Application of SSR markers in the construction of Australian barley genetic maps

G. A. Ablett, A. Karakousis, L. Banbury, M. Cakir, T. A. Holton, P. Langridge and R. J. Henry

Abstract

Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers.

Keywords: microsatellite, database, genotyping.

Australian Journal of Agricultural Research 54(12) 1187 - 1195 (2003) doi:10.1071/AR02222