Genome-wide in-silico identification and characterization of simple sequence repeats in onion (Allium cepa L.)

Onion (Allium cepa L.) is a globally significant vegetable crop with a large genome that presents challenges for genetic study and breeding. A study was undertaken to identify and characterize simple sequence repeats (SSRs) in the onion genome using in-silico method to develop new molecular markers for breeding and genetic diversity analysis. Using the KRAIT tool, 470,700 SSRs were identified from the onion genome, with dinucleotide repeats being the most abundant. Primers were designed for 171 SSR loci and tested on a subset of onion genotypes, resulting in 18 primers displaying clear amplification and polymorphism. These primers were further validated on 22 onion genotypes and Allium fistulosum, revealing a total of 49 alleles with an average polymorphic information content (PIC) value of 0.456. The study demonstrated the potential of these SSR markers in genetic diversity analysis and breeding programs for onion. The newly developed SSR markers enhance the genomic resources available for Allium cepa and provide valuable tools for future molecular breeding efforts.