Functional markers in wheat: technical and economic aspects

Speed and cost–effective techniques for evaluation of plant materials to provide information before entering the next cycle of selection are critical for success in plant breeding. Whether or not a ‘new’ technique realizes its potential depends on technical and economic considerations. Biotechnology-based research tools such as doubled haploid technology and molecular markers have already demonstrated their value for application in plant breeding. In the area of genomics, implementation of functional markers (FMs) is currently of particular interest. The pipeline from plant materials to FM data points for any application includes maceration of plant material, DNA isolation and sample preparation. For each step of this pipeline, a number of techniques are available, and no single method is ideally suited for all applications. The challenge is to meet the needs of many different scenarios which are present in a modern breeding programme such as the use of (1) few markers for genotyping hundreds of samples (e.g., marker assisted backcrossing (MAB)), (2) few markers in thousands of samples (e.g., screening for GMO), (3) hundreds to thousands of markers for hundreds to thousands of samples (e.g., genetic characterization of breeding materials (fingerprinting)). This paper compares different techniques for each of the steps from plant material to FM data point, with the main emphasis on SNP detection platforms, assuming that multiple FMs will become available in the near future. We focus on technical and economic aspects and discuss which techniques are most suitable for each of the scenarios using wheat as a model.