Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality
RESEARCH ARTICLE

An informative set of SNP markers for molecular characterisation of Australian barley germplasm

M. J. Hayden A B E , T. L. Tabone A C , T. M. Nguyen A , S. Coventry A , F. J. Keiper D , R. L. Fox A , K. J. Chalmers A , D. E. Mather A and J. K. Eglinton A

A Molecular Plant Breeding CRC and School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.

B Current address: Primary Industries Research Victoria, Victorian AgriBioscience Center, La Trobe Research and Development Park, Bundoora, Vic. 3082, Australia.

C Current address: Ludwig Institute for Cancer Research, PO Box 2008, Royal Melbourne Hospital, Parkville, Vic. 3050, Australia.

D South Australian Research and Development Institute, GPO Box 397, Adelaide, SA 5001, Australia.

E Corresponding author. Email: matthew.hayden@dpi.vic.gov.au

Crop and Pasture Science 61(1) 70-83 http://dx.doi.org/10.1071/CP09140
Submitted: 10 May 2009  Accepted: 31 August 2009   Published: 17 December 2009

Abstract

The identification of genetic variation using molecular markers is fundamental to modern plant breeding and research. The present study was undertaken to develop a resource of informative single nucleotide polymorphism (SNP) markers for molecular characterisation of Australian barley germplasm. In total, 190 SNP markers were developed and characterised using 88 elite barley lines and varieties, sampling genetic diversity relevant to Australian breeding programs, and a core set of 48 SNPs for distinguishing among the barley lines was identified. The utility of the core 48-SNP set for distinguishing barley lines and varieties using DNA extracted from grain samples was also assessed. Finally, the 48 SNPs in the core set were converted into simple PCR markers to enable co-dominant SNP genotyping on agarose gel. The SNP markers developed, and in particular the core 48-SNP set, provide a useful marker resource for assessing genetic relationships between individuals and populations of current Australian barley germplasm. They are also useful for identity and purity testing of inbred lines in research, breeding, and commercial applications.

Additional keywords: SNPs, genotyping, genetic diversity.


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