The genetic heritage of Alpine local cattle breeds using genomic SNP data

Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead...

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Main Authors: Gabriele Senczuk, Salvatore Mastrangelo, Elena Ciani, Luca Battaglini, Filippo Cendron, Roberta Ciampolini, Paola Crepaldi, Roberto Mantovani, Graziella Bongioni, Giulio Pagnacco, Baldassare Portolano, Attilio Rossoni, Fabio Pilla, Martino Cassandro
Format: Article
Language:deu
Published: BMC 2020-07-01
Series:Genetics Selection Evolution
Online Access:http://link.springer.com/article/10.1186/s12711-020-00559-1
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spelling doaj-a00fdaa3d38a4c14ac724f89f239bf052020-11-25T03:07:20ZdeuBMCGenetics Selection Evolution1297-96862020-07-0152111210.1186/s12711-020-00559-1The genetic heritage of Alpine local cattle breeds using genomic SNP dataGabriele Senczuk0Salvatore Mastrangelo1Elena Ciani2Luca Battaglini3Filippo Cendron4Roberta Ciampolini5Paola Crepaldi6Roberto Mantovani7Graziella Bongioni8Giulio Pagnacco9Baldassare Portolano10Attilio Rossoni11Fabio Pilla12Martino Cassandro13Dipartimento di Agricoltura, Ambiente e Alimenti, University of MoliseDipartimento Scienze Agrarie, Alimentari e Forestali, University of PalermoDipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of BariDipartimento di Scienze Agrarie Forestali e Alimentari, University of TorinoDipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of PadovaDipartimento di Scienze Veterinarie, University of PisaDipartimento di Scienze Agrarie ed Ambientali - Produzione, Territorio, Agroenergia, University of MilanoDipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of PadovaIstituto Sperimentale Italiano Lazzaro SpallanzaniIstituto di Biologia e Biotecnologia Agraria (IBBA), CNRDipartimento Scienze Agrarie, Alimentari e Forestali, University of PalermoItalian Brown Cattle Breeders’ AssociationDipartimento di Agricoltura, Ambiente e Alimenti, University of MoliseDipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of PadovaAbstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.http://link.springer.com/article/10.1186/s12711-020-00559-1
collection DOAJ
language deu
format Article
sources DOAJ
author Gabriele Senczuk
Salvatore Mastrangelo
Elena Ciani
Luca Battaglini
Filippo Cendron
Roberta Ciampolini
Paola Crepaldi
Roberto Mantovani
Graziella Bongioni
Giulio Pagnacco
Baldassare Portolano
Attilio Rossoni
Fabio Pilla
Martino Cassandro
spellingShingle Gabriele Senczuk
Salvatore Mastrangelo
Elena Ciani
Luca Battaglini
Filippo Cendron
Roberta Ciampolini
Paola Crepaldi
Roberto Mantovani
Graziella Bongioni
Giulio Pagnacco
Baldassare Portolano
Attilio Rossoni
Fabio Pilla
Martino Cassandro
The genetic heritage of Alpine local cattle breeds using genomic SNP data
Genetics Selection Evolution
author_facet Gabriele Senczuk
Salvatore Mastrangelo
Elena Ciani
Luca Battaglini
Filippo Cendron
Roberta Ciampolini
Paola Crepaldi
Roberto Mantovani
Graziella Bongioni
Giulio Pagnacco
Baldassare Portolano
Attilio Rossoni
Fabio Pilla
Martino Cassandro
author_sort Gabriele Senczuk
title The genetic heritage of Alpine local cattle breeds using genomic SNP data
title_short The genetic heritage of Alpine local cattle breeds using genomic SNP data
title_full The genetic heritage of Alpine local cattle breeds using genomic SNP data
title_fullStr The genetic heritage of Alpine local cattle breeds using genomic SNP data
title_full_unstemmed The genetic heritage of Alpine local cattle breeds using genomic SNP data
title_sort genetic heritage of alpine local cattle breeds using genomic snp data
publisher BMC
series Genetics Selection Evolution
issn 1297-9686
publishDate 2020-07-01
description Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.
url http://link.springer.com/article/10.1186/s12711-020-00559-1
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