Microsatellite and SNP Markers in Wheat Breeding

Abstract

Bread wheat (Triticum aestivum L.) is one of the most important crop plants. Due to its hexaploid nature consisting of three different genomes (A, B and D) and its large genome size of approximately 15 billion base pairs, it is also one of the most complex crop genomes. This has rendered the use of molecular markers in wheat genome analysis and breeding slow and difficult. Mainly, through the use of microsatellite or SSR (simple sequence repeat) markers, wheat molecular marker analysis has gained momentum during the last ten years. The advantage of microsatellite markers is that they detect an unsurpassed level of polymorphism in this recently polyploidised organism with a generally low level of sequence variation. Furthermore, a large proportion of the microsatellite markers is genome-specific, thus amplifying a defined single product from one of the three wheat genomes. Currently, 2.000 to 2.500 mapped microsatellite markers are available for the wheat genome. With microsatellite markers, the chromosomal position of many relevant breeding traits such as disease resistance genes and quality traits has been identified and they are increasingly used in marker-assisted selection during wheat breeding. For the future, high expectations are being put into another marker type that is called single nucleotide polymorphisms (SNPs) since their number in the wheat genome should be much higher and cost-efficient, highly multiplexed technologies are available for the analysis of SNP markers in plants. SNP marker development and use are, however, still in their infancy. Based on recent results, we discuss here the advantages and disadvantages of SNPs compared to microsatellite markers for future wheat breeding.