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Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds

SIMPLE SUMMARY: Linkage disequilibrium (LD) of genomic markers is related to various evolutionary forces, such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutations, and hence is an essential parameter to examine population history. In this analysis, we examined...

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Autores principales: Fabbri, Maria Chiara, Dadousis, Christos, Bozzi, Riccardo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341513/
https://www.ncbi.nlm.nih.gov/pubmed/32545850
http://dx.doi.org/10.3390/ani10061034
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author Fabbri, Maria Chiara
Dadousis, Christos
Bozzi, Riccardo
author_facet Fabbri, Maria Chiara
Dadousis, Christos
Bozzi, Riccardo
author_sort Fabbri, Maria Chiara
collection PubMed
description SIMPLE SUMMARY: Linkage disequilibrium (LD) of genomic markers is related to various evolutionary forces, such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutations, and hence is an essential parameter to examine population history. In this analysis, we examined the LD pattern of three Italian local beef breeds (Calvana, Mucca Pisana, and Pontremolese) facing the risk of extinction, using the commercial Limousin beef breed as a control. Our results provide important information on the population history and the current status of the breeds and they can be further used for conservation and breeding purposes. ABSTRACT: The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r(2)) across autosomes. Moreover, r(2) values were used to calculate historical and contemporary effective population size (N(e)) in each breed. Average r(2) was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in N(e) across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.
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spelling pubmed-73415132020-07-14 Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds Fabbri, Maria Chiara Dadousis, Christos Bozzi, Riccardo Animals (Basel) Article SIMPLE SUMMARY: Linkage disequilibrium (LD) of genomic markers is related to various evolutionary forces, such as inbreeding, nonrandom mating, population bottleneck, drift, recombination, and mutations, and hence is an essential parameter to examine population history. In this analysis, we examined the LD pattern of three Italian local beef breeds (Calvana, Mucca Pisana, and Pontremolese) facing the risk of extinction, using the commercial Limousin beef breed as a control. Our results provide important information on the population history and the current status of the breeds and they can be further used for conservation and breeding purposes. ABSTRACT: The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r(2)) across autosomes. Moreover, r(2) values were used to calculate historical and contemporary effective population size (N(e)) in each breed. Average r(2) was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in N(e) across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation. MDPI 2020-06-14 /pmc/articles/PMC7341513/ /pubmed/32545850 http://dx.doi.org/10.3390/ani10061034 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Fabbri, Maria Chiara
Dadousis, Christos
Bozzi, Riccardo
Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title_full Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title_fullStr Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title_full_unstemmed Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title_short Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds
title_sort estimation of linkage disequilibrium and effective population size in three italian autochthonous beef breeds
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341513/
https://www.ncbi.nlm.nih.gov/pubmed/32545850
http://dx.doi.org/10.3390/ani10061034
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