B-G.10: Assessing SNV and SV Callers using HiFi Long Read WGS to Find Causal Variants for Mendelian Traits in Goats
Authors
Laura Voitl
University of Bern
Rémy Bruggmann
University of Bern
Cord Drögemüller
University of Bern
Anna Letko
University of Bern
[sponser-meet-now-chat][/sponser-meet-now-chat]
Long-read whole-genome sequencing (LR-WGS) has the advantage of enabling detection of large and repetitive structural variants (SV) compared to short-read (SR-WGS). Here, we sequenced 20 Swiss goat genomes representing 10 local breeds using PacBio Revio. To broaden the diversity of our dataset, we included 12 publicly available genomes from the European Nucleotide Archive. We aligned all samples using pbmm2 to the T2T-goat1.0 Inner Mongolia cashmere goat reference available on NCBI.
We subsequently constructed variant catalogs based on the aligned genomes using a reference-based approach. We used two tools for SNV calling (DeepVariant and clair3) and SV calling (Sniffles2 and Sawfish2) respectively. SNV calls were also compared to SR-WGS data of the Swiss cohort. Our aim was to compare the output of each caller by investigating which variants were called by each tool. We also tested for the presence of known caprine variants for Mendelian traits from the Online Mendelian Inheritance in Animals (OMIA) database.
Both shared and unique variants were detected across the different callers. Known variants of interest included copy number variants affecting coat color, a complex SV on chromosome 1 causing polled intersex syndrome, and variants present in CSN1S1, which affect milk protein. We confirmed the expected presence of these different variants in the Swiss goats and evaluated their occurrence in the public dataset.
This work shows the benefit of using LR-WGS to detect the full spectrum of genetic variation in goats. The variant catalogs provide a valuable and sustainable resource for small ruminant genomics.
Co-authors: Rémy Bruggmann, Cord Drögemüller, Anna Letko
Contact Attendee
Warning: Attempt to read property "user_email" on string in /home/1276969.cloudwaysapps.com/ydbgzhdjeq/public_html/wp-content/plugins/my-conference-now/functions.php on line 2826