| Acronym | EXBARDIV | |||||||||
| Title | Genomics-Assisted Analysis and Exploitation of Barley Diversity | |||||||||
| Duration | 1 October 2007 - 1 October 2010 | |||||||||
| Project leader | Andrew J. Flavell, University of Dundee, UK | |||||||||
Project partners | Søren K. Rasmussen, Copenhagen University, Denmark | |||||||||
| Funding | Denmark | Danish Agency for Science, Technology and Innovation (DASTI) | ||||||||
| Finland | The Academy of Finland (AKA) | |||||||||
| Germany | The German Research Foundation (DFG) | |||||||||
| Italy | Ministry of University and Research (MUR) | |||||||||
| United Kingdom | Biotechnological and Biological Sciences Research Council (BBSRC) and the Scottish Funding Council | |||||||||
| Total granted budget | € 2,020,953 | |||||||||
| Abstract | ||||||||||
Crop plants have evolved from their wild ancestors through domestication and selective breeding over approximately the last 10 000 years. This process has captured many useful gene alleles for breeders but, unfortunately, many other potentially useful alleles have also been lost during this process. There is therefore a need to identify and recruit new alleles from the wild, including niche adaptation, stress tolerance and morphology development for sustainable, environmentally benign crop production in the face of climate change. The association genetics approach potentially offers a powerful way to achieve this, by building upon extensive genomics information and detailed phenotypic analysis. Unfortunately, whole genome association mapping in wild samples requires hundreds of thousands of gene-linked markers, owing to the low levels of linkage disequilibrium in these populations. We propose an experimental strategy to overcome this problem, which exploits the fact that linkage disequilibrium decays at dramatically different rates in different populations. Our approach will use barley as a paradigm for investigating the effectiveness of association mapping in identifying useful gene alleles from the wild. Our second objective is to recruit these new useful gene alleles, into advanced back-cross breeding programs derived from wide crosses between wild barley (H. spontaneum) germplasm and elite cultivars. This will allow us to determine the efficiencies of identification and extraction of useful alleles in barley breeding programs based upon wide crosses. Our third major project objective is to use the huge DNA and marker data set obtained in the project to determine important population genetic parameters for barley. | ||||||||||
| Progress | ||||||||||
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ERA-NET Plant Genomics is supported by the Sixth Framework Programme
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ERA-PG / File repository / Call 2006 / / EXBARDIV
The first phase of the EXBARDIV project has involved the selection and expansion of plant samples for our germplasm collections, namely the Hordeum vulgare Cultivar Collection (HVCC), the Landrace Collection (LRC), the Hordeum spontaneum Collection (HSC) and Advanced Backcross Collections (ABC). Following extensive discussions, 451 candidate lines were selected for the HVCC. Seed for these, obtained from germplasm collections, breeders and our own resources, were grown over the summer of 2007, before the project formally commenced (see Figure 1) in duplicate locations to avoid accidental losses. For each line, seed was collected from a single plant to ensure genetic purity.
These seed samples were grown in bulk plots in North Italy over the Winter-Spring to increase stocks (Figure 2) and a small sample of each line was also grown in the greenhouse in Scotland (Figure 3) to provide reference seed stocks and DNAs for subsequent use in the project and for posterity. Some lines were lost due to poor fertility and we expect the HVCC to be finalised at roughly 400 lines, following the harvest in Italy in early July 2008. DNAs for these lines were extracted in June 2008 and these will all be analysed using 1536 gene-targetted Single Nucleotide Polymorphism (SNP) molecular markers over the summer of 2008. For the LRC we were fortunate to have access to a well-studied population of 480 lines carefully collected from multiple recorded locations in Syria and Jordan. 
We received 100 pure seed per sample from our generous external collaborator (Dr Stefania Grando, ICARDA), avoiding the need for the first growth step. These seed have been treated in exactly the same way as the HVCC (as described above) thereafter (Figures 2 and 3). For the HSC we decided to concentrate on wild barley lines collected from the ‘Fertile Crescent’ – the region where barley was first domesticated from the wild by Neolithic early farmers roughly 10 000 years ago. 
This region contains all the collection sites for the LRC, allowing us to compare the genetic structure of wild barley germplasm with the primitive cultivated material still grown in the same area. We have benefited from the generosity of two external colleagues – Drs Brian Steffenson (University of Minnesota) and Eyal Fridman (Hebrew University of Jerusalem), both of whom have well-characterised collections of H. spontaneum. A total of 486 lines distilled from these two collections have been growing in Scotland in Spring 2008, to provide reference seed and DNA for the project (Figure 3). The ABC comprises the progeny of various crosses between wild barley H. spontaneum and a cultivars (named Scarlett or Thuringia). ABC lines contain relatively small regions of the genomes from wild barley, superimposed upon the cultivated genome (Figure 4). The idea is to search for useful new gene alleles from the wild to enrich the cultivated germplasm.