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Barley Association Genetics

 

Association Genetics of UK Elite Barley (SA302)

Description
The main aim of this project is to accurately identify the genomic regions which control economically important traits in elite UK barley through linkage disequilibrium analyses to associate phenotypes of interest with marker genotypes.

The advances in the genomics of human and several animal model systems have made possible the development of linkage disequilibrium based mapping methods to search for genes that influence complex traits of medical or evolutionary importance.  The use of association genetic analyses in plants has, to date, been limited and largely focused on out-breeding species such as maize.  The objective of this project is thus to apply these methodologies to the inbreeding species, barley, for the analysis of traits of biological and agronomic importance.  The project takes advantage of recent developments in barley genomic research and modern marker technology to rapidly generate genotypic data that can then be used in the analysis of the wealth of phenotypic data that has been generated through the official UK barley trialling system over the last ten years.  The use of elite barley lines for the project brings many advantages not least of which is the alignment of genomic studies with the allelic variation that has been and is being used to develop varieties that will underpin future sustainable agriculture in the UK. 

Objectives
1. Genotyping 1000 elite barley lines for 3000 SNP marker loci developed from 1000-1500 genes (2-3 SNPs/gene) to give 1-2cM resolution necessary for association genetics studies in barley

2. Assembly and analysis of phenotypic data for economically important traits from extant official trial and breeders’ data,

3. The generation of novel phenotypic data by additional field and glasshouse studies.  These will include in particular detailed characterisation of disease resistance in the material.

4. Analysis of the genotypic data to determine the genome-wide distribution of linkage disequilibrium, to predict haplotype structures and to test for various evolutionary factors that shaped the observed linkage disequilibrium patterns.

5. Identification of those linkage disequilibrium and/or haplotype structures that explain highly significant proportions of genetic variation for the traits under investigation. The traits studied will include a wide spectrum varying from highly heritable traits such as heading date for which several candidate genes/genomic regions are known to other biologically and agronomically important traits (such as yield, quality and durable disease resistance) that have to date proved less tractable through traditional linkage studies. 

6. Development and exploration of theoretical approaches for modelling linkage and linkage disequilibrium between polymorphic markers and quantitative trait loci in populations with and without genealogical information and, from this, the development of data-specific statistical methods and computational tools for analyzing the data generated in this project.

7. The development of a web accessible public/private data base that will store the genotypic and phenotypic data and the results of association genetic analysis.

Time-scale
From: 01/10/05
To: 30/09/09

Partners
National Institute of Agricultural Botany, SCRI, University of Birmingham, Brewing Research International, Calibre Control International Ltd, CPB Twyford Ltd, Coors Brewers Ltd, HGCA, The Maltsters Association of Great Britain (MAGB), Mylnefield Research Services Ltd, Syngenta Seeds Ltd, Nickerson (UK) Ltd, Serasen, Secobra/Dalgety, Svalof Weibull AB, SWRI.