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Objective: Lop sheep species exhibit remarkable adaptability to desert pastures and extreme arid climates, demonstrating tolerance to rough feeding and high resistance to stress. However, little is known about the population genetic diversity of Lop sheep and the genetic mechanisms underlying their adaptability to extreme environments. Methods: Blood samples were collected from a total of 110 individuals comprising 80 Ruoqiang Lop sheep and 30 Yuli Lop sheep. A total of 110 Lop sheep were subjected to whole genome resequencing to analyze genetic diversity, population structure, and signatures of selection in both regions. Results: The genetic diversity of the Lop sheep population is substantial, and the degree of inbreeding is low. In comparison to the Lop sheep in Yuli County, the genetic diversity and linkage disequilibrium analysis results for the Lop sheep population in Ruoqiang County are slightly lower. Population structure analysis indicates that Ruoqiang and Yuli Lop sheep have differentiated into two independent groups. Using Yuli Lop sheep as the reference group, an analysis of the extreme environmental adaptability selection signal of Lop sheep was conducted. The FST and π ratio under the 1% threshold identified 1686 and 863 candidate genes, respectively, with their intersection yielding a total of 122 candidate genes. Functional annotation revealed that these genes are associated with various traits, including immune response (SLC12A2, FOXP1, PANX1, DYNLRB2, RAP1B, and SEMA4D), heat and cold resistance (DNAJC13, PLCB1, HIKESHI, and PITPNC1), desert adaptation (F13A1, PANX1, ST6GAL1, STXBP3, ACTN4, and ATP6V1A), and reproductive performance (RAP1B, RAB6A, PLCB1, and METTL15). Conclusions: These research findings provide a theoretical foundation for understanding the survival and reproductive characteristics of Lop sheep in extreme environments, and they hold practical value for the conservation and utilization of Lop sheep genetic resources, as well as for genetic improvement efforts.

The Lop sheep (LOP), a unique local breed from Xinjiang, exhibits remarkable resilience to the harsh conditions of a desert arid climate and frequent sandstorms, alongside notable fecundity characteristics. This study aims to investigate the adaptability of LOP within this challenging environment by collecting whole blood samples from 110 LOP individuals in the Lop Nur region of Xinjiang for genome resequencing. The resulting data will be compared with whole genome resequencing information from 22 local sheep breeds worldwide to analyze the origin and evolution of LOP. Additionally, comparisons will be made with HUS sheep from warm and humid regions to identify genomic differences through selection signal analysis, thereby assessing the impact of a desert arid climate on the extreme living conditions of LOP. Finally, qPCR was used to preliminarily analyse the impact of the desert arid climate on the genome of the Bactrian sheep. Genetic diversity results indicate that LOP exhibits a relatively stable genetic structure alongside high genetic diversity. The results of population structure analysis and gene flow indicate that we can tentatively posit that LOP is a breed that originated from the Middle East, subsequently mixing with MGS upon its arrival in Xinjiang. Chinese local sheep breeds trace their origins to AMS, with the gene flow evolving from west to east, progressing through mountainous hills (BSBS), basins (LOP, HTS, CLHS, DLS), plains (MGS, TANS), and coastal areas (HUS). LOP is associated with ALTS, BSBS, HTS, CLHS, and DLS, as well as with MGS, HUS, TANS, WDS, and SSSP, in a context of gene exchange, with the degree of exchange diminishing in that order. Selection signal analysis revealed that the candidate genes identified are closely related to adaptation to desert arid climates and disease resistance (PDGFD, NDUFS3, ATP1B2, ITGB8, and CD79A), using HUS as the reference group. qPCR results demonstrated that LOP was significantly upregulated in cardiac, splenic, and lung tissues compared to HUS, suggesting that LOP plays a crucial role in cardiac function, immune response, and respiratory capacity.