Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks wer...
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doaj-81017dd7dd334ffcb4255f3d3cd9d26a2020-11-25T03:37:53ZengMDPI AGAnimals2076-26152020-08-01101441144110.3390/ani10081441Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken BreedsFilippo Cendron0Francesco Perini1Salvatore Mastrangelo2Marco Tolone3Andrea Criscione4Salvatore Bordonaro5Nicolaia Iaffaldano6Cesare Castellini7Margherita Marzoni8Arianna Buccioni9Dominga Soglia10Achille Schiavone11Silvia Cerolini12Emiliano Lasagna13Martino Cassandro14Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, ItalyDepartment of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, ItalyDepartment of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, ItalyDepartment of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, ItalyDepartment of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, ItalyDepartment of Agricultural, Environment and Food, University of Molise, Via De Sanctis s/n, 86100 Campobasso, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, ItalyDepartment of Veterinary Science, University of Pisa, Viale delle Piagge 2, 56124 Pisa, ItalyDepartment of Agriculture, Food, Environment and Forestry, University of Firenze, Via di San Bonaventura, 50145 Firenze, ItalyDepartment of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, ItalyDepartment of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, ItalyDepartment of Veterinary Science, University of Milano, Via Trentacoste, 2, 20134 Milano, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, ItalyThe genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (F<sub>ROH</sub>), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.https://www.mdpi.com/2076-2615/10/8/1441biodiversitylocal breedsgenetic diversitysafeguardpoultry |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Filippo Cendron Francesco Perini Salvatore Mastrangelo Marco Tolone Andrea Criscione Salvatore Bordonaro Nicolaia Iaffaldano Cesare Castellini Margherita Marzoni Arianna Buccioni Dominga Soglia Achille Schiavone Silvia Cerolini Emiliano Lasagna Martino Cassandro |
spellingShingle |
Filippo Cendron Francesco Perini Salvatore Mastrangelo Marco Tolone Andrea Criscione Salvatore Bordonaro Nicolaia Iaffaldano Cesare Castellini Margherita Marzoni Arianna Buccioni Dominga Soglia Achille Schiavone Silvia Cerolini Emiliano Lasagna Martino Cassandro Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds Animals biodiversity local breeds genetic diversity safeguard poultry |
author_facet |
Filippo Cendron Francesco Perini Salvatore Mastrangelo Marco Tolone Andrea Criscione Salvatore Bordonaro Nicolaia Iaffaldano Cesare Castellini Margherita Marzoni Arianna Buccioni Dominga Soglia Achille Schiavone Silvia Cerolini Emiliano Lasagna Martino Cassandro |
author_sort |
Filippo Cendron |
title |
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds |
title_short |
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds |
title_full |
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds |
title_fullStr |
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds |
title_full_unstemmed |
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds |
title_sort |
genome-wide snp analysis reveals the population structure and the conservation status of 23 italian chicken breeds |
publisher |
MDPI AG |
series |
Animals |
issn |
2076-2615 |
publishDate |
2020-08-01 |
description |
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (F<sub>ROH</sub>), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers. |
topic |
biodiversity local breeds genetic diversity safeguard poultry |
url |
https://www.mdpi.com/2076-2615/10/8/1441 |
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