The project takes advantage of several unique features of elite UK barleys to carry out association-genetics analysis to dissect the genetic control of those traits that are of agronomic and/or ecological importance to the future sustainability of the UK ’s crop production and environment.
The project will involve the genotyping of 1000 elite barley lines with 3000 SNP marker loci developed from 1000-1500 genes (2-3 SNPs/gene). The germplasm will be based on all spring and winter lines that have completed the second year of National List (NL) trials since 1993 so that the lines have at least two years phenotypic data, from treated and untreated trials. This material will be supplemented by confidential elite lines chosen by each of the breeding companies, by known key progenitors of the elite genepool and small numbers of unselected progeny from a number of elite crosses to give additional phenotypic and genetic mapping data.
The SNPs will largely be drawn from those currently being developed in the BBSRC/SEERAD funded ExGen project that is focussed on the genes involved in the abiotic stress, in particular drought. These will be complemented by additional SNP markers from other genes that are candidates for the control of particular agronomic traits or known targets of past introgression and selection.
This genotype data will be analysed to determine the level and extent of linkage disequilibrium, haplotype structure and complicating factors such as population substructure and combined with assembled phenotypic data for economically important traits from the extant official trial and breeders’ data. This phenotypic data set will be supplemented by generation of novel phenotypic data by additional field and glasshouse studies which will be based on subsets of the lines and include in particular detailed characterisation of disease resistance and certain quality parameters in depth for malting, brewing and distilling.
The combined data sets will be used for the association of the genotypic and phenotypic data to determine the patterns of genetic control of qualitative and quantitative traits in barley. The analysis offers considerable challenges and will necessitate the development of novel theory and methods to predict the distribution of linkage disequilibrium structure and haplotype blocks in the barley genome, the combination of linkage disequilibrium and linkage analyses for high-resolution mapping and identification of quantitative trait loci in populations with and without genealogical information and the implementation of data-specific statistical methods and computational tools for full analysis.
The development of a web accessible public/private data-base will allow the storage of genotypic and phenotypic data and the results of association genetic analysis in an easily understood/retrievable form, necessary for information exchange between the project’s partners but also with the wider community. The database will be crucial to the projects success and its envisaged longer-term impact on UK barley research.
For further information on this project please contact Bill Thomas (firstname.lastname@example.org) from the James Hutton Institute.