# ASIP, AHCY and ITCH Genes Are Associated with the Coat Color of Local Goats (Capra hircus) of Southwestern China

## TL;DR

This study identifies genes linked to coat color variation in Chongqing goats from Southwestern China, offering insights for breed improvement and conservation.

## Contribution

The study discovers ASIP, AHCY, ITCH, and TPK1 as novel genes associated with coat color in local Chinese goats.

## Key findings

- ASIP and AHCY genes are linked to black coat color in Chongqing goats.
- ITCH gene is potentially associated with white coat color expression.
- TPK1 is newly identified as a gene related to coat color in goats.

## Abstract

Coat color is an important economic trait in goats, influencing breed identification and market value. Chongqing goats, representative local breeds in Southwestern China, exhibit diverse coat colors; however, the genetic basis underlying this variation remains poorly understood. In this study, we identified genes associated with the coat color of Chongqing goats via a genome-wide association study (GWAS). The results revealed that the ASIP, AHCY, and ITCH genes on chromosome 13 play a significant role in coat color variation in Chongqing goats. Further haplotype and functional analyses supported the association of these genes with coat color, with ASIP and AHCY related to black coat color and the ITCH gene potentially influencing white coat color expression. These findings enhance our understanding of the genetic mechanisms regulating coat color in goats and provide valuable genetic resources for breed conservation and improvement.

The local goat breeds of Chongqing represent the typical goat populations of Southwestern China and play a significant role in global goat research. However, studies on these goats remain limited. Chongqing goats exhibit diverse coat colors, a crucial economic trait essential for individual and breed identification. In this study, we performed genome-wide association analysis (GWAS) of Chongqing goats to identify candidate genes associated with coat color. The results of the GWAS revealed that the ASIP, AHCY, and ITCH genes on chromosome 13 are significantly associated with coat color variation in Chongqing goats. Furthermore, haplotype analysis, gene function annotation, and pathway analysis enrichment further confirmed that a significant region on chromosome 13 is associated with coat color in local Chongqing goats, and that ASIP and AHCY are related to black coat color, whereas ITCH is potentially associated with white coat expression. Additionally, we also identified TPK1 as being associated with coat color in goats, which has hardly been reported. The newly identified genes expand our understanding of the complex genetic architecture underlying pigmentation traits in livestock. Our study identifies the genes related to coat color in local goats, which enriches the genetic resource pool of goats and contributes to a deeper understanding of the genetic mechanisms underlying coat color in these breeds.