Murdoch University Research Repository

Welcome to the Murdoch University Research Repository

The Murdoch University Research Repository is an open access digital collection of research
created by Murdoch University staff, researchers and postgraduate students.

Learn more

Selection of a core set of informative gene-derived SSR and SNP markers for assaying the genetic variation in germplasm collections of barley for abiotic stress tolerance

Varshney, R.K.ORCID: 0000-0002-4562-9131, Thiel, T., Valkoun, J., Grando, S., Baum, M., Chabane, K. and Graner, A. (2004) Selection of a core set of informative gene-derived SSR and SNP markers for assaying the genetic variation in germplasm collections of barley for abiotic stress tolerance. In: 17th EUCARPIA General Congress, 8 - 11 September 2004, Tulln, Austria

Abstract

A core set of informative gene (EST)-derived SSR (simple sequence repeat or microsatellite) and SNP (single nucleotide polymorphism) markers was selected for the analysis of the genetic background and to make inferences about population structure of a set of >220 barley lines comprising landraces, accessions, cultivars. In this direction, a total of 50 SSR and 50 SNP markers from the transcript map of barley were used with a set of 6 highly diverse barley accessions by employing fluorescence-based fragment analysis (for SSR) and allele-specific sequencing (for SNP) techniques. Finally, a core set of 28 SSR and 28 SNP markers was identified on the basis of the following criteria: (i) randomly distributed markers (2 markers per chromosome arms), (ii) high PIC (polymorphic information content) value, and (iii) producing good quality peaks. Details on different features like PIC, number of alleles or SNPs detected per marker, the haplotypes, and the calculated nucleotide diversity index (π value) for selected SSR and SNP markers are discussed. With the help of SNP2CAPS tool (http://pgrc.ipk-gatersleben.de/snp2caps/), putative restriction enzymes were identified for 20 of 28 targeted SNPs; therefore, they can be assayed on agarose gel by using CAPS marker assay. Furthermore, comparison of SSR and SNP marker data for cladistic analysis suggest that both marker types yield similar groupings.

Item Type: Conference Paper
URI: http://researchrepository.murdoch.edu.au/id/eprint/65122
Item Control Page Item Control Page