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Untangling the Copy Number Variation at the Basis of Belted Phenotypes in Cattle Using Long-Read Sequencing
Rensco A H Hogers1, Mirte Bosse1,2, Annemieke P Rattink1,3
1Animal Breeding and Genomics, Wageningen University & Research, Gelderland, the Netherlands.
Animal Genetics
|July 17, 2026
Summary
The belted phenotype in cattle is caused by a copy number variant (CNV) upstream of TWIST2. This CNV is essential for belt formation, but other genetic factors influence belt width and completeness.
Area of Science:
- Genetics
- Animal breeding
- Molecular biology
Background:
- The belted phenotype in cattle, characterized by a white midsection, is linked to a copy number variant (CNV) near the TWIST2 gene.
- Understanding the genetic basis for variations in belt width and completeness is crucial for cattle breeding and genetics.
Purpose of the Study:
- To investigate the genetic underpinnings of the belted phenotype in Dutch Belted cattle, focusing on belt width and completeness.
- To identify the specific genetic variant responsible for the belted phenotype and explore potential modifiers.
Main Methods:
- Generated a de novo genome assembly of Dutch Belted cattle.
- Analyzed short- and long-read sequencing data from cattle with varying belt phenotypes.
- Utilized coverage analysis and quantitative PCR (qPCR) to confirm the copy number variant (CNV).
- Performed genome-wide scans to assess nucleotide diversity and identify potential selective sweeps.
Main Results:
- A 6kb tandem array copy number variant (CNV) located upstream of TWIST2 was identified as the cause of the belted phenotype.
- CNV copy number did not correlate with variations in belt width or completeness.
- No unique variants within the CNV or TWIST2 were found in individuals with narrow belts, suggesting extragenic modifiers.
- The CNV region exhibited extremely low nucleotide diversity, indicative of a strong selective sweep in Dutch Belted cattle.
Conclusions:
- The identified CNV is necessary but not sufficient for the belted phenotype in cattle.
- Genetic modifier loci located elsewhere in the genome likely control the variation in belt width and completeness.
- Artificial selection has significantly impacted the genetic diversity around the CNV region in the Dutch Belted breed.
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