Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert

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.