HAPPAN : Haplotype and pan-genome exploration of the multiparental wild barley population HEB-25 to access its full potential for breeding improved barley cultivars better adapted to changing environments.

• Applicants: Professor Dr. Klaus Pillen; Dr. Thomas Schmutzer
• Subject Area: Plant Breeding and Plant Pathology
• Term: from 2020 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 433162815

Wild relatives of crops are an important source of genetic diversity with a high potential to enhance elite cultivars and ensure stable food production, however, their gene repertoire remains largely unexplored. Barley is a major crop in Germany and Europe and the pace to breed improved barley cultivars, which are better adapted to climatic and environmental changes is required to accelerate. The genetic diversity among wild barley accessions is a centerpiece of the multi-parental wild barley population HEB-25 ("Halle Exotic Barley"), which carries defined chromosomal segments from 25 wild barleys inserted into the genome background of the elite barley cultivar 'Barke' (Hordeum vulgare L.). We aim to sequence the 25 wild barley donor accessions to illuminate the horizon for a first wild barley pan-genome. Subsequently the pan genome data will be used to decode the entire population of 1,420 lines of the wild barley nested association mapping (NAM) population HEB-25. This will allow to detect large sequence variations and define an ultra-high density genome-wide set of DNA markers, including novel variations and genes that are untapped in domesticated barley lines. To exploit the full potential of the HEB-25 population, HAPPAN will first construct a genome reference for a wild barley. An assembly of a high-quality reference in barley is a grand challenge because of its large genome size (5.1 Gbp) and highly repetitive sequence (>80%). The wild barley genomic resource will be completed by prediction of gene models and annotation of their function. The complete HEB-25 population will be assessed to construct the first wild barley pan-genome. This will allow deep calling of variations in coding and regulatory regions to investigate SNPs, presence/absence and structural variations between HEB-25 lines and available domesticated barley cultivars. With this comprehensive approach HAPPAN is expected to reveal novel alleles of diversity, but also find novel genes that are most likely derived from duplication and sub-functionalisation events. HAPPAN will define haplotypes and provide an ultra-high resolution of DNA markers. With the definition of haplotype groups for the diverse wild barley panel we will enter a new era of haplotype based analysis for barley breeding and research.Since 2014, the set of 1,420 NAM lines of the HEB-25 population are continuously analysed in regional and global field trials for variation in important agronomical traits like plant development, yield formation, pathogen resistance and stress tolerance. Based on the HAPPAN pan genome data this large phenotypic data collection will be exploited to map and, ultimately clone the causative genes controlling the studied traits. We believe that the accuracy and precision of this novel resource will allow to substantially accelerate the pace of breeding improved barley cultivars better adapted to changing environments.

• DFG Programme: Research Grants