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Aldersey JE, Liu N, Tearle R, Low WY, Breen J, Williams JL, Bottema CDK. Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue. Anim Genet 2023. [PMID: 36990727 DOI: 10.1111/age.13322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300-kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus- and Brahman-specific Hi-C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus- and Brahman-specific Hi-C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.
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Affiliation(s)
- J E Aldersey
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
| | - N Liu
- South Australian Health & Medical Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - R Tearle
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
- Alkahest Inc, San Carlos, California, USA
| | - W Y Low
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
| | - J Breen
- South Australian Health & Medical Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - J L Williams
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
- Department of Animal Science, Food and Technology, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - C D K Bottema
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, South Australia, Australia
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