Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep
SM Ghoreishifar, H Moradi-Shahrbabak… - Archives Animal …, 2019 - aab.copernicus.org
Archives Animal Breeding, 2019•aab.copernicus.org
This research aimed to measure the extent of linkage disequilibrium (LD), effective
population size (N e), 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 (r 2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20
kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between
SNP pairs (40–60 kb). The N e of Zandi sheep in past (approximately 3500 generations ago) …
population size (N e), 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 (r 2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20
kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between
SNP pairs (40–60 kb). The N e of Zandi sheep in past (approximately 3500 generations ago) …
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.
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