Genome skimming and development of simple sequence repeat marker for the characterization of high-value drought endurant legume moth bean (Vigna aconitifolia J.)

This research presents a comprehensive analysis of the Gujarat Moth Bean 2 (GMO-2) genome, employing next-generation sequencing technology and subsequent functional annotation. The genome assembly resulted in 155.49 Mb, comprising 206,446 contigs with an N50 value of 1329 bp. Functional annotation identified genes involved in diverse biological processes, cellular components, and molecular functions. Gene prediction using AUGUSTUS pipelines revealed 57,665 genes and 112,269 transcripts, offering insights into the genomic landscape. Comparative genome analysis highlighted homology with various species, with the highest similarity observed with Arabidopsis thaliana. Within the Vigna genus, the GMO-2 genome exhibited the closest resemblance to Vigna radiata. Repetitive element analysis unveiled a prevalence of mononucleotide repeats, providing valuable information on the repetitive landscape. The research also focused on simple sequence repeat (SSR) marker development, resulting in 575 primers with varying repeat motifs. Subsequent validation and polymorphism assay of a subset of SSR primers identified 10 markers exhibiting high polymorphism among 44 moth bean genotypes. Diversity analysis using Jaccard’s similarity coefficient and Unweighted Pair Group Method with Arithmetic Mean clustering revealed distinct genetic clusters, emphasizing the moderate genetic diversity among moth bean genotypes. This research contributes valuable genomic resources for moth bean, offering insights into its genetic makeup, functional elements, and diversity. The developed SSR markers hold promise for further genetic research and crop improvement initiatives in moth bean.