Exploring sequence-related amplified polymorphism (SRAP) markers for assessing genetic diversity in onion (Allium cepa L.) genotypes and their wild relatives

This study used custom-designed sequence-related amplified polymorphism (SRAP) markers to amplify specific regions in the onion genome, resulting in reproducible and informative DNA fingerprints. By analysing various onion accessions, including red, white, and wild types, we identified unique genetic profiles, particularly within Allium roylei and Allium negianum, by using the me2-em6 marker. The findings demonstrated the effectiveness of SRAP markers in distinguishing between different onion cultivars, categorising them into distinct groups where red and white onions were separated from wild species and two specific white genotypes. We used 20 SRAP marker combinations to assess genetic diversity among 17 onion (Allium cepa L.) cultivars, 3 germplasm samples, and 10 wild species. The polymorphic information content value ranged from 0.06 to 0.44, indicating moderate diversity. We identified 107 loci, of which 81 exhibited polymorphisms. The onion cultivar Bhima Shweta displayed the highest polymorphism at 45.26%. Clustering analysis revealed three major clusters comprising 30 Allium species. The genotypes Bhima Super and Red 3 exhibited the highest similarity, whereas the wild onion Allium negianum and Allium consanguineum had the least similarity. These 20 SRAP marker pairs serve as valuable tools for targeted and effective onion breeding, thereby offering benefits for the onion industry and consumers. Furthermore, this approach enhances our understanding of the genetic diversity present among cultivated onion genotypes and their wild relatives.