The construction of a cattle pangenome for 14 French dairy and beef breeds provides new insights into their genetic diversity.
Résumé
The current cattle genome reference assembly, based on a single Hereford cow fails to capture the whole spectrum of genetic variations within the species. Structural variations (SVs), defined as genomic variations longer than 50 nucleotides, can have a potential impact on both complex and Mendelian phenotypic variations. However they are difficult to detect using only standard approaches of either short or long-read sequence mapping to the current bovine genome assembly. Thanks to the recent advances in long-read sequencing technologies coupled with the development of appropriate bioinformatics tools, it’s now possible to construct de novo genome assemblies for a large number of animals across various cattle breeds. It also offers the opportunity to study a broader range of both small and more complex genome-wide variations. Using these technologies, we have produced a comprehensive cattle pangenome incorporating genetic diversity from 64 high-quality de novo assemblies representing 14 French bovine dairy and beef breeds. We applied a combination of complementary approaches to characterize a wide spectrum of SVs and we report the identification of several megabases of novel genome sequences that are absent in the current cattle genome reference assembly. Further work is currently in progress to investigate the gene content of these non-reference sequences. This work was conducted in the SeqOccIn project, funded by the Occitanie region, FEDER, and Apis-Gene. Valentin Sorin’s PhD is supported by INRAE.
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