# Genome-Wide Association Study and Whole-Genome Resequencing Reveal Key lincRNA and Candidate Gene for Polled Phenotype in Yak

## TL;DR

This study identifies a key lincRNA and candidate genes linked to the polled (hornless) trait in yaks, offering insights for breeding.

## Contribution

The study reveals a conserved genetic basis for the polled trait across different yak breeds using GWAS and resequencing.

## Key findings

- A 273.6 kb region on chromosome 1 was significantly associated with the polled trait in Xueduo yaks.
- Candidate genes EPCIP, OLIG1, and PAXBP1 were identified near the associated region.
- Ashdan and Xueduo yaks share the same candidate genes and some genetic variants for the polled trait.

## Abstract

The polled trait enhances yak breeding and management efficiency, making it a key breeding objective aligned with the developmental goals of modern animal husbandry. In this study, horned Xueduo yaks, polled Xueduo yaks, and Ashdan yaks (a polled breed derived from Datong yaks) were selected as research subjects. Using genome-wide association study (GWAS) technology, we aimed to identify key genes regulating the polled trait in yaks and to clarify whether the same genetic loci underlie the polled phenotype across different yak breeds, thereby providing theoretical support and technical guidance for polled yak breeding.

Yaks are important livestock in high-altitude regions, and their polled trait can effectively improve breeding and management efficiency. In this study, whole-genome resequencing combined with a GWAS was employed to identify a significantly associated region of approximately 273.6 kb on chromosome 1 (36,313,286–36,586,879 bp) in Xueduo yaks. This region contains 1001 significant single-nucleotide polymorphism (SNP) loci and is located within a long intergenic non-coding RNA (lincRNA) region. Candidate genes EPCIP, OLIG1 and PAXBP1 adjacent to this region were identified. Among these, the PAXBP1 gene plays a crucial role in neural crest development, suggesting that it may be a core gene regulating horn development in yaks. Further analysis of Ashdan yaks (a polled breed developed from Datong yaks) indicated that the two breeds share the same candidate genes and a subset of associated genetic variants for the polled trait, suggesting a degree of genetic conservation underlying this trait across yak breeds. This study provides a theoretical basis for polled yak breeding.