Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds
The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-02-01
|
| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579120307756 |
| _version_ | 1818452386280112128 |
|---|---|
| author | F. Cendron S. Mastrangelo M. Tolone F. Perini E. Lasagna M. Cassandro |
| author_facet | F. Cendron S. Mastrangelo M. Tolone F. Perini E. Lasagna M. Cassandro |
| author_sort | F. Cendron |
| collection | DOAJ |
| description | The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds. |
| first_indexed | 2024-12-14T21:22:16Z |
| format | Article |
| id | doaj.art-b65cd8fb63cc4f43a5be08795784c473 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-12-14T21:22:16Z |
| publishDate | 2021-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-b65cd8fb63cc4f43a5be08795784c4732022-12-21T22:46:55ZengElsevierPoultry Science0032-57912021-02-011002441451Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breedsF. Cendron0S. Mastrangelo1M. Tolone2F. Perini3E. Lasagna4M. Cassandro5Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy; Corresponding author:Department of Agricultural, Food and Forest Sciences, University of Palermo 90128 Palermo, PA, ItalyDepartment of Agricultural, Food and Forest Sciences, University of Palermo 90128 Palermo, PA, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia 06121 Perugia, PG, ItalyDepartment of Agricultural, Food and Environmental Sciences, University of Perugia 06121 Perugia, PG, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, ItalyThe aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds.http://www.sciencedirect.com/science/article/pii/S0032579120307756genetic diversitypopulation structurelocal poultry breedSNP markerruns of homozygosity |
| spellingShingle | F. Cendron S. Mastrangelo M. Tolone F. Perini E. Lasagna M. Cassandro Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds Poultry Science genetic diversity population structure local poultry breed SNP marker runs of homozygosity |
| title | Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds |
| title_full | Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds |
| title_fullStr | Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds |
| title_full_unstemmed | Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds |
| title_short | Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds |
| title_sort | genome wide analysis reveals the patterns of genetic diversity and population structure of 8 italian local chicken breeds |
| topic | genetic diversity population structure local poultry breed SNP marker runs of homozygosity |
| url | http://www.sciencedirect.com/science/article/pii/S0032579120307756 |
| work_keys_str_mv | AT fcendron genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds AT smastrangelo genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds AT mtolone genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds AT fperini genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds AT elasagna genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds AT mcassandro genomewideanalysisrevealsthepatternsofgeneticdiversityandpopulationstructureof8italianlocalchickenbreeds |