Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds

Abstract

Knowledge of linkage disequilibrium (LD), genetic structure and genetic diversity are some key parameters to study the breeding history of indigenous small ruminants. In this study, the OvineSNP50 Bead Chip array was used to estimate and compare LD, genetic diversity, effective population size (Ne) and genomic inbreeding in 186 individuals, from three Iranian indigenous sheep breeds consisting of Baluchi (n = 96), Lori-Bakhtiari (n = 47) and Zel (n = 47). The results of principal component analysis (PCA) revealed that all animals were allocated to the groups that they sampled and the admixture analysis revealed that the structure within the populations is best explained when separated into three groups (K = 3). The average r2 values estimated between adjacent single nucleotide polymorphisms (SNPs) at distances up to 10Kb, were 0.388±0.324, 0.353±0.311, and 0.333±0.309 for Baluchi, Lori-Bakhtiari and Zel, respectively. Estimation of genetic diversity and effective population size (Ne) showed that the Zel breed had the highest heterozygosity and Ne, whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using FROH (based on the long stretches of consecutive homozygous genotypes) showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that could be due to higher pressure of artificial selection on Baluchi breed. The results of genomic inbreeding and Ne showed an increase in sharing haplotypes in Baluchi, leading to the enlargement of LD and the consequences of linkage disequilibrium and haplotype blocks confirmed this point. Also, the persistence of the LD phase between Zel and Lori-Bakhtiari was highest indicating that these two breeds would be combined in a multi-breed training population in genomic selection studies.

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds

“…It can be used for analysis of animal admixture and monitoring of effective population size rather than census size for effective conservation programs [ 41 ]. Besides, the STRUCTURE analysis result gives the idea of introgression of alleles (i.e., breed admixture/ dilution) and the historical migration of individuals among the populations as well as common ancestry, if any, for different numbers of clusters [ 42 ].…”

Long-range linkage disequilibrium events on the genome of dromedary camels as a signal of epistatic and directional positive selection

“…This statistic, which ranges between 0 (no-disequilibrium) to 1 (complete disequilibrium) is preferred in animal populations LD analyses due to its low sensitivity to small sample sizes and low allele frequency markers [ 2 ]. Using these different estimators, the LD level and extent of LD decay have been widely investigated in different animal species, e.g., sheep [ 3 , 4 ], horse [ 5 , 6 ], cattle [ 7 , 8 ], and in Bactrian and dromedary camels [ 9 , 10 ]. The estimation of such LD pattern can be used to infer different evolutionary events, such as effective population size, level of genetic drift, and footprints of selection [ 1 ].…”