Genomics-Assisted Analysis and Exploitation of Barley Diversity

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 are testing an experimental strategy to overcome this problem, which exploits the fact that linkage disequilibrium decays at dramatically different rates in different populations. Our approach is using 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.