# Whole-Genome Resequencing Analysis of Athletic Traits in Grassland-Thoroughbred

## TL;DR

This study identifies genes linked to athletic performance in a new Chinese horse breed using genome sequencing and selection analysis.

## Contribution

The study introduces a new racehorse breed and identifies genes associated with athletic traits through whole-genome resequencing and selection signal analysis.

## Key findings

- Strong selection pressure was detected on chromosomes 1 and 3 in racing-type horses.
- 215 candidate genes were identified using π ratio, iHS, Fst, and XP-EHH methods.
- Genes like PPARGC1A and FOXO1 are linked to muscle function and metabolism in racehorses.

## Abstract

Enhancing speed remains the primary objective in racehorse breeding programs. In this study, whole-genome resequencing was conducted on 30 racing-type and 30 non-racing-type Grassland-Thoroughbreds, with an average sequencing depth of 25.63×. Selection signals were detected using multiple methods, including π ratio, iHS, Fst, and XP-EHH, revealing strong selective pressure on chromosomes 1 and 3 and identifying a total of 215 candidate genes. Additionally, Fst analysis of Indels yielded 661 more candidate genes. Functional enrichment analysis indicated that pathways related to immune regulation, neural signal transmission, muscle contraction, and energy metabolism play crucial roles in differences in athletic performance. Among the identified genes, PPARGC1A, FOXO1, SGCD, FOXP2, PRKG1, SLC25A15, CKMT2, and TRAP1 are closely associated with muscle function, metabolism, and neural regulation, suggesting their significant roles in shaping racehorse traits.

Speed is not only the primary objective of racehorse breeding but also a crucial indicator for evaluating racehorse performance. This study investigates a newly developed racehorse breed in China. Through whole-genome resequencing, we selected 60 offspring obtained from the crossbreeding of Thoroughbred horses and Xilingol horses for this study. This breed is tentatively named “Grassland-Thoroughbred”, and the samples were divided into two groups based on racing ability: 30 racehorses and 30 non-racehorses. Based on whole-genome sequencing data, the study achieved an average sequencing depth of 25.63×. The analysis revealed strong selection pressure on chromosomes (Chr) 1 and 3. Selection signals were detected using methods such as the nucleotide diversity ratio (π ratio), integrated haplotype score (iHS), fixation index (Fst), and cross-population extended haplotype homozygosity (XP-EHH). Regions ranked in the top 5% by at least three methods were designated as candidate regions. This approach detected 215 candidate genes. Additionally, the Fst method was employed to detect Indels, and the top 1% regions detected were considered candidate regions, covering 661 candidate genes. Functional enrichment analysis of the candidate genes suggests that pathways related to immune regulation, neural signal transmission, muscle contraction, and energy metabolism may significantly influence differences in performance. Among these identified genes, PPARGC1A, FOXO1, SGCD, FOXP2, PRKG1, SLC25A15, CKMT2, and TRAP1 play crucial roles in muscle function, metabolism, sensory perception, and neurobiology, indicating their key significance in shaping racehorse phenotypes. This study not only enhances understanding of the molecular mechanisms underlying racehorse speed but also provides essential theoretical and practical references for the molecular breeding of Grassland-Thoroughbreds.