Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

A 'core set' of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32-0.72 (average 0.58) and 0.28-0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marker.