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

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 (N(e)...

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Autores principales: Barani, S., Nejati-Javaremi, A., Moradi, M. H., Moradi-Sharbabak, M., Gholizadeh, M., Esfandyari, H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10237446/
https://www.ncbi.nlm.nih.gov/pubmed/37267244
http://dx.doi.org/10.1371/journal.pone.0286463
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author Barani, S.
Nejati-Javaremi, A.
Moradi, M. H.
Moradi-Sharbabak, M.
Gholizadeh, M.
Esfandyari, H.
author_facet Barani, S.
Nejati-Javaremi, A.
Moradi, M. H.
Moradi-Sharbabak, M.
Gholizadeh, M.
Esfandyari, H.
author_sort Barani, S.
collection PubMed
description 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 (N(e)) 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 r(2) 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 (N(e)) showed that the Zel breed had the highest heterozygosity and N(e), whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using F(ROH) (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 N(e) 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.
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spelling pubmed-102374462023-06-03 Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds Barani, S. Nejati-Javaremi, A. Moradi, M. H. Moradi-Sharbabak, M. Gholizadeh, M. Esfandyari, H. PLoS One Research Article 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 (N(e)) 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 r(2) 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 (N(e)) showed that the Zel breed had the highest heterozygosity and N(e), whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using F(ROH) (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 N(e) 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. Public Library of Science 2023-06-02 /pmc/articles/PMC10237446/ /pubmed/37267244 http://dx.doi.org/10.1371/journal.pone.0286463 Text en © 2023 Barani et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Barani, S.
Nejati-Javaremi, A.
Moradi, M. H.
Moradi-Sharbabak, M.
Gholizadeh, M.
Esfandyari, H.
Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title_full Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title_fullStr Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title_full_unstemmed Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title_short Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds
title_sort genome-wide study of linkage disequilibrium, population structure, and inbreeding in iranian indigenous sheep breeds
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10237446/
https://www.ncbi.nlm.nih.gov/pubmed/37267244
http://dx.doi.org/10.1371/journal.pone.0286463
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