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Background Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum ), produces devastating symptoms on whole plants of watermelon ( Citrullus lanatus ) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties. Results In this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F 2 population developed from C. lanatus lines, ‘PI 279461’ ( resistant ) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1 , ClGSB10.1 , and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs ( ClC01G014900 and ClC01G015010 ), two WRKY transcription factors ( ClC01G014910 and ClC01G014990 ), and one AvrRpt-cleavage domain protein ( ClC01G015130 ). Conclusion Two high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB.

Plasmodiophora brassicae , an obligate biotrophic pathogen-causing clubroot disease, can seriously affect Brassica crops worldwide, especially Chinese cabbage. Understanding the transcriptome and metabolome profiling changes during the infection of P. brassicae will provide key insights in understanding the defense mechanism in Brassica crops. In this study, we estimated the phytohormones using targeted metabolome assays and transcriptomic changes using RNA sequencing (RNA-seq) in the roots of resistant (BrT24) and susceptible (Y510-9) plants at 0, 3, 9, and 20 days after inoculation (DAI) with P. brassicae . Differentially expressed genes (DEGs) in resistant vs. susceptible lines across different time points were identified. The weighted gene co-expression network analysis of the DEGs revealed six pathways including “Plant–pathogen interaction” and “Plant hormone signal transduction” and 15 hub genes including pathogenic type III effector avirulence factor gene ( RIN4 ) and auxin-responsive protein ( IAA16 ) to be involved in plants immune response. Inhibition of Indoleacetic acid, cytokinin, jasmonate acid, and salicylic acid contents and changes in related gene expression in R-line may play important roles in regulation of clubroot resistance (CR). Based on the combined metabolome profiling and hormone-related transcriptomic responses, we propose a general model of hormone-mediated defense mechanism. This study definitely enhances our current understanding and paves the way for improving CR in Brassica rapa .

Background TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done. Objective The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions. Methods The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein–protein interactions were analyzed using various databases and webtools. Results A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification. Conclusion This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.

Anthocyanins are the resultant end-point metabolites of phenylapropanoid/flavonoid (F/P) pathway which is regulated at transcriptional level via a series of structural genes. Identifying the key genes and their potential interactions can provide us with the clue for novel points of intervention for improvement of the trait in strawberry. We profiled the expressions of putative regulatory and biosynthetic genes of cultivated strawberry in three developmental and characteristically colored stages of fruits of contrastingly anthocyanin rich cultivars: Tokun, Maehyang and Soelhyang. Besides FaMYB10, a well-characterized positive regulator, FaMYB5, FabHLH3 and FabHLH3-delta might also act as potential positive regulators, while FaMYB11, FaMYB9, FabHLH33 and FaWD44-1 as potential negative regulators of anthocyanin biosynthesis in these high-anthocyanin cultivars. Among the early BGs, Fa4CL7, FaF3H, FaCHI1, FaCHI3, and FaCHS, and among the late BGs, FaDFR4-3, FaLDOX, and FaUFGT2 showed significantly higher expression in ripe fruits of high anthocyanin cultivars Maehyang and Soelhyang. Multivariate analysis revealed the association of these genes with total anthocyanins. Increasingly higher expressions of the key genes along the pathway indicates the progressive intensification of pathway flux leading to final higher accumulation of anthocyanins. Identification of these key genetic determinants of anthocyanin regulation and biosynthesis in Korean cultivars will be helpful in designing crop improvement programs.

Recent advances in high-throughput genome sequencing technologies are now making the genetic dissection of the complex genome of cultivated strawberry easier. We sequenced Maehyang (short-day cultivar) × Albion (day-neutral cultivar) crossing populations using double digest restriction-associated DNA (ddRAD) sequencing technique that yielded 978,968 reads, 80.2% of which were aligned to strawberry genome allowing the identification of 13,181 high quality single nucleotide polymorphisms (SNPs). Total 3051 SNPs showed Mendelian segregation in F 1 , of which 1268 were successfully mapped to 46 linkage groups (LG) spanning a total of 2581.57 cM with an average interval genetic distance of 2.22 cM. The LGs were assigned to the 28 chromosomes of Fragaria  ×  ananassa as determined by positioning the sequence tags on F. vesca genome. In addition, seven QTLs namely, qRU-5D, qRU-3D1, qRU-1D2, qRU-4D, qRU-4C, qRU-5C and qRU-2D2 were identified for runner production with LOD value ranging from 3.5–7.24 that explained 22–38% of phenotypic variation. The key candidate genes having putative roles in meristem differentiation for runnering and flowering within these QTL regions were identified. These will enhance our understanding of the vegetative vs sexual reproductive behavior in strawberry and will aid in setting breeding targets for developing perpetual flowering and profuse runnering cultivar.

Melon is a commercially important crop, yet its adaptation and genetic enhancement, particularly in regions like Bangladesh, remain limited by insufficient comprehensive evaluations of the agronomic performance of diverse global germplasm. This study integrates morphometric evaluation and marker-assisted selection to assess melon germplasm and select superior genotypes for further breeding programs. The morphometric evaluation involved 364 F 2 genotypes, examining growth, flowering, and fruit characteristics. Significant phenotypic variation was observed across various traits, including plant height, fruit weight, sweetness, and flowering time. Principal Component Analysis identified key traits influencing phenotypic diversity and highlighted genotypes with strong potential for improving yield and fruit quality under local agro-climatic conditions. The marker-assisted evaluation utilized seven molecular markers to assess genotypic variation in 18 selected genotypes, particularly for traits linked to fruit quality and disease resistance. Identified promising genotypes like HDM.3.14 and HDM.3.16 with high yield (8746 g and 4368 g, respectively), °Brix (12.4 and 12.7, respectively), and consumer preference (4 and 4.29, respectively) can be advanced to the next generations and be used in variety developments. This study provides a framework for the improvement of melon cultivars, integrating phenotypic and molecular approaches. The findings will facilitate future breeding efforts aimed at developing high-yielding, stress-resistant melon varieties optimized for local environments.

Diamondback moth (DBM), L., is a devastating pest of cabbage worldwide whose feeding attributes are influenced by glucosinolate profiles of the plant. Identifying the specific glucosinolates associated with plants' resistance mechanism can provide cues to novel points of intervention in developing resistant cultivars. We studied the DBM larval feeding preference and extent of damage on cabbage leaves via controlled glass-house and multiple- and two-choice feeding tests. These feeding attributes were associated with the individual glucosinolate profiles, analyzed by HPLC, of each of the eight cabbage genotypes using multivariate analytical approach to identify the glucosinolates that may have roles in resistance. Both the glass-house and multiple-choice feeding tests identified the genotype BN4303, BN4059, and BN4072 as the least preferred (resistant) and Rubra, YR Gold and BN3383 as most preferred (susceptible) genotypes by DBM larvae. The principal component analysis separated the genotypes based on lower feeding scores in association with higher contents of glucobrassicin, glucoiberin, glucoiberverin in one direction and 4-hydroxyglucobrassicin, glucoerucin, glucoraphanin, and progoitrin in opposite direction in a way to explain the major variation in resistant versus susceptible genotypes based on their extent of preference and leaf area damage. The simultaneous presence (or higher contents) of glucobrassicin, glucoiberin, and glucoiberverin and the absence (or lower contents) of 4-hydroxyglucobrassicin, glucoerucin, glucoraphanin, and progoitrin in the least preferred genotypes and in most preferred genotypes indicated their apparent role as putative repellents and attractants of DBM larvae in cabbage genotypes, respectively. These novel findings add to the current knowledgebase on the roles of glucosinolates in plant-herbivore interactions and will be helpful in setting breeding priorities for improving the resistance against DBM in cabbage using conventional and biotechnological approaches.

Watermelon (Citrullus lanatus), an economically important and nutritionally rich Cucurbitaceous crop grown worldwide, is severely affected by bacterial fruit blotch (BFB). Development of resistant cultivar is the most eco-friendly, cost-effective, and sustainable way to tackle this disease. This requires wider understanding of the genetics of resistance to BFB. In this study, we identified quantitative trait loci (QTLs) associated with BFB resistance in an F2 mapping population developed from BFB-resistant ‘PI 189225’ (Citrullus amarus) and -susceptible ‘SW 26’ (C. lanatus) genotypes based on the polymorphic markers identified by genotyping by sequencing (GSB). A linkage map covering a total genetic distance of 3377.1 cM was constructed. Two QTLs for BFB resistance, namely, ClBFB10.1 and ClBFB10.2, both located on chromosome 10 explaining 18.84 and 15.41% of the phenotypic variations, respectively, were identified. Two SNP-based high-resolution melting (HRM) markers WmBFB10.1 and WmBFB10.2 having high positive correlation with resistance vs. susceptible alleles were developed. The efficacy of the markers was validated in another F2 population derived from SW34 × PI 189225. The highest phenotypic variation was found in the locus ClBFB10.2, which also contains three putative candidate genes for resistance to BFB. These findings will accelerate the development of BFB-resistant watermelon varieties via molecular breeding.

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is the most devastating cabbage disease and causes substantial economic losses worldwide. Among the eleven known Xcc races, races 1 and 4 are the most devastating to Brassica oleracea. Therefore, the deployment of regional race-specific resistant cultivars could be an effective way to safeguard cabbage production. Unfortunately, the racial diversity and distribution of black rot pathogens are not well understood in many countries, including South Korea. This study aimed to investigate the Xcc races and their distribution in the northwestern region of Jeju Island, a major cabbage-growing region in South Korea. Black rot-infected cabbage and broccoli leaves were collected from 19 locations across 5 different regions of Jeju Island. Pathogens (Xcc) were isolated and cultured from the infected leaves, and distinct individual colonies of Xcc (10 colonies per location) were selected for further experimentation. Using Xcc pathovar-specific PCR-based markers, 183 colonies were confirmed as Xcc. Race-typing was performed using race 1 to race 6 specific markers which identified race 1 in 12 locations and race 4 in two locations. In addition, both races were present in one location, indicating the prevalence of races 1 and 4 on Jeju Island. This is the first study to demonstrate the uses of the race-specific molecular markers to identify the Xcc races. The races of the remaining colonies were determined. Similarly, a nationwide survey of Xcc races is necessary to develop regional and race-specific resistant varieties.

Acidovorax citrulli (A. citrulli) strains cause bacterial fruit blotch (BFB) in cucurbit crops and affect melon significantly. Numerous strains of the bacterium have been isolated from melon hosts globally. Strains that are aggressively virulent towards melon and diagnostic markers for detecting such strains are yet to be identified. Using a cross-inoculation assay, we demonstrated that two Korean strains of A. citrulli, NIHHS15-280 and KACC18782, are highly virulent towards melon but avirulent/mildly virulent to the other cucurbit crops. The whole genomes of three A. citrulli strains isolated from melon and three from watermelon were aligned, allowing the design of three primer sets (AcM13, AcM380, and AcM797) that are specific to melon host strains, from three pathogenesis-related genes. These primers successfully detected the target strain NIHHS15-280 in polymerase chain reaction (PCR) assays from a very low concentration of bacterial gDNA. They were also effective in detecting the target strains from artificially infected leaf, fruit, and seed washing suspensions, without requiring the extraction of bacterial DNA. This is the first report of PCR-based markers that offer reliable, sensitive, and rapid detection of strains of A. citrulli causing BFB in melon. These markers may also be useful in early disease detection in the field samples, in seed health tests, and for international quarantine purposes.