Efficiency of RAPD and SSR markers in assessing genetic diversity in summer onion (Allium cepa L.) genotypes

Abstract

The genetic diversity assessment of agricultural crops is crucial for breeding programs aimed at enhancing crop yield, resistance to diseases, and adaptation to changing environmental conditions. In the present investigation, a comparative genetic relationship in sixteen onion genotypes was assessed utilizing dominant (RAPD) and co-dominant (SSR) marker systems. Ten RAPD and nine SSR markers showed genetic diversity remarkably and produced 503 and 107 amplicons respectively. Spearman rank correlation was used to compare the different efficiency parameters in two marker systems with respect to sixteen onion genotypes. The genetic relationship based on similarity matrix values between a pair of cultivars was higher for SSR markers than for the RAPD marker system. OPC-04 (RAPD primer) and ACM-004 (SSR primer) witnessed the highest poly-morphic bands along with other polymorphic markers that proved to be useful in grouping onion genotypes. Finally, dendrograms were constructed and compared following the mantel test to find out the genetic diversity among the germplasms. This study will be effective for a selection of efficient primers and suitable marker systems to distinguish the onion genotypes in the future.

Keywords

• amplicons
• genetic diversity
• RAPD
• Spearmen rank correlation
• SSR
• summer onion