# Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS

## TL;DR

This study identifies genes linked to growth and milk production in three Anatolian goat breeds using genome-wide analysis, offering insights for breeding strategies.

## Contribution

The study reveals breed-specific candidate genes for growth and milk traits in Anatolian goats using GWAS.

## Key findings

- ID4 and CXCR4 genes directly affect birth weight and milk yield in Honamlı goats.
- Eight protein-coding genes influence live weight at 90 days in Hair and Kabakulak goats.
- 103 additional genes show potential effects on growth and milk traits through suggestive SNPs.

## Abstract

This study aimed to identify candidate genes related to birth weight (BW), live weight at 90th day (90-LW), and lactation milk yield (LMY) in Hair (HAI), Honamlı (HNM), and Kabakulak (KBK) goats, providing a genome-wide basis for further selection strategies. The genome-wide efficient mixed model association approach was assessed with 309.342 bi-allelic single nucleotide polymorphisms (SNPs) across 481 animals to detect significant variants and their corresponding genomic regions. False discovery rate (FDR) correction and suggestive significance threshold were applied to identify SNPs having direct and potential effects on traits of interest, respectively. A total of 138 outlier SNPs (20 in HNM, 47 in HAI, and 71 in KBK) exceeded suggestive significance, of which 12 SNPs were identified to meet Benjamini-Hochberg’s FDR criterion, suggesting that the overlapped protein-coding genes directly influence the phenotypic traits of interest. This approach revealed that the ID4 and CXCR4 genes directly affect BW and LMY traits in HNM goats, whereas no significant associations were observed regarding these traits in HAI and KBK goats. Additionally, a total of 8 protein-coding genes were identified to directly influence the 90-LW trait in HAI (MFSD1, CHMP4C, and MAP1B) and KBK (IGSF21, RALY, ZNF507, SLC38A10, and PGBD5) goats. The remaining 126 suggestive SNPs, on the other hand, either overlapped or were located near 103 protein-coding genes, indicating their potential effects on growth and milk yield. Both direct and potential protein-coding genes identified in this study seem promising for designing comprehensive selection strategies to improve growth and milk traits in Anatolian goats.

The online version contains supplementary material available at 10.1007/s00335-026-10203-w.