Han Zhi-Peng, Zhang Lu-Lu, Li Xiao-Peng, Zhu Li-Jun, Zhang Xue-Chen, Zhou Wen, Liu Shudong
College of Animal Science and Technology, Tarim University, Alar, 843300, China.
Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China.
BMC Genomics. 2025 Mar 18;26(1):267. doi: 10.1186/s12864-025-11445-9.
Runs of Homozygosity (ROH) are homozygous genomic fragments inherited from parents to offspring. ROH can be used to indicate the level of inbreeding, as well as to identify possible signatures of artificial or natural selection. Indigenous sheep populations on the southern edge of the Taklimakan Desert have evolved unique genetic traits adapted to extreme desert environments. In an attempt to better understand the adaptive mechanisms of these populations under harsh conditions, we used Illumina® Ovine SNP50K BeadChip to perform a genomic characterization of three recognized breeds (Duolang: n = 36, Hetian: n = 84, Qira black: n = 189) and one ecotypic breed (Kunlun: n = 27) in the region. Additionally, we assessed genomic inbreeding coefficients through ROH analysis, revealing insights into the inbreeding history of these populations. Subsequently, we retrieved candidate genes associated with economic traits in sheep from ROH islands in each breed. To better understand the autozygosity and distribution of ROH islands in these indigenous sheep breeds relative to international breeds, we also included three commercial mutton breeds (Poll Dorset: n = 108, Suffolk: n = 163, Texel: n = 150). The study revealed that among seven sheep breeds, Hetian exhibited the shortest linkage disequilibrium (LD) decay distance, while Kunlun demonstrated the highest LD levels. A total of 10,916 ROHs were obtained. The number of ROHs per breed ranged from 34 (Kunlun) to 2,826 (Texel). The length of ROH was mainly 1-5 Mb (63.54%). Furthermore, 991 candidate genes specific to indigenous sheep breeds were identified, including those associated with heat tolerance, adaptability, energy metabolism, reproduction, and immune response. These findings elucidate the genetic adaptation of indigenous sheep in the Taklimakan Desert, uncovering distinctive characteristics of indigenous sheep formation, and advocating for the conservation and genetic enhancement of local sheep populations.
纯合性片段（ROH）是从亲代遗传给子代的纯合基因组片段。ROH可用于指示近亲繁殖水平，以及识别可能的人工选择或自然选择特征。塔克拉玛干沙漠南缘的本土绵羊种群已经进化出适应极端沙漠环境的独特遗传特性。为了更好地了解这些种群在恶劣条件下的适应机制，我们使用Illumina®绵羊SNP50K芯片对该地区三个公认品种（多浪羊：n = 36，和田羊：n = 84，策勒黑羊：n = 189）和一个生态型品种（昆仑羊：n = 27）进行了基因组特征分析。此外，我们通过ROH分析评估了基因组近亲繁殖系数，揭示了这些种群的近亲繁殖历史。随后，我们从每个品种的ROH岛中检索了与绵羊经济性状相关的候选基因。为了更好地了解这些本土绵羊品种相对于国际品种的纯合性和ROH岛分布情况，我们还纳入了三个商业肉羊品种（无角陶赛特羊：n = 108，萨福克羊：n = 163，特克塞尔羊：n = 150）。研究表明，在七个绵羊品种中，和田羊的连锁不平衡（LD）衰减距离最短，而昆仑羊的LD水平最高。共获得10916个ROH。每个品种的ROH数量从34个（昆仑羊）到2826个（特克塞尔羊）不等。ROH的长度主要为1 - 5 Mb（63.54%）。此外，还鉴定出991个本土绵羊品种特有的候选基因，包括与耐热性、适应性、能量代谢、繁殖和免疫反应相关的基因。这些发现阐明了塔克拉玛干沙漠本土绵羊的遗传适应性，揭示了本土绵羊形成的独特特征，并倡导对当地绵羊种群进行保护和遗传改良。
