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.
Final Report Abstract
HAPPAN constructed 25 complete, pseudomolecule-level, fully annotated reference sequences and utilized this extraordinary resource to build the wild barley pangenome. This allowed us to study the barley genetic diversity within at an unprecedented new level, revealing 191.5M high-quality SNPs, 1.4M reliable structural variations and even large chromosomal translocations. Although the project start was challenging, due to difficulties in establishing an optimized protocol for HMW DNA extraction for PacBio sequencing, we finally succeeded with the establishment of a compelling genomic resource. This led to one of our most important achievements, the integration of our genome resource into the publication of the IPBGv2 in the Nature journal. In summary, we are very happy that the HAPPAN project completed with an extraordinary performance by providing a genomic milestone - the wild barley pangenome. Our results are very promising and to express our strong confidence in the importance of the resource we plan to submit a follow up proposal to the DFG. Here, the established knowledge should be lifted to the next level (wild barley pan-transcriptome). The intention is that the gene models for wild barley accessions become of equal quality as for the domesticated barleys. In addition to the central outcome of the project, we established a strong expertise for sequencing and pan genomics. This led to building an own long-read sequencing infrastructure at the MLU, comprising both specialized wet lab and bioinformatics skills. Throughout the HAPPAN project we show the importance of the constructed resources on multiple levels. In a genome-wide association study (GWAS) we utilize SNP as well as structural variation data and link this novel genomic information with phenotypic traits. Using two core genes with high impact on agronomic application we dive into the pangenome perspective. The first example is the ELF3 gene, a central gene regulating flowering time in barley. The second example is the P5CS1 gene complex, where variations in the promoter region of the gene regulate drought response. With these two genes, we will illustrate how our wild barley pangenome elucidates the large genetic diversity between the 25 exotic barleys, offering a plethora of small and large structural variations. In addition to the genecentric view, our deep sequencing of this collection revealed several chromosomal translocations. For the first time, we could link that these large structural variations have a direct consequence to the F1 generation where, for several wild barleys, we observed semisterility. An effect that underlines an additional complexity in crop breeding where that inadvertent selection of germplasm with SVs can create obstacles for the use of plant genetic resources. In summary, this emphasizes the importance of our wild barley pangenome and its broad application for research and breeding toward improved resilience in barley.
Publications
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Structural variation in the pangenome of wild and domesticated barley. Nature, 636(8043), 654-662.
Jayakodi, Murukarthick; Lu, Qiongxian; Pidon, Hélène; Rabanus-Wallace, M. Timothy; Bayer, Micha; Lux, Thomas; Guo, Yu; Jaegle, Benjamin; Badea, Ana; Bekele, Wubishet; Brar, Gurcharn S.; Braune, Katarzyna; Bunk, Boyke; Chalmers, Kenneth J.; Chapman, Brett; Jørgensen, Morten Egevang; Feng, Jia-Wu; Feser, Manuel; Fiebig, Anne ... & Stein, Nils
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A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity. Nature Genetics, 57(2), 441-450.
Guo, Wenbin; Schreiber, Miriam; Marosi, Vanda B.; Bagnaresi, Paolo; Jørgensen, Morten Egevang; Braune, Katarzyna B.; Chalmers, Ken; Chapman, Brett; Dang, Viet; Dockter, Christoph; Fiebig, Anne; Fincher, Geoffrey B.; Fricano, Agostino; Fuller, John; Haaning, Allison; Haberer, Georg; Himmelbach, Axel; Jayakodi, Murukarthick; Jia, Yong ... & Waugh, Robbie
