Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys

Abstract

A set of 16 expressed sequence tag (EST)-derived simple sequence repeat (SSR) and 15 EST-derived single nucleotide polymorphism (SNP) markers together with 4 amplified fragment length polymorphism (AFLP) primer combinations were analyzed on 43 wild ( Hordeum vulgare ssp. s pontaneum – HS), 35 cultivated ( H. vulgare ssp. vulgare – HV) and 12 elite ( H. vulgare ssp. vulgare – from EU) barley lines. SSR markers were found most polymorphic with an average PIC value of 0.593 and eight alleles per marker, while AFLP markers showed the highest effective multiplex ratio (26.4) and marker index (5.042). The effective marker index (EMI) was recorded highest (0.468) for AFLP markers and lowest (0.341) for the SNP markers while the SSR markers had an intermediate EMI (0.442). Cluster analysis on combined set of SSR, SNP and AFLP genotyping data classified wild, cultivated and elite barley lines in three distinct groups. The present study suggests the SNP markers as the best class of markers for characterizing and conserving the genebank materials and the AFLP and SSR markers more suitable for diversity analysis and fingerprinting.