# Genetic Structure and Selective Signature Analysis of Xinjiang Local Sheep Populations

## TL;DR

This study explores the genetic makeup and adaptations of Xinjiang's local sheep breeds, revealing how they survive extreme environments and how their traits could be used in breeding programs.

## Contribution

The study provides a comprehensive genomic analysis of seven Xinjiang sheep breeds, identifying unique genetic adaptations to extreme environments and traits related to body size.

## Key findings

- Kirgiz sheep have genetic variants in DNA repair and energy metabolism genes, aiding high-altitude survival.
- Turpan Black sheep possess genetic markers linked to heat stress response and pigmentation.
- Candidate genes for body size regulation were identified, including CUX1 and KIT.

## Abstract

Xinjiang harbors numerous local sheep breeds that have adapted to extreme environments, including high-altitude plateaus and hot deserts; however, their genetic background remains poorly understood. In this study, we analyzed whole-genome sequences from 140 individuals representing seven indigenous Xinjiang breeds to investigate their genetic diversity, population structure, and the genetic basis of their adaptations to harsh environments and variation in body size. All breeds exhibited comparable levels of genetic diversity, and geographic isolation likely contributed significantly to the observed genetic differentiation among populations. Kirgiz sheep from the Pamir Plateau harbor unique genetic variants in genes involved in DNA repair, energy metabolism, and nervous system development—traits that may facilitate survival under high-altitude conditions. Turpan Black sheep, which are adapted to extreme heat, carry genetic variants potentially associated with heat stress response and coat pigmentation. We also identified several candidate genes linked to body size that may influence growth and development. These findings provide valuable genomic insights to support future breeding programs and conservation efforts for Xinjiang’s indigenous sheep breeds.

The unique ecological gradients of Xinjiang have fostered a rich reservoir of genetic resources in local sheep populations. However, the population genetic structure, adaptive mechanisms to extreme environments, and the genetic basis underlying key economic traits of these breeds remain poorly understood. To address this gap, we performed whole-genome resequencing of 140 individuals from seven indigenous sheep populations—Altay, Bayinbuluke, Kazakh, Kirgiz, Bashibai, Turpan Black, and Yemule White—identifying 18,700,507 high-quality SNPs. Genetic diversity analyses revealed that all populations exhibited comparable levels of genetic diversity, with modest variation across breeds, with Turpan Black sheep exhibiting the highest observed heterozygosity (Ho = 0.3110) and proportion of polymorphic sites, whereas Kirgiz sheep showed comparatively lower values. Population structure analyses consistently indicated that geographic isolation is the primary driver of genetic differentiation, with Kirgiz sheep from the Pamir Plateau in southern Xinjiang displaying the greatest genetic distance relative to northern Xinjiang populations. By integrating multiple selection signature detection methods—including F_ST, π ratio, and XP-CLR—we found that genes under selection in Kirgiz sheep were significantly enriched in biological pathways related to stem cell pluripotency regulation (e.g., BMPR1B), DNA repair (e.g., DDB2), and neural development, thereby elucidating their unique genetic adaptations to high-altitude environments. In contrast, Turpan Black sheep appear to cope with heat stress through mechanisms involving basal transcriptional regulation (e.g., GTF2I), maintenance of protein homeostasis (e.g., DNAJB14), and melanin biosynthesis (e.g., MC1R). Furthermore, comparative analysis of body size identified a suite of candidate genes associated with growth and development (e.g., CUX1, KIT), which are primarily involved in transcriptional regulation, protein kinase activity, and the ubiquitin-mediated proteolytic system, thereby revealing a multi-layered genetic regulatory network governing body conformation. Collectively, this study provides a comprehensive genomic framework for understanding the genetic structure, adaptive evolution, and molecular basis of economically important traits in indigenous sheep breeds from Xinjiang, offering valuable candidate targets for future functional validation and precision breeding programs.