Molecular markers as a breeder's tool: a glimpse into the future
2001
Koebner, R.
First generation DNA marker systems have not lived up to initial expectations as universal genotyping assays, particularly in wheat. Both RFLP and RAPD suffer from a poverty of polymorphism, and while the former is not readily scalable to a breeding programme context, the latter has problems of non-reproducibility. Since the latter half of the 1990's, second-generation molecular markers have been developed, and as these can exploit variation in the repetitive DNA fraction of the genome, which makes up over 80% of the overall genome of wheat, levels of polymorphism have been much improved. The three major markers in this class - AFLP, microsatellites, and most recently, various retrotransposon-based assays - are all PCR-based. However, their use in plant breeding programmes as selection aids remains limited by the difficulty of scale-up and automation, largely because they all rely on a gel assay. Much attention is now being focused on techniques which dispense with gel electrophoresis as a core technology, since this is among the most rate limiting of the steps involved in detecting specific DNA fragments. The primary candidates for these third generation markers are Single Nucleotide Polymorphisms (SNPs), each of which represents a defined position at a chromosomal site at which the DNA sequence of two individuals differs by a single base. SNPs are ubiquitous and dispersed, and provided that appropriate assay techniques can be developed, they have the potential to markedly increase levels of both efficiency (throughput and unit cost) and discrimination power (polymorphism) compared to current assays, allowing a realistic application of marker assisted selection to large scale cereal breeding programmes. The talk will focus on current SNP assay technologies, and the prospects for laboratory-based of small grained cereals
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