Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana)...

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Autores principales:	Maria Chiara Fabbri, Christos Dadousis, Francesco Tiezzi, Christian Maltecca, Emmanuel Lozada-Soto, Stefano Biffani, Riccardo Bozzi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/02acf068e2804e36a672aaccef5b9dab
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spelling	oai:doaj.org-article:02acf068e2804e36a672aaccef5b9dab2021-11-04T06:09:18ZGenetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity1932-6203https://doaj.org/article/02acf068e2804e36a672aaccef5b9dab2021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8544844/?tool=EBIhttps://doaj.org/toc/1932-6203In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.Maria Chiara FabbriChristos DadousisFrancesco TiezziChristian MalteccaEmmanuel Lozada-SotoStefano BiffaniRiccardo BozziPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maria Chiara Fabbri Christos Dadousis Francesco Tiezzi Christian Maltecca Emmanuel Lozada-Soto Stefano Biffani Riccardo Bozzi Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
description	In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
format	article
author	Maria Chiara Fabbri Christos Dadousis Francesco Tiezzi Christian Maltecca Emmanuel Lozada-Soto Stefano Biffani Riccardo Bozzi
author_facet	Maria Chiara Fabbri Christos Dadousis Francesco Tiezzi Christian Maltecca Emmanuel Lozada-Soto Stefano Biffani Riccardo Bozzi
author_sort	Maria Chiara Fabbri
title	Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
title_short	Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
title_full	Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
title_fullStr	Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
title_full_unstemmed	Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
title_sort	genetic diversity and population history of eight italian beef cattle breeds using measures of autozygosity
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/02acf068e2804e36a672aaccef5b9dab
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Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

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