BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme

Database (Oxford). 2025 Jan 18;2025:baaf039. doi: 10.1093/database/baaf039.

ABSTRACT

Bitter gourd, scientifically known as Momordica charantia L. with 2n = 22, is a widely recognized medicinal vegetable, renowned for its multifaceted health benefits, primarily acclaimed for its lipid- and glucose-lowering effects. Its growing demands as a food source and for industrial applications necessitate value addition in ongoing breeding initiatives to enhance genotypic traits in multifarious ways. A thorough understanding of the underlying molecular footprint is warranted for characterization, which still remains underexplored relative to other cash crops. Though a chromosome-level genome assembly of bitter gourd is available, scattered and fragmented information becomes an obstacle for assisted breeding and gene editing. Therefore, it is crucial to further dissect structural and molecular variants, noncoding RNAs (ncRNAs), transcription factors, and transcripts from whole-genome and resequencing projects. The present study leads to the development of a comprehensive genomic resource, BgDB (Bitter Gourd Resource Database) at a single platform, vital for advanced bitter gourd breeding programmes for raising bitter gourd varieties with traits of significant social and economic value. BgDB, available at https://bgdb.daasbioinfromaticsteam.in/index.php, is a user-friendly, three-tier database that offers a comprehensive interface with detailed analysed information, including 114 598 transcripts, 4914 differentially expressed genes, 32 570 predicted simple sequence repeat markers, and 162 850 primers for downstream applications. It also catalogues extensive annotations of bitter gourd-specific single nucleotide polymorphisms/insertions and deletions, long noncoding RNAs, circular RNAs, microRNAs, 1220 transcription factors, 295 transcription regulators, and 146 quantitative trait loci (QTL) distributed throughout the chromosomes. This genomic resource is poised to significantly advance genetic diversity analyses, population and varietal differentiation, and trait optimization. It further facilitates the exploration of regulatory ncRNA elements, key transcripts, and essential transcription factors and regulators. The discovery of QTL will aid in the development of improved bitter gourd varieties in the endeavour of enhanced productivity. Beyond comprehensive datasets, the future integration of multi-omics resources could profoundly advance and fully unlock the potential of databases. Database URL: https://bgdb.daasbioinfromaticsteam.in/index.php.

PMID:40625145 | PMC:PMC12462627 | DOI:10.1093/database/baaf039