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.
Domaines
Génétique animale| Origine | Fichiers produits par l'(les) auteur(s) |
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