Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Authors: TRIGO, BEATRIZ - Sao Paulo State University (UNESP); UTSUNOMIYA, ADAM - International Atomic Energy Agency (IAEA); FORTUNATO, ALVARO - Sao Paulo State University (UNESP); MILANESI, MARCO - Sao Paulo State University (UNESP); TORRECILHA, RAFAELA - International Atomic Energy Agency (IAEA); LAMB, HARRISON - University Of Queensland; HAYES, BEN - University Of Queensland; NGUYEN, LOAN - University Of Queensland; ROSS, ELIZABETH - University Of Queensland; PADULA, ROMULO - Pontifical Catholic University; SUSSAI, THAYLA - Pontifical Catholic University; ZAVAREZ, LUDMILLA - International Atomic Energy Agency (IAEA); CIPRIANO, RAFAEL - Pontifical Catholic University; CAMINHAS, MARIA - Sao Paulo State University (UNESP); LOPES, FLAVIA - Sao Paulo State University (UNESP); LUNG, LAIZA - Crv Lagoa; PELLE, CASSIANO - Crv Lagoa; LEEB, TOSSO - University Of Bern; BANNASCH, DANIKA - University Of Bern; Bickhart, Derek; Smith, Timothy - Tim; GARCIA, JOSE - Sao Paulo State University (UNESP); UTSUNOMIYA, YURI - Sao Paulo State University (UNESP)

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2021
Publication Date: 4/28/2021
Citation: Trigo, B.B., Utsunomiya, A.T., Fortunato, A., Milanesi, M., Torrecilha, R.B., Lamb, H., Hayes, B., Nguyen, L., Ross, E., Padula, R.C., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M., Lopes, F.L., Lung, L.H., Pelle, C., Leeb, T., Bannasch, D., Bickhart, D.M., Smith, T.P.L, Garcia, J.F., Utsunomiya, Y.T. 2021. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution. 53. Article 40. https://doi.org/10.1186/s12711-021-00633-2.
DOI: https://doi.org/10.1186/s12711-021-00633-2

Interpretive Summary: The coat color of cattle breeds has long fascinated breeders. Many cattle breeds are solely defined based on colorful patterns in their external coats of hair. The genetics of coat color are incredibly complex with many genes found to influence pigment colors and patterns. This study identified one gene that influences the white coat color of the Nelore cattle breed. This white coat color may play a role in the breed's adaptation to tropical climates.

Technical Abstract: Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair-coat length and color are traits that may impact heat tolerance. The Nellore breed have had intense selection for white coat color in females, but bulls generally exhibit darker hair ranging from light gray to black on the head, neck, hump, and knees. We performed a Genome-wide association study (GWAS) analysis for darkness of hair coat in Nellore cattle using data from 432 bulls genotyped for >777k single nucleotide polymorphisms (SNPs). A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole genome sequencing (WGS) of 21 bulls revealed functional variants associated with darker hair, including a structural rearrangement (ASIP-CNVR1) consisting of a ~1 kbp deletion followed by a >150 bp insertion of a transposable element that may impact the recruitment of ASIP non-coding exons. Oxford nanopore sequencing of 10 Australian Brahman bulls further showed segregation of ASIP-CNVR1 in Brahman cattle and confirmed its structural arrangement. Overall, our results indicate that the mutant ASIP sequence causes partial loss of melanin dilution in specific body regions.