Applied Molecular Marker Technology
Molecular markers have been exploited by the group in four main areas of application:
1. Genetic Diversity and Variety Identification: A question we have addressed in detail is the issue of whether the reduction in number of breeding programs over the past 60 years or so has led to a decline in the available biodiversity in major crops. This question was first addressed in wheat and barley at the UK level, leading to the conclusion that while qualitative shifts in genetic diversity could be noted over time, there was no trend over the last 60 years towards an inexorable decline in diversity (Donini et al., 2000; Koebner et al., 2003). Similar work on durum wheat has shown a widening in the diversity base of that crop (Maccaferri et al., 2003). A broader perspective on the problem is being gained from work in progress within the EU FP5 Gediflux project which looks at temporal trends in diversity in wheat, barley, potato and maize at the European level.
2. DUS testing: The applications of SSRs as tools for DUS (Distinctness, Uniformity and Stability pre-requisite criteria for the award of plant breeders rights) testing have been explored in oilseed rape (Tommasini et al., 2001) and wheat (in preparation).
3. Food Provenance and Authenticity: As the need arises, often as part of projects with wider aims, we develop and/or refine novel marker sets for less well-studied species. The species studied are typically non-UK crops that are consumed in the UK in the form of high value processed foods, where there is a consumer-driven demand to authenticate and trace premium quality varieties all along the food chain (“from farm to fork”). Recent studies include tea (Freeman et al., 2004), coffee and olive.
4. Functional markers: Increasingly, the emphasis is shifting away from anonymous markers to gene-based markers.
• Microsatellite motifs found within genes provide a convenient source of polymorphism through which different allelic forms of the genes in question are effectively tagged (e.g. Leigh et al., 2003).
• Derivatives of the AFLP profiling method have been explored where the amplified fragments are targeted to classes of gene characterised by specific sequence motifs e.g. tubulin genes, NBS-LRR genes etc. (e.g. Bardini et al., 2004).
• As the amount of DNA sequence available grows exponentially, it is becoming increasingly feasible to derive SNP information from in silico analyses. We have functional SNP programs currently running in barley and olive.