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Type: Journal article
Title: Comparison of SNP and CAPS markers application in genetic research in wheat and barley
Author: Shavrukov, Y.
Citation: BMC Plant Biology, 2016; 16(Suppl. 1):11-47-11-51
Publisher: BioMed Central
Issue Date: 2016
ISSN: 1471-2229
Statement of
Yuri Shavrukov
Abstract: Background: Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic ‘bottle-neck’ created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. Results: Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary ‘in silico’ search databases for assessing the potential value of SNPs have yet to be developed. Conclusions: This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.
Keywords: Barley; CAPS; high-throughput technology; molecular markers; SNP; SNP frequency; wheat
Rights: © 2016 Shavrukov. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
DOI: 10.1186/s12870-015-0689-9
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