Watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] is one of the economically most important fruit crops of the Cucurbitaceae family. Among different watermelon traits, disease resistance and fruit quality are the important traits for growers and consumers. The single nucleotide polymorphism (SNP) markers similar to those traits can potentially and cost-effectively distinguish the genetic variations among these traits. Consequently, we developed 33 SNP makers linked to different watermelon traits associated with fruit quality and disease resistance, and validated in the genetic resources of watermelon and F1 breeding lines using ‘Fluidigm SNP Genotyping’ assay. Most of the SNP markers distinguished the alleles into three different types such as reference allele, alternative allele and heterozygous from watermelon genotypes for various traits. The SNP markers ‘ZymFL-T81P’ (ZYMV- resistance), ‘FON1-U161’ and ‘FON1-S075’ (Fusarium wilt-resistance), ‘Pmr21-Cla831’ (PM-resistance), and ‘ClGBS-J168’ and ‘GBS-GC230’ (GSB-resistance) can successfully differentiate resistant (R), susceptible (S) and heterozygous watermelon genotypes. Similarly, the SNP marker associated with sugar content, citrulline content, arginine content, rind hardness, flesh firmness, fruit shape, rind strip pattern of watermelon fruit and seed coat colour can successfully distinguished the watermelon genetic resources and F1 breeding lines as reference allele (A) type, alternative allele (B) type and heterozygous (H). These SNP markers could be utilized for marker assisted selection as well as screening of a large number of watermelon germplasm for fruit quality and disease resistance. However, further validation like artificial inoculation of pathogens for the traits related to disease resistance is required in watermelon crops.

Powdery mildew (PM), caused by the biotrophic fungus Podosphaera xanthii, drastically reduces the yield and quality of melon (Cucumis melo L.). Knowledge of the genetic control and high throughput molecular markers linked with resistance against this disease are essential for breeding programs. The bioassay study of the F1 and F2 populations derived from the parents, ‘PMR 5’ (♂) and ‘SCNU1154’ (♀) revealed a monogenic dominant nature of resistance to the devastating race, race 5. Besides, we developed three SNP based high resolution melting markers, PMm-HRM-1, PMm-HRM-2, and PMm-HRM-3, based on the previously identified SNPs on chromosome 12 and validated them using 8 melon lines and 137 F2 populations. Among these, the SNP of marker PMm-HRM-1 causes a missense mutation in the LRR region of MELO3C002393 and we were able to distinguish the resistant vs susceptible genotypes from eight diverse melon accessions and the segregating F2 population with more than 90% genotyping efficiency. The other two markers were based on intergenic SNPs and had more than 80% genotyping efficiency in F2 population. These markers will be helpful to melon breeders to develop melon cultivars resistant to P. xanthii race 5 via marker assisted breeding programs.

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• Developing DNA Markers based on Male-Specific Chromosomal Regions for Selecting Male Plants in Hop (Humulus lupulus)
  Tae hyun Ha, Jae Il Lyu, So Young Yi, Si-Yong Kang
  Plant Breeding and Biotechnology.2024;[Epub]     CrossRef
• 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

Squash (Cucurbita moschata D.) is an economically important vegetable of the Cucurbitaceae family. The genetic purity of commercial hybrid seed is crucial for the success of hybrid seed production. The molecular markers like single nucleotide polymorphism (SNP) can efficiently and cost-effectively distinguish the genetic differences among F₁ hybrid cultivars. Therefore, in this study, we used ‘Fluidigm SNP Genotyping’ assay using 27 SNPs to distinguish and purity analysis of registered commercial F₁ hybrid cultivars and F₁ breeding lines of squash. Of these, eight SNP markers, including CMo-A01, CMo-A02, CMo-A04, CMo-A05, CMo-A12, CMo-A16, CMo-A20 and CMo-A25 can successfully identified heterozygotes from the registered commercial F₁ hybrid squash cultivars with 100% accuracy and partial contamination was detected for F₁ hybrid squash breeding lines which resulted due to outcrossing. Moreover, the HRM analysis of a registered commercial F₁ hybrid cultivar ‘Parangsae’ with CMo-A03 SNP marker showed 96.30-100% purity of the cultivar. Our results suggest that the ‘Fluidigm SNP Genotyping’ technology could be a rapid and cost-effective method for cultivar differentiation and genetic purity analysis of F₁ hybrids and squash cultivars.

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• Unlocking the Potential of Cucurbitaceae Seed Oils: A Narrative Review on Phytochemical, Pharmacological, and Biotechnological Applications
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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
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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
  Jalal Eldeen Chol Atem, Longcai Gan, Wenlin Yu, Fan Huang, Yanyan Wang, Amanullah Baloch, Chinedu Charles Nwafor, Alpha Umaru Barrie, Peng Chen, Chunyu Zhang
  Plant Science.2024; 347: 112175.     CrossRef
• 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
  Mingzhao Zhu, Yong Wang, Shujin Lu, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv, Zhiyuan Fang, Xilin Hou
  Horticultural Plant Journal.2022; 8(1): 68.     CrossRef
• 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
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• 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
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• 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
  Physiological and Molecular Plant Pathology.2021; 114: 101640.     CrossRef
• 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
  Julia Badstöber, Claire M. M. Gachon, Jutta Ludwig-Müller, Adolf M. Sandbichler, Sigrid Neuhauser
  Scientific Reports.2020;[Epub]     CrossRef
• Expression and Role of Response Regulating, Biosynthetic and Degrading Genes for Cytokinin Signaling during Clubroot Disease Development
  Rawnak Laila, Arif Hasan Khan Robin, Jong-In Park, Gopal Saha, Hoy-Taek Kim, Md. Abdul Kayum, Ill-Sup Nou
  International Journal of Molecular Sciences.2020; 21(11): 3896.     CrossRef
• Biocontrol arsenals of bacterial endophyte: An imminent triumph against clubroot disease
  Ayesha Ahmed, Shahzad Munir, Pengfei He, Yongmei Li, Pengbo He, Wu Yixin, Yueqiu He
  Microbiological Research.2020; 241: 126565.     CrossRef

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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• Black rot of crucifers: recent advances and future perspectives
  Dinesh Singh
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• Complete genome sequence of Xanthomonas campestris pv. campestris strain NSTU_AG-1 causing black rot disease isolated from infected cabbage leaves in Bangladesh
  Arnab Goswami, Maksudur R. Nayem, Pijush K. Jhan, Amena Khatun, A.B.Z. N. Rahman, Mahmudul Hasan, Swagato Dutta, Md T. Islam, Jong-In Park, Mehede H. Rubel, Leighton Pritchard
  Microbiology Resource Announcements.2026;[Epub]     CrossRef
• Race-specific resistance in Brassica oleracea cultivars against Xanthomonas campestris pv. campestris: insights from Turkish isolates
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  Journal of Plant Diseases and Protection.2026;[Epub]     CrossRef
• Constructing a Novel Disease Resistance Mechanism Model for Cruciferous Crops: An Example From Black Rot
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  Molecular Plant Pathology.2025;[Epub]     CrossRef
• Molecular marker development for specific amplification of Xanthomonas campestris pv. campestris race 8 causing black rot disease in Brassica crops
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• Molecular-genetic marking of Brassica L. species for resistance against various pathogens: achievements and prospects
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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
  Botanical Studies.2024;[Epub]     CrossRef
• 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
  Horticulture Research.2024;[Epub]     CrossRef
• Inheritance of Resistance to Race 5 of Powdery Mildew Fungus Podosphaera xanthii in Melon and Development of Race 5-Specific High Resolution Melting Markers
  Jeong-Eui Hong, Mohammad Rashed Hossain, Hee-Jeong Jung, Ill-Sup Nou
  Plant Breeding and Biotechnology.2022; 10(4): 272.     CrossRef
• 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
  Horticulture, Environment, and Biotechnology.2020; 61(2): 347.     CrossRef
• 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
  Phytopathology®.2020; 110(12): 1970.     CrossRef
• PCR-Based InDel Marker Associated with Powdery Mildew-Resistant MR-1
  Yu-Ri Choi, Jae Yong Lee, Seongbin Hwang, Hyun Uk Kim
  Agronomy.2020; 10(9): 1274.     CrossRef
• 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
  The Plant Pathology Journal.2018; 34(3): 182.     CrossRef

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
  Journal of Plant Pathology.2019; 101(1): 129.     CrossRef

Identification and authentication of parentage are important for effective pear breeding. Within Korean pear cultivars discrepancies are often reported between parents and offspring in skin color of fruits and also in S-genotypes suggesting that reported parentage was often inappropriate. In Korea, the parentage of the most of pear cultivars was never confirmed at the molecular level. Simple sequence repeat (SSR) genotyping and S-genotype analysis are considered effective in identifying parents. In this study, parentage of nine Korean bred cultivars was confirmed using SSR genotyping and S-genotype analysis. A total of 53 SSR markers were used. Six different haplotype-specific endonucleases were used for restriction cleavage of S-genotypes. Most of the Korean bred cultivars had six comparatively shorter S-RNase, S¹, S³, S⁴, S⁵, S⁶, or S⁷ of 450 bp in length whereas the Japanese control cultivars had four other comparatively longer S-RNase. Out of nine pear cultivars only ‘Chuwhangbae’ and ‘Whangkeumbae’ had identical SSR genotypes and S-genotype with previously reported parents. For another cultivar, ‘Sujeonbae’, the parents were the mutants of reported parent, ‘Niitaka’. For four other cultivars, SSR and S-genotypes of offspring matched with only one reported parent ‘Niitaka’ but those of another parent did not match. For the two other pear cultivars ‘Soowhangbae’ and ‘Sooyoung’ none of reported parents were confirmed by SSR genotyping and S-genotype analysis. Historically, the parent ‘Niitaka’ was predominant in the Korean pear breeding programs because of its high yield potential and quality. The methods have been used in this study could be used to identify pear cultivars with diverse S-genotypes to eliminate any existing obscure parent-offspring relations.

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  Horticulturae.2025; 11(7): 854.     CrossRef
• Quantitative Trait Loci Analysis Related to Fruit Quality Traits in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (Pyrus spp.)
  Keumsun Kim, Haewon Jung, Kyungho Won, Seok Kyu Yun, Young Sik Cho, Eu Ddeum Choi, Ung Yang
  Korean Journal of Breeding Science.2025; 57(4): 455.     CrossRef
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Flowering time is a very important agronomic trait in Brassica crops and regulation of the time is one of major factor in the breeding program. To understand the control of flowering time in Brassica rapa, we have carried out Br300K microarray with two contrasting Brassica inbred lines, Rapid Cycling B. rapa (RCBr) as rapid cycling type and B. rapa ssp. pekinensis inbred line Chiifu as slow flowering phenotype. Reproductive process-related genes were specifically expressed in RCBr, whereas environmental stimuli-responsive genes in Chiifu. Flowering stimulating genes, such as BrFT and BrSOC1, were preferentially expressed in RCBr, while flowering repressing genes, such as BrFLC and BrMAF4, expressed in Chiifu. Several paralogues present in B. rapa, BrFLCs and BrCOLs, were expressed with paralog-specific pattern depending on flowering phenotypes: i.e., BrFLC1 and BrFLC2, major floral repressors, were expressed in Chiifu, BrFLCL/BrFLC5 in RCBr and BrFLC3 in both plants. The expression of several flowering repressing genes was gradually decreased in RCBr growth, but increased in Chiifu growth. However, the expression of genes involved in photoperiodic flowering was no difference between these two plants under LD and SD conditions, indicating photoperiodic pathway is not major factor to distinguish fast vs. slow flowering in B. rapa. The mechanism underlined in the rapid or fast flowering of RCBr would be further elucidated in association with the controlling mechanism of its short life span.

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• Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters
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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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• Biochar Enhances Nutrient Uptake, Yield, and NHX Gene Expression in Chinese Cabbage Under Salinity Stress
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• Genome-Wide Identification of GYF-Domain Encoding Genes in Three Brassica Species and Their Expression Responding to Sclerotinia sclerotiorum in Brassica napus
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• Effects of Short-Term Root Cooling before Harvest on Yield and Food Quality of Chinese Broccoli (Brassica oleracea var. Alboglabra Bailey)
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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.

Grafting has widely used in the agriculture of fruit-bearing crops and trees because rootstocks have a profound influence on many aspects of scion development and scion responses to the environmental changes including biotic and abiotic stress tolerance. These effects appear to result from the change of gene expression on scion, but only limited numbers of papers have been published demonstrating it. To identify altered expression of genes in Chinese cabbage, Chiifu(Brassica rapa ssp. pekinensis, inbred line) shoot was grafted on three Brassica rootstocks: mustard, turnip and broccoli. After head formation, Br300K microarray experiment was conducted using total RNAs from scion leaves collected in two different seasons, spring (June) and fall (October). A large number of differentially expressed genes (DEGs) were identified both in two seasonal samples, but DEGs were more notable in June sample than in October sample. However, the number of DEGs by three rootstocks were high in October with respect to up-regulation, but high in June for down-regulation. Categories of DEGs included metal ion binding, response to hormonal stimuli, response to endogenous stimuli, regulation of transcription, oxidation reduction and response to stress. Up-regulated genes in both June and October samples were similar in mustard and turnip rootstocks, but different in broccoli rootstock. Two genes were found to respond to all experimental conditions: Brapa_ESTC049008 (hypothetical protein) as an up-regulated gene and Brapa_ESTC016027 (CNGC12) as a down-regulated gene. Together with the previous reports, these results suggest that grafting-induced gene expression depends on the species involved.

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• Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages
  Changhe Wei, Ming Li, Jia Qin, Yunfan Xu, Yizheng Zhang, Haiyan Wang
  Genes & Genomics.2019; 41(8): 895.     CrossRef
• Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis
  Thomas K. Uthup, Rekha Karumamkandathil, Minimol Ravindran, Thakurdas Saha
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A novel allele of the putative soybean raffinose synthase gene, RS2, was discovered in PI200508 that is associated with the low raffinose and stachyose content. Soybean line PI200508 was identified as expressing reduced levels of raffinose and stachyose as well as elevated levels of sucrose. The RS2 mutant gene shows three base pairs InDel with the normal gene. Based on InDel region we developed novel co-dominant and dominant marker. The aim of this study was to develop Korean soybean cultivars, Daewon, Cheongja, and Danmiput, containing low levels of raffinose and stachyose. A specific markers assay for the PI200508 RS2 allele was developed to allow direct selection of the low raffinose and stachyose phenotype. Our findings highlight the efficiency of allele-specific markers in selection, which is evident in the matching genotype and results of the HPLC in the F₂ generations of Daewon×PI200508 population.

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• Breeding a black soybean line with green cotyledon free from lectin, KTI, P34, lipoxygenase, and stachyose
  Sarath Ly, Byeong Eon Park, Sang In Shim, Min Chul Kim, Jin Young Moon, Jong Il Chung
  Euphytica.2024;[Epub]     CrossRef
• Breeding of Penta Null Soybean [Glycine max (L.) Merr.] for Five Antinutritional and Allergenic Components of Lipoxygenase, KTI, Lectin, 7S α′ Subunit, and Stachyose
  Sang Woo Choi, Sarath Ly, Jeong Hwan Lee, Hyeon Su Oh, Se Yeong Kim, Na Hyeon Kim, Jong II Chung
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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  Nick Lord, Chao Shang, Luciana Rosso, Bo Zhang
  Crop Science.2021; 61(2): 966.     CrossRef
• Effect of a mutation in Raffinose Synthase 2 (GmRS2 ) on soybean quality traits
  Luiz Cláudio Costa Silva, Larissa Martins Mota, Letícia Assis Barony Vasconcelos Fonseca, Rafael Delmond Bueno, Newton Deniz Piovesan, Elizabeth Pacheco Batista Fontes, Maximiller Dal-Bianco
  Crop Breeding and Applied Biotechnology.2019; 19(1): 62.     CrossRef
• Stachyose increases absorption and hepatoprotective effect of tea polyphenols in high fructose‐fed mice
  Wenfeng Li, Di Huang, Anning Gao, Xingbin Yang
  Molecular Nutrition & Food Research.2016; 60(3): 502.     CrossRef

The functions of DUF640/ALOG (Arabidopsis LSH1 and Oryza G1) domain proteins, which are found in most land plants, have not been well characterized, but some of these proteins regulate inflorescence architecture in rice and specify organ boundaries in Arabidopsis. Arabidopsis DUF640-domain genes are initially identified as LIGHT-SENSITIVE HYPOCOTYLS (LSH) genes. Chinese cabbage leaves have large, white midribs and photosynthetic leaf blades (or lamina). A DUF640 domain gene of Brassica rapa, BrLSH2, is specifically expressed in the midrib of Chinese cabbage. Arabidopsis and rice possess ten LSH family genes, but B. rapa has 24 LSH genes, which can be categorized into two or four groups based on sequence identity. Here, we examined the expression patterns of the LSHs in various Brassica species and analyzed the promoter sequence of the BrLHS2 gene. The transcript levels of most LSH genes were very high in the midrib but low in the leaf blade. These genes were evenly expressed throughout the petiole region of Korean cabbage and highly expressed in the leaf base region near the stem and in the border area in B. oleracea. In addition, BrLSHs were expressed in both bundle and mesophyll cells of the midrib. These expression patterns suggest the possible use of these genes to generate leafy vegetables with altered leaf morphology. The BrLSH2 promoter, which contains auxin- and cytokinin-responsive elements as well as leaf development-related elements, may confer midrib-specific expression, suggesting that this promoter may be useful for the production of midrib-targeted transgenic Chinese cabbage.

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• Genome-wide analysis of LSH genes reveals evolutionary patterns in Rosaceae and a positive role for MdLSH10b in adventitious root formation
  Xi Li, Shuyang Gu, Donglin Huang, Liu Cong, Yawen Shen, Yujie Zhao, Wanyu Xu, Pengbo Hao, Kunxi Zhang, Miaomiao Wang, Jian Jiao, Chunhui Song, Ran Wan, Jiangli Shi, Tuanhui Bai, Shangwei Song, Yu Liu, Jiancan Feng, Xianbo Zheng
  Plant Physiology and Biochemistry.2026; 231: 110983.     CrossRef
• Genome-wide identification and characterization of ALOG domain genes in Rosa
  Feng Chen, Bo Lv, Jiaqi Guo, Jurong Song, Cong Guo, Jie Yang, Jianguo Lin, Yuanyuan Yang, Fayun Xiang
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  Gouranga Upadhyaya, Vishmita Sethi, Annayasa Modak, Sreeramaiah N Gangappa, Kishore Panigrahi
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• The Characterization of Constitutive Promoters in Chrysanthemum (Chrysanthemum morifolium Ramat)
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• Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis)
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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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• Genetics Behind Sexual Incompatibility in Plants: How Much We Know and What More to Uncover?
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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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