Robert J. Cooke

Temporal trends in the diversity of UK wheat

Abstract The common assertion that scientific plant breeding leads to a narrowing in crop diversity has been examined. We have characterised the dominant UK winter wheat varieties from the period 1934–1994 using two types of PCR-based DNA profiling (AFLPs, amplified fragment length polymorphisms, and SSRs, simple-sequence repeats, microsatellites), seed storage protein analysis and morphological descriptors. The varieties were grouped into a series of decadal groups on the basis of their first appearance on the ’Recommended List’, and by analysis of molecular variance it was shown that an overwhelming proportion of the overall observed variance occurred within, rather than between, decades. A further range of statistical indices provided little evidence for any significant narrowing of overall diversity over the time studied. Principal co-ordinate analysis showed that the diversity in the time periods overlapped and that the most modern group of varieties encompassed the majority of the diversity found in earlier decades. The consistent indication is that plant breeding has resulted, over time, in a qualitative, rather than a quantitative, shift in the diversity of winter wheat grown in the UK.

DNA profiling and plant variety registration. III : The statistical assessment of distinctness in wheat using amplified fragment length polymorphisms

The use of AFLP analysis to produce DNA profiles from a set of 55 wheat varieties, commonly grown in the UK over the past 60 years, is described. Using six different primer pairs, 90 polymorphic bands were readily recognised and recorded. These AFLP bands are not significantly clustered and hence can be used with some confidence, even though they are not mapped. Statistical approaches to the analysis of the data were developed such that the discrimination between the varieties achieved by the use of the six primer pairs, both separately and in combination, could be derived and compared to that achieved by a common set of morphological descriptors. Various criteria for the definition of distinctness in terms of the number of band differences required between pairs of varieties were also compared. In general, higher levels of discrimination were achieved by the inclusion of greater numbers of bands in the analysis. The optimal number of polymorphic bands appears to be between v and 2v, where v is the number of varieties under test. Discrimination levels were adversely affected if the number of bands was below v/2. Distinctness levels achieved by the use of molecular markers can be calibrated so that they reproduce those seen with morphological characters. The results are discussed in relation to the possible use of DNA profiling methods for distinctness, uniformity and stability testing.

Gel electrophoresis for the identification of plant varieties

Abstract The use of various types of gel electrophoresis for distinguishing between and identifying plant varieties is well established. This review describes how different electrophoretic techniques [native polyacrylamide gel electrophoresis (PAGE), sodium dodecyl sulphate PAGE, isoelectric focusing and two-dimensional methods] have been utilised in a wide range of crop species. The fact that there are different types of plant variety, varying in genetic structure, is emphasized, and the way in which this influences the choice of technique is discussed. Other factors which need to be borne in mind when discussing identification in its broad sense are also outlined. Some practical applications of electrophoresis in this area are mentioned and finally future trends for the use of electrophoresis in plant variety identification studies are considered.

Minimising inter-laboratory variation when constructing a unified molecular database of plant varieties in an allogamous crop.

The construction of large-scale databases of molecular profiles of plant varieties for variety identification and diversity analyses is of considerable interest. When varieties of an allogamous species such as oilseed rape are analysed and described using molecular markers such as microsatellites, care is needed to represent the variety in a meaningful yet useful way. It is possible to characterise such heterogeneous genotypes by analysing bulked samples comprising more than one individual seed or plant, but this approach may result in complex microsatellite profiles. Intuitively it would be reasonable to represent a variety by the common ‘major alleles’ in a profile, but how to define these ‘major alleles’ remains problematic. This paper describes methods of analysing DNA microsatellite data that will allow independent and objective data production at a number of laboratories. Methods for establishing allele scoring rules (thresholding) are described and the effect of these rules on the utility of the data is discussed.

The impact of breeding on genetic diversity and erosion in bread wheat

This paper examines the fate of alleles and changes of genetic diversity in old ( ca 1930s) versus more modern ( ca 1990s) UK bread wheat varieties using 14 mapped DNA microsatellite (simple sequence repeat, SSR) loci and morphological markers. The allelic constitution of varieties belonging to three time periods (early, intermediate, late) was determined. While at certain loci one or more SSR alleles were gained between early and late periods, at others the allelic representation remained constant, although a shift in allelic frequencies could sometimes be detected. No locus showed a clear, net loss in the total number of alleles over the time period. In a further group of loci, there was neither clear gain nor loss, but rather a dynamic flux of alleles. A comparison of the allelic constitution of the UK variety set with a larger genetic pool (non-UK varieties) showed that some loci were rather similar in allelic constitution, while others possessed additional diversity. Certain SSR alleles appeared to be associated with old or modern varieties, possibly indicating associations with chromosome regions under selection pressure. The same exercise was conducted on the basis of 14 of the morphological characteristics recorded in the course of distinctness, uniformity and stability testing of varieties. Overall, this analysis generated a similar picture of changes in diversity to that obtained from the microsatellite data.