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 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.

Keywords: Indigenous sheep; Linkage disequilibrium; ROH islands; Runs of homozygosity; Taklamakan desert.

Fig. 1

Geographic distribution of the four indigenous sheep populations from the southern edge of the Taklamakan Desert in Xinjiang, China

Fig. 2

(a) LD decay map measured by r² over distance between SNPs in seven sheep populations; (b) Estimated Ne for 10,000 ancestral generations of four Chinese indigenous sheep breeds

Fig. 3

The average sum of ROH of each breed in different ROH length classes

Fig. 4

Number of ROH found on each chromosome in seven sheep populations

Fig. 5

The total genomic length covered by ROH per individual (x axis) and total number of ROH per individual (y axis)

Fig. 6

(A) Distribution of the runs of homozygosity inbreeding coefficient (F_ROH) within each breed; (B) Trend plot of F_ROH and F_HOM for each sheep breed

Fig. 7

(a) Manhattan plot of SNPs in ROH islands on different chromosomes of four indigenous sheep breeds; (b) Manhattan plot of SNPs in ROH islands on different chromosomes of three commercial meat sheep breeds; (c) Wayne diagram of candidate genes of four indigenous sheep breeds; (d) Wayne diagram of candidate genes of three commercial meat sheep breeds; (e) Wayne plots of candidate genes in four indigenous sheep breeds versus three commercial meat sheep breeds