# Whole-Genome Sequencing Reveals Breed-Specific SNPs, Indels, and Signatures of Selection in Royal White and White Dorper Sheep

## TL;DR

This study uses whole-genome sequencing to compare Royal White and White Dorper sheep, identifying genetic differences linked to traits like growth, immunity, and reproduction.

## Contribution

The first whole-genome sequencing-based comparison of Royal White and White Dorper sheep, revealing breed-specific genetic markers and selection signatures.

## Key findings

- Royal White sheep showed genetic differences in growth and health-related regions.
- White Dorper sheep exhibited genetic variations in immunity and reproduction-related regions.
- Over 21 million SNPs and nearly 2.9 million indels were identified in Royal White sheep.

## Abstract

Royal White and White Dorper sheep are two breeds raised for meat in the U.S., yet little is known about their genomes. In this study, we examined the genome-wide DNA variation to identify unique regions that define each breed. We found that some of these genetic changes are likely linked to economically important traits such as parasite resistance, body growth, reproduction, and meat quality. For example, Royal White sheep showed genetic differences in regions related to growth and health, while White Dorper sheep showed differences in regions related to immunity and reproduction. These findings improve our understanding of the biology of these breeds and may help farmers refine breeding practices in the future.

Whole-genome sequencing (WGS) is a powerful tool for uncovering genome-wide variation, identifying selection signatures, and guiding genetic improvement in livestock. Royal White (RW) and White Dorper (WD) sheep are economically important meat-type hair breeds in the U.S., yet their genomic architecture remains poorly characterized. In this study, WGS was performed on 20 ewes (n = 11 RW, n = 9 WD) to identify and annotate SNPs and small insertions and deletions (indels). Functional annotation, gene enrichment, population structure, and selective sweep analysis were also performed. Selective sweep analysis was conducted by integrating the fixation index (FST), nucleotide diversity (π), and Tajima’s D to identify candidate regions under putative recent positive selection. A total of 21,957,139 SNPs and 2,866,600 indels were identified in RW sheep, whereas 18,641,789 SNPs and 2,397,368 indels were identified in WD sheep. In RW sheep, candidate genes under selection were associated with health and parasite resistance (NRXN1, HERC6, TGFB2) and growth traits (JADE2). In WD sheep, selective sweep regions included genes linked to immune response and parasite resistance (TRIM14), body weight (PLXDC2), and reproduction (STPG3). These findings were supported by sheep-specific quantitative trait loci (QTL) annotations and previously reported SNP–trait associations. This study provides the first WGS-based genomic comparison between RW and WD sheep, establishing a foundation for future genetic improvement, including targeted selection for enhanced immune function, disease resistance, and other economically important traits in these breeds.