Abstract
This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD () for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was but rapidly decreased to by increasing the distance between SNP pairs (40–60 kb). The of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long ( Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.
Highlights
The population of sheep in Iran, consisting of many different breeds, is estimated to be approximately 50 million, which constitutes the most important economic area in the livestock industry of the country (Moradi et al, 2012)
There is potential to increase genetic gain in Zandi sheep by adopting genomic selection technology; the success of genomic selection relies on the level of genome-wide linkage disequilibrium (LD) between markers and causal mutations (Hayes et al, 2013)
The aims of this research were to (1) measure the amount and pattern of LD, (2) examine genetic diversity by measuring Ne and runs of homozygosity (ROHs)-based inbreeding, and (3) estimate the minimum number of single-nucleotide polymorphism (SNP) required for robust genomic selection and genome-wide association studies (GWASs) in Zandi sheep
Summary
The population of sheep in Iran, consisting of many different breeds, is estimated to be approximately 50 million, which constitutes the most important economic area in the livestock industry of the country (Moradi et al, 2012). Because of its large population in Iran (about 2 million heads), there is much interest in genetically improving Zandi sheep for growth traits (Ghafouri-Kesbi et al, 2008; Mohammadi et al, 2013). The adoption of such new technologies as genomic selection can play an essential role in satisfying the demand for meat production. There is potential to increase genetic gain in Zandi sheep by adopting genomic selection technology; the success of genomic selection relies on the level of genome-wide linkage disequilibrium (LD) between markers and causal mutations (Hayes et al, 2013).
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