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Genome-wide association study of genetic markers of coat color patterns in Sumatran native cattle

Hartati H 1 , Putra WPB 2 , Handiwirawan E 1 , Ramon E 1 , Firison J 1 , Zubir Z 1 Show all authors , Suretno ND 3 , Mariyono M 1 , Yusriani Y 1 , Robba DK 1 , Destomo A 1 , Anggraeni T 4 , Anwar P 5 , Irmawanti S 1 , Aprisal A 6 , Elieser S 1 , Kurniawati D 7

Affiliations 

  • 1 Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
  • 2 Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
  • 3 Research Center for Sustainable Production System and Life Cycle Assessment, National Research and Innovation Agency (BRIN), Banten, Indonesia
  • 4 Directorate of Laboratory Management, Research Facilities, and Science and Technology Areas, Deputy for Research and Innovation Infrastructure, National Research and Innovation Agency (BRIN), Indonesia
  • 5 Department of Animal Science, Faculty of Agriculture, Islamic University of Kuantan Singingi, Teluk Kuantan Riau, Indonesia
  • 6 Department of Animal Husbandry and Veterinary Science, West Sumatra Provincial Government, Rasuna Said Street No. 68 Padang, Indonesia
  • 7 Department of Animal Science, Faculty of Agriculture, University of Lampung 35145, Indonesia
Vet World, 2024 Nov;17(11):2537-2543.
PMID: 39829673 DOI: 10.14202/vetworld.2024.2537-2543

Abstract

BACKGROUND AND AIM: Coat color is a phenotypic trait that is affected by many functional genes. In addition, coat color is an important characteristic of breeds in livestock. This study aimed to determine functional genes for coat color patterns in Sumatran native cattle in Indonesia using a genome-wide association study method.

MATERIALS AND METHODS: A bovine single nucleotide polymorphism (SNP) 50K BeadChip was used for the investigation. A total of 46. Sumatran native cattle of three colors as follows: Brown (36 animals), white (9 animals), and black (1 animal), were used as experimental animals.

RESULTS: Results showed that the SNP markers ARS-BFGL-NGS-75486 (p = 2.46 × 10-7) and BTB-01992588 (p = 1.06 × 10-5) were selected as two genetic markers for coat color variation in animals under study, which were located at the cytoplasmic FMR1-interacting protein 2 (CYFIP2) gene at BTA7 and small G protein signaling modulator 1(SGSM1) genes at BTA17, respectively. The polymorphic informative content values of both SNP markers were 0.33 (ARS-BFGL-NGS-75486) and 0.13 (BTB-01992588). In this study, a genetic marker for coat color patterns in Sumatran native cattle was obtained based on the haplotypes of both SNP markers.

CONCLUSION: It can be concluded that CYFIP2 and SGSM1 are two coloration genes that affect the phenotype characteristics of Sumatran native cattle.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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