses. The stress responsive, pathogens related genes are involved in tolerance or resistance to stress in plants that are cross-talk with different types of stress components in signal transduction pathways. The plants have their own mechanism to overcome biotic and abiotic stresses to follow the abscisic acid (ABA)-dependent and ABA-independent pathways. Several transcription factors such as WRKY, Alfin-like, MYB, NAC, DREB, CBF are integrating to various stress signals and controlling the gene expression through networking with their related cis-elements. To develop stress tolerance and/or resistant crops plants, there is need to realize both of the plant and pathogenic disease development mechanisms. Therefore, this article is focused on (i) major and devastating stresses on vegetable crops, (ii) role of genes to overcome the stresses, and (iii) differential genes expressed under biotic and abiotic stresses in Brassica oleracea and B. rapa for getting insight of the mechanisms of development of resistance lines.

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Rapeseed is a member of family Brassicaceae, cultivated as oil crop. Rapeseed oil is being utilized from early civilization, but its popularity being declined from the mid-nineteenth century due to presence of erucic acid (C22:1) and glucosinolates. Thereby, several attempts have been made to develop cultivars free from those toxins. In the past 20 years, breeders got success in developing ‘00’-quality rapeseed, known as ‘Canola’. The target mutagenesis of fae-1 and fae-2 of Brassica napus ensured such success. Thereafter, ‘canola’ regains its market as a healthy vegetable oil. Moreover, high oleic acid rapeseed lines, with 86% oleic acid, have been developed by using chemical mutagenesis of FAD2 alleles responsible for desaturation of oleic acid (C18:1) to linoleic acid (C18:2). Recently, high erucic acid rapeseed oil regained interest for biodegradable plastic, cosmetic, emollient industries and for biodiesel. Therefore, breeding approaches have been pursued; unfortunately, that were failed to reach erucic acid level beyond 50% in seed-oil. Rapeseed genotypes over-expressed with Ld-LPAAT separately and Ld-LPAAT-FAE chimaric construct together were tried but failed to reach the erucic acid content more than 60%. Thereof, combined effort of conventional breeding and transgenic approaches are brought together to overcome three hypothesized bottlenecks; reviewed in this article, which restricted erucic acid level near to 60%. Finally, rapeseed genotypes with 78% erucic acid were developed successfully. This material is now available in Germany for using in emollient industries and for biodiesel. Therefore, this article is reviewed on the current status and future outlook for modification of fatty acid profiles of rapeseed oil for its end-use as food, industrial feed-stock and biodiesel.

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MADS-box genes are well known for the ABC model of flower development. In this study, we investigated the expressions of A, B and C functions Brassica rapa MADS-box genes in different Ogura cytoplasmic male sterile (CMS) lines of B. juncea, B. oleracea, and their wild types. We observed two AP1-like (BjAP1 and BoCAL1), three PISTILLATA-like (PI-like; BjPI1, BoPI1, and BoPI2) and six AGAMOUS-like (AG-like; BjAGL1, BjAGL2, BjAGL3, BjAGL4, BoAGL1, and BoAGL2) genes to be altered their expressions in the CMS B. juncea and B. oleracea compared to their wild types. Partial and complete petaloidy in the third whorl (stamen) were observed of two CMS B. juncea lines J26 and J27, respectively. Besides, a sepaloidy structure was evident in the third whorl of CMS B. oleracea line 25053. Altered expressions of BjAP1 and BjPI1 in the fourth whorl (pistil) can be correlated with curved and robust stature of pistils in CMS B. juncea. Furthermore, an in silico protein interaction analysis revealed that AP-like, PI-like, and AG-like proteins are in close association with different MADS-box proteins and LEAFY (LFY), UNUSUAL FLORAL ORGANS (UFO), SEUSS (SEU), LEUNIG (LUG) for different floral organ development. We suggest that expressions of MADS-box genes might be dependent on mitochondrial signaling for cytoplasmic homeosis in CMS B. juncea and B. oleracea. The expression dataset on A, B, and C functions MADS-box genes of CMS and wild type B. juncea and B. oleracea presented in this study might be useful for the development of CMS in different Brassica species.

DNA barcoding is a technique that provides rapid identification of species without using morphological cues. The method employs relatively small-standardized DNA fragments as tags to define or discover species. In plants, the mitochondrial genome evolves much more slowly than in animals. There is currently no consensus on which candidate markers comprise the best plant DNA barcoding region; however, DNA barcodes such as rbcL, matK, psbA-trnH and ITS have been proposed for the plant kingdom. And also very recently the chloroplast intergenic spacer (IGS) like trnE-trnT, trnT-psbD, ndhF-rpl32 and rpl14-rpl16 were also employed for discriminating the cultivar species. The region ITS2 showed better intra-species variation, followed by psbA-trnH. Several analyses reveal that the ITS2 region is able to distinguish all tested species of the plant kingdom, but evaluations of DNA barcodes have to be conducted for more species covering many genera to confirm the above results. In this review we discussed the current view of DNA barcoding.

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Molecular genetic studies of self-incompatibility (SI) are the most accentuating part in the way of advancement of reproductive mechanisms in flowering plants. In the Brassicaceae plants, self-incompatibility has been mapped genetically to a single chromosomal location where several closely linked genes have been identified. Recently, various studies have provided a novel insight into the basis of specificity in the S-receptor kinase (SRK) and S-locus protein 11 or S-locus Cysteine-rich (SP11/SCR) interaction, the nature of the signaling cascade that culminates in the inhibition of ‘self’ pollen, and the physiological and morphological changes that are associated with transitions between the outbreeding and inbreeding modes of mating in the Brassicaceae. In this review, we discuss the current view of the molecular genetic aspects of the self-incompatibility in Brassicaceae.

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Cabbage (Brassica oleracea) is a very important vegetable worldwide and biotic stress is a crucial issue for this crop. Enhancement of resistance by exploiting stress resistance-related genes offers the most efficient approach to address this issue. Among the stress resistance-related genes, thaumatin-like proteins (TLPs) play a vital role in enhancement of resistance against stresses. In this study, we identified 12 TLPs from B. oleracea genomic DNA sequencing database, analyzed their sequences and compared with other published pathogenesis-related TLPs, and found a high degree of homology with them. In addition, these genes showed an organ-specific expression, three of which expressed differentially after Pectobacterium carotovorum subsp. carotovorum infection in cabbage plants. Data obtained in this study suggest the probable involvement of TLPs in resistance against soft rot disease of Brassica.

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