Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

Abstract

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 $0.21\pm 0.25$ but rapidly decreased to $0.10\pm 0.16$ by increasing the distance between SNP pairs (40-60 kb). The $N_e$ 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 ( $>10$ 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.

Figure 1

PCA plot based on a genomic relationship matrix. The first two principal components (PCs) and the variance explained by each component is shown on the corresponding axis. The amount of variance explained by the first two components is relatively small (10.5 %), representing a great deal of genetic diversity among samples.

Figure 2

Estimation of effective population size ($N_{\mathrm{e}}$) of Zandi sheep using genome-wide linkage disequilibrium ($r^{\mathrm{2}}$) between SNPs. $N_{\mathrm{e}}$ was estimated using average $r^{\mathrm{2}}$ between markers at different distances by SNeP software. The $N_{\mathrm{e}}$ in the past (approximately 3500 generations ago) was 6475, which decreased to 3000 approximately 500 generations ago and then continued to decrease more rapidly until recent generations. The $N_{\mathrm{e}}$ of recent populations (up to five generations ago) was estimated to be 122.

Figure 3

Frequency and proportion of detected ROHs with different lengths (Mb). In total, 558 ROHs (with average length of $\mathrm{10.77}\pm \mathrm{8.36}$ Mb) were detected in 89 sheep, and in 7 remaining sheep no ROHs were found. The ROH segments with the length of 4–10 Mb were the most frequent (62.2 %), and those with the length of $\mathit{>}\mathrm{30}$ Mb were the least frequent (3.2 %).

Figure 4

Number of detected ROHs and percent of coverage per autosome. In total, 558 ROHs were detected. For each autosome, the average length of a ROH (for the sheep with at least one ROH) was divided by the length of the chromosome to calculate the percentage of each autosome covered by ROHs. OAR1 with 60 ROHs (average length of $\mathrm{12.9}\pm \mathrm{8.8}$ Mb) had the highest number of ROHs, and OAR14, OAR16, and OAR24 with 9 ROHs (average length of $\mathrm{10.3}\pm \mathrm{5.9}$ Mb) had the lowest number of ROHs.