A comparative study of Inter Simple Sequence Repeat (ISSR), Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) loci in assessing genetic diversity in Amaranthus

Abstract

Genetic diversity in a set of 31Amaranthus accessions was analysed using RAPD, ISSR and SSR markers. Polymorphic Information Content (PIC) values of the polymorphic RAPD, SSR and ISSR markers ranged from 0.067 to 0.471, 0.178 to 0.452 and 0.11 to 0.362 with an average of 0.229, 0.371 and 0.441 per primer, respectively. Gene diversity for RAPD, SSR and ISSR markers respectively ranged from 0.032 to 0.487, 0.11 to 0.362 and 0.104 to 0.384. The similarity metrics values for the accessions ranged from 0.58 to 0.98 with RAPD, 0.70 to 1.00 with SSR and from 0.44 to 0.88 with ISSR markers. The dendrogram generated by the markers had five major clusters in case of RAPD markers, two distinct clusters in case of SSR markers and six clusters in case of ISSR markers. Amongst all, ISSR markers provided greater confidence for the assessment of genetic diversity in comparison to SSR and RAPD markers. All the accessions studied were found genetically diverse which may be useful in breeding for improving the genotypes of Amaranthus.