Identification of TYR gene variants associated with white coat color in Hanwoo cattle using whole-genome sequencing

TL;DR

This study identifies genetic variants in the TYR gene linked to white coat color in rare White Hanwoo cattle, revealing reduced genetic diversity and potential inbreeding in this population.

Contribution

The study identifies a functionally relevant missense variant in the TYR gene associated with white coat color in Hanwoo cattle.

Findings

White Hanwoo cattle show reduced genetic diversity and higher inbreeding compared to Brown Hanwoo.

A missense variant in the TYR gene is associated with white coat color and may affect melanin biosynthesis.

Genome-wide association identified 3,482 SNPs significantly related to coat color in Hanwoo cattle.

Abstract

Hanwoo cattle, a native Korean breed, display diverse coat colors, with White Hanwoo being extremely rare. Understanding the genetic basis of white coat color is essential for preserving genetic diversity and uncovering pigmentation mechanisms. This study aims to explore genetic differences between White and Brown Hanwoo and identify coat color-associated variants through genome-wide association study.

Population structure analysis revealed clear genetic difference between the Brown Hanwoo (B×B) and White Hanwoo (W×W) groups. The W×W_White population exhibited the highest number of runs of homozygosity (ROH, n = 423) and the highest identity-by-descent (IBD) value (0.3547), suggesting reduced genetic diversity and potential inbreeding due to artificial selection. In contrast, the B×B_Brown group showed lower ROH (n = 78) and IBD (0.2956), indicating greater genetic variability. Genome-wide association study identified 3,482 SNPs significantly related to coat color. Notably, five missense variants were discovered in TYR, FAT3, ENSBTAG00000051637, and SPTY2D1, including a G-to-C substitution in exon 2 of the TYR gene. This mutation caused a glycine-to-arginine amino acid change, and structural modeling indicated a potential alteration in TYR protein conformation and hydrogen bonding, suggesting its involvement in melanin biosynthesis and coat color expression.

This study highlights significant genomic differences between White and Brown Hanwoo populations, including reduced genetic diversity in White Hanwoo due to potential inbreeding. In addition, it confirms the TYR gene as a critical determinant of coat color through the identification of a functionally relevant missense variant. These findings provide valuable insights for Hanwoo breeding and conservation strategies and lay the foundation for further functional studies on pigmentation-related genes.

The online version contains supplementary material available at 10.1186/s12864-025-12458-0.

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