Gene function & annotation

Genomic information from long read sequencing in DSN cattle and its impact on genomic features

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Abstract

German Black Pied (DSN, Deutsches Schwarzbuntes Niederungsrind) is an endangered cattle breed valued for its genetic diversity, robustness, and high milk fat and protein content. Previous studies using short-read sequencing data have primarily identified SNPs and small insertions/deletions (indels). However, structural variants (SVs), which include large deletions, duplications, inversions, and translocations, have largely remained unexplored due to the limitations of short-read sequencing data. This study utilizes long-read sequencing technology (PacBio Sequel II HiFi and PacBio Revio HiFi) to assess SVs in 13 DSN cattle including two parent-offspring trios and to determine individual methylation patterns. SVs were identified using sniffles2 v.2.6.1 and functionally annotated using the Ensembl Variant Effect Predictor. A total of 56,673 SVs were identified, with large indels being the predominant type. Functional annotation of SVs revealed 1 start lost, 76 stop lost, and 129 frameshift SVs. Previously identified QTLs for milk and meat traits in DSN were screened for locally relevant SVs. For example, in a QTL for with milk protein yield, FGF12 (fibroblast growth factor 12) contains the top associated SNP and harbors four SVs affecting the length of 3 out of 4 introns. All of the SVs are in low linkage disequilibrium (LD) with the top SNP. The methylation level in the promoter was higher in the calf (0.28) than in the cow (0.08), suggesting that increased gene activation may be important for milk protein production in females. In a QTL for body weight at 7 months, a 126 bp insertion causes a frameshift in exon 35 out of 82 in the VPS13C (vacuolar protein sorting 13 homolog C) gene. VPS13C is necessary for proper mitochondrial function and lipid transport. No differential methylation was found in this gene region, indication that the gene is active independently of age or gender. This study provides novel insights into the potential impact of SVs. Further investigation is needed on the molecular level to evaluate the functional impact of the SVs on gene regulation, protein function, and ultimately, associated traits. The results obtained on DNA methylation signals provide additional insight into the potential regulation of genes in QTL regions.

Keywords: 2026

How to Cite:

Brockmann, G., Korkuć, P., Neumann, G. & Strucken, E., (2026) “Genomic information from long read sequencing in DSN cattle and its impact on genomic features”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286942. doi: https://doi.org/10.31274/wcgalp.24177

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