GrainGenes Reference Report: PEU-04-213
Reference
PEU-04-213
Title
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
Contained in
(2004) Genetic variation for plant breeding. Proceedings of the 17th EUCARPIA General Congress, Tulln, Austria, 8-11 September 2004.
Year
2004
Pages
213-217
Author
Varshney RK
[ Show all 10 ]
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 ( pi 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
Keyword
allele
[ Show all 21 ]
GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.
GrainGenes Reference Report: PEU-04-213
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GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture. | |||