Breed wheat pangenome graph provides access to gene diversity, structural variations and key agronomic loci architecture
Résumé
Bread Wheat (Triticum aestivum) is one of the most important staple crops, widely cultivated world-wide with more than 215 million hectares grown each year. To meet the demand of a growing global population, and to face the increasing impact of climate change on yield, there is an urgent need to accelerate wheat breeding. With recent higher accessibility of reliable long-read sequencing technolo-gies, high-quality reference genomes became more achievable in wheat, providing essential resources to examine genetic diversity. However, wheat is characterized by a large (15 Gb), hexaploid (2n = 6x = 42; genomes AABBDD) and complex (85% of repeats) genome with numerous structural variations, hampering rapid genetic gain. To address this difficulty, we produced a wheat pangenome graph with Minigraph-Cactus pipeline [1] from 13 publicly available genomes [1–3] and one genome recently sequenced and assembled by our team. Using GrAnnoT, we were able to transfer public gene annotation through the graph, and thus to characterize the core, shell and cloud genomes. Transposable elements (TE) of the 14 genomes were annotated with CLARI-TE_smk, a snakemake workflow integrating CLARI-TE [4], in order to ana-lyse TE dynamics and to detect insertion variations between wheat accessions using panREPET pipe-line [5]. In addition, a global structural variant calling was obtained directly from the graph to supply association studies and genomic selection. Finally, a key agronomic locus carrying storage protein coding genes was further investigated by extracting a sub-graph and revealed gene copy number vari-ations. Altogether, these results give access to a wider diversity for comparative genomics studies compared to linear reference genome, and provide genomic feature variations to be exploited in wheat breed-ing, of which gene presence absence variations. Leveraging this wheat pangenome will help to im-prove our understanding of genetic diversity.
