Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert
Abstract 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 Takli...
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2025-03-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11445-9 |
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| author | Zhi-peng Han Lu-lu Zhang Xiao-peng Li Li-jun Zhu Xue-chen Zhang Wen Zhou Shudong Liu |
| author_facet | Zhi-peng Han Lu-lu Zhang Xiao-peng Li Li-jun Zhu Xue-chen Zhang Wen Zhou Shudong Liu |
| author_sort | Zhi-peng Han |
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| description | Abstract 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. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-03-01 |
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| spelling | doaj-art-9448bf4cdab645aead6f0483ed6a363d2025-08-20T03:41:49ZengBMCBMC Genomics1471-21642025-03-0126111610.1186/s12864-025-11445-9Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desertZhi-peng Han0Lu-lu Zhang1Xiao-peng Li2Li-jun Zhu3Xue-chen Zhang4Wen Zhou5Shudong Liu6College of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityCollege of Animal Science and Technology, Tarim UniversityAbstract 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.https://doi.org/10.1186/s12864-025-11445-9Taklamakan desertIndigenous sheepRuns of homozygosityLinkage disequilibriumROH islands |
| spellingShingle | Zhi-peng Han Lu-lu Zhang Xiao-peng Li Li-jun Zhu Xue-chen Zhang Wen Zhou Shudong Liu Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert BMC Genomics Taklamakan desert Indigenous sheep Runs of homozygosity Linkage disequilibrium ROH islands |
| title | Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert |
| title_full | Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert |
| title_fullStr | Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert |
| title_full_unstemmed | Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert |
| title_short | Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert |
| title_sort | single nucleotide polymorphism based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern taklamakan desert |
| topic | Taklamakan desert Indigenous sheep Runs of homozygosity Linkage disequilibrium ROH islands |
| url | https://doi.org/10.1186/s12864-025-11445-9 |
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