13 ERA-CAPS BARLEY NAM - Locating exotic genes that control agronomic traits under stress in a wild barley nested association mapping (NAM) population

Delivering sustainable food production in the face of climate change with reduced fertilizer and pesticide input requires a revolution in crop improvement. Meanwhile, modern crops are becoming increasingly depleted in gene biodiversity. Extending crop biodiversity and supporting future crop improvements can be achieved by 'mining' allelic variants of genes from ancestral wild germplasm. Novel strategies to utilize multi-parental breeding populations and apply the genomics revolution offer a promising route towards exploitation of exotic germplasm for breeding. We will test both approaches using wild barley (Hordeum vulgare ssp. spontaneum) as a model to improve agronomic performance of cultivated barley under abiotic and biotic stress conditions. For this, we will explore a nested association mapping (NAM) approach using the first cereal NAM population HEB-25 ('Halle Exotic Barley') to simultaneously test 25 wild barley accessions for beneficial gene effects. HEB-25 consists of 1,420 BC1S3 lines, each of which carrying ca. 25% of wild barley genome from one of 25 exotic donors on a 75% genetic background of the recipient spring barley cultivar Barke.
First, the HEB-25 lines will be assessed for allele content, employing state-of-the-art Exome Capture with Next Generation Sequencing (EC-Seq) to discover single nucleotide polymorphisms (SNP) for 21,643 genes in each of the 1,420 HEB-25 lines. We expect to map roughly 400,000 SNPs, giving several SNPs per gene with the goal to distinguish any wild barley allele from the recipient Barke allele.
Second, the HEB-25 lines will be cultivated in field trials in Germany, Scotland and Israel, to assess phenotypic stress performance under either nitrogen deficiency, drought or pathogen attack. Morphologic, agronomic, and nutrient content traits will be scored, as well as resistances against the important barley diseases leaf rust, yellow rust and net blotch. In addition, agronomic performance will be modeled in Israel by up-to-date remote sensing technology, to establish non-invasive phenotype prediction models.
Third, the collected data sets will be archived and further processed in a central data warehouse at Halle, built around a custom web-accessible relational database, enabling universal access to the project outputs.
Fourth, the resulting genotypic and phenotypic data sets will be combined in a Genome-Wide Association Scan (GWAS) to identify wild barley alleles that improve plant performance under stress. Because the gene resolution is extremely high this study will yield individual high confidence candidate alleles that putatively regulate the studied traits.
Fifth, to validate the identified trait-improving exotic alleles in follow up studies, high-resolution offspring populations derived from the originally studied HEB-25 lines will be developed in Halle by backcrossing.
The expected outcome of the BARLEY-NAM project will be beneficial in two directions. On one hand, the molecular regulation of new HEB properties will be studied in detail using the developed backcross lines. On the other hand, trait improving exotic alleles will be used in future breeding programs. This will ultimately lead to new elite barley cultivars with improved properties and, simultaneously, extend the biodiversity of our modern elite barley gene pool due to the incorporation of wild barley germplasm.

Delivering sustainable food production in the face of climate change with reduced fertilizer and pesticide input requires a revolution in crop improvement. Meanwhile, modern crops are becoming increasingly depleted in gene biodiversity. Extending crop biodiversity and supporting future crop improvements can be achieved by 'mining' allelic variants of genes from ancestral wild germplasm. New experimental breeding populations offer a promising route towards exploitation of wild germplasm for breeding. We will use wild barley as a model to improve the performance of cultivated barley under stress conditions that mimic future challenging environmental conditions. We will explore a nested association mapping (NAM) approach to simultaneously test 25 wild barley samples for beneficial gene effects.
Each individual in the population will be assessed for its genetic makeup, employing state-of-the-art Next Generation Sequencing technology. Second, the population will be grown in field trials in Germany, Scotland and Israel, to assess performance of each individual under stress from either fertilizer deficiency, drought or microbe attack, using (where necessary) up-to-date remote sensing technology. The collected data sets will be archived in a central data warehouse, enabling universal access to the project results. The final genetic and trial data sets will be combined to identify wild barley gene variants that improve plant performance under stress. The expected outcome of the BARLEY-NAM project will be beneficial by providing new sources of genes that can be used in future breeding programs. This will ultimately lead to new elite barley cultivars with improved properties and increased biodiversity in European cultivated barley.

Barley is the model Triticeae cereal and this family together constitutes the major sector of UK agricultural and food chain activity in the UK. Information on the beneficial gene diversity in the wild barley genome that will be gained in this project will in the longer term lead to advances in genetics/plant breeding and biotechnology. In this regard the beneficiaries of the project will be commercial sector organisations that breed new varieties and the farmers that grow these new varieties in their fields. Additionally, barley has a considerable extra value to the UK economy because it supports the brewing and a large part of the distilling industries. Four of the seven largest brewers in the world are European, and the total annual government revenue across Europe deriving from this activity is roughly £45Bn. Also, cereal straw has a big role in animal nutrition and the second-generation bioenergy sector. Lastly, our discoveries in barley potentially impact upon activity in the other cereal grasses such as forage/turf rye grasses, wheat and rye that are less accessible to genomic studies.

The gene sequence data and its embracing genome context information will facilitate the identification of genes and gene networks conferring traits including yield, food and feed quality, abiotic stress tolerance and biotic stress resistance. The gene sequences we will explore provide the raw material for allele mining and genomics-derived crop improvement. The UK brewing sector relies upon regular high quality barley production and this in turn guarantees additional downstream employment in supply, retail, and hospitality sectors. Barley is also an important part of the livestock industry (as feed). It also has potential in health-promoting human nutrition, with high content of beneficial nutrients such as beta glucans, arabinoxylans, sterols and stenols. In this regard, the US FDA recently stated that barley products have a role in reducing the risk of heart disease.

Advances in crop genomics flow rapidly into marker-assisted breeding activities in the plant breeding sector and then diffuse outwards to the food, feed and drinks industries. The UK has an efficient and successful commercial cereal breeding sector (largely with EU parent companies) and our research group (including our close colleagues in the James Hutton Institute) has close and longstanding collaborations with the major European barley breeders. We engage enthusiastically with this user community via open days and a variety of collaborative activities, many of which have received significant UK and EU funding. Internationally, the International Barley Sequencing Consortium has links with the breeding and brewing sectors. We have broad experience in web-accessible databasing of our experimental outputs and we thus have the necessary ability to ensure that our results can be accessed rapidly and effectively by the broad user community.