Melon (Cucumis melo L.) is a highly diversified and economically important crop species of the family Cucurbitaceae that is cultivated in temperate, tropical and sub-tropical regions over the world. It is an economically important agricultural crop in terms of cultivation and consumption.
However, this crops are being harshly affected by bacterial fruit blotch (BFB) disease, caused by Acidovorax citrulli (A. citrulli) is an aerobic, gramnegative, rod shaped as well as seed-borne bacterium and is a destructive disease, which has been responsible for extensive economic losses of melon crops worldwide. Many strains of this 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. For designing primers, we used a whole-genome alignment-based approach to identify genomic fragments that are only present in A. citrulli strains that are particularly virulent towards melon. We developed three primer sets (AcM13, AcM380, and AcM797) that are specific to melon host strains, from three pathogenesis-related genes. These markers effective in detecting the target strains from artificially infected leaf, fruit, and seed washing suspensions, without requiring the extraction of bacterial DNA. Moreover, we molecularly characterized a Korean devastating A. citrulli strain
NIHHS15-280, belonging to A. citrulli group I, which predominantly infects non-watermelon cucurbits (virulent to melon) by partially sequencing the 16S rRNA gene using PCR-based markers. Additionally, the development of resistant cultivars against BFB has been considered is the worthwhile and sustainable way of BFB management. In this aspects, we identified four lines (PI 353814, PI 140471, PI420145, and SCNU1154) and two cultivars (ME6 and ME5) highly/moderately resistance to BFB (A. citrulli strain NIHHS15-280) by an intensive screening of thirty five melon genotypes. In addition, no molecular studies (genetic loci or markers) have focused on BFB resistance in melon. Nucleotide binding site (NBS)-encoding resistance (R) genes play important roles in plant defense responses to several pathogens, but there is not known about the role of NBS-encoding genes in disease resistance in melon. So, we explored eight (MELO3C023441, MELO3C016529, MELO3C022157, MELO3C022146, MELO3C022144, MELO3C025518, MELO3C005452 and MELO3C034399) BFB resistance NBS-encoding R genes through genome-wide expression analysis in resistant and susceptible melon lines after inoculation of A. citrulli at different time points. Furthermore, development of molecular markers is very much essential to explore BFB resistance genotypes from a diverse source of germplasm. For this, we determined the inheritance pattern of BFB resistance from a segregating population of 491 F2 individuals raised by crossing BFB-resistant (PI 353814) and -susceptible (PI 614596) parental lines. All F1 plants were resistant to A. citrulli strain KACC18782, and F2 plants segregated with 3:1 ratio for resistant and susceptible phenotypes, respectively, in a seedling bioassay experiment, indicating monogenic dominant inheritance of the disease. Besides, investigation of length polymorphism in 57 genes across the genome encoding proteins containing nucleotide binding site (NBS) domains identified only one TIR-NBS-LRR gene, MELO3C022157, showing length polymorphism between resistant and susceptible parents. Sequencing of this gene (from resistant and susceptible parent) revealed multiple insertion/deletions (InDels) and single nucleotide polymorphisms (SNPs), of which the SNP A2035T in the second exon of the gene caused loss of the LRR domain and a truncated protein in the susceptible line. The InDel marker MB157-2, based on the large (504 bp) insertion in the first intron of the susceptible line, was able to distinguish resistant and susceptible lines among 491 F2 and 22 commercial inbred lines with 98.17% and 100% detection accuracy, respectively. Over all, our study provides some markers for early disease detection of A. citrulli (virulent to melon host) in the field samples, in seed health tests, and for international quarantine purposes; molecularly characterized A. citrulli strain NIHHS15-280 (group I) and identified resistant lines; fundamental insights into the NBS-encoding candidate genes in melon in response to A. citrulli infection; novel PCR-based, co-dominant InDel marker (MB157-2) represents a practical tool for marker-assisted breeding aimed at developing BFBresistant melon lines.