Genetic Insights into Cumin (Cuminum cyminum L.): First Draft Genome Sequencing and Mining of SSR Markers

Abstract

Cumin (Cuminum cyminum L.) is a globally significant spice crop, highly valued for its distinctive aromatic volatile oil content and its natural drought tolerance. To accelerate molecular breeding for these traits, this paper presents the first de novo draft genome assembly of the widely cultivated Indian variety Gujarat Cumin 4 (GC-4), a cultivar known for its high yield. The genome was sequenced using a hybrid strategy, combining high-accuracy Ion S5 short reads with long-read PacBio sequencing technology to generate an initial draft genome resource. More than 69 million sequencing reads contributed to an assembled genome of approximately 835 Mbp. The resulting assembly was fragmented, comprising 15,088 scaffolds, with a scaffold N50 of 6.85 kb and a maximum scaffold length of 92.9 kb; therefore, it should be regarded as an initial draft rather than a highly contiguous or chromosome-level reference genome. Nevertheless, the assembly supported extensive downstream genome mining and annotation. A total of 37,342 protein-coding genes were predicted, with 16,920 genes assigned Gene Ontology terms and 9,463 genes mapped to KEGG pathways. Candidate genes associated with important biological and quality-related traits were identified, including 21 flavonoid-related genes, 9 chalcone synthase (CHS) genes, 15 terpene synthase (TPS) genes, and 89 disease-resistance-related genes. Genome-wide analysis also identified 133,814 SSR loci, predominantly dinucleotide repeats, providing a substantial resource for subsequent molecular marker development. Collectively, these results demonstrate the utility of the assembly as an initial genomic resource for gene discovery, functional annotation, candidate-gene mining, and marker development, while recognizing that improved long-read coverage and chromosome-scale scaffolding will be required for a more complete reference genome.