Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations
Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analys...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-01-01
|
| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124011210 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832591815903019008 |
|---|---|
| author | Medhat S. Saleh Vincenzo Landi Martijn F.L. Derks Gerardo Centoducati Martien A.M. Groenen Pasquale De Palo Elena Ciani Maria G. Strillacci Alessandro Bagnato Nicola Pugliese Elena Circella Antonio Camarda |
| author_facet | Medhat S. Saleh Vincenzo Landi Martijn F.L. Derks Gerardo Centoducati Martien A.M. Groenen Pasquale De Palo Elena Ciani Maria G. Strillacci Alessandro Bagnato Nicola Pugliese Elena Circella Antonio Camarda |
| author_sort | Medhat S. Saleh |
| collection | DOAJ |
| description | Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. We used new data from 73 WGS samples (12X) representing five turkey populations, together with previous data from 107 birds genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array from 11 populations. The PCA and Admixture show a relatively strong isolation effect between the populations. Moreover, the values of genomic inbreeding based on ROH (FROH) showed marked differences among populations and ranged from 0.096 to 0.643. Selective sweeps were identified using the integrated haplotype score (iHS) within the local group, the commercial line, and the Narragansett breed, resulting in the identification of 20, 19, and 27 regions with a total of 73, 48, and 90 candidate genes, respectively. Some of these genes such as FAM107B, MSTN, PDZRN4, HSF2 and GJA1 are associated with heat stress, growth, and carcass traits. We conclude that our results improve our understanding of the genomic architecture of the Italian turkey populations. The findings of iHS suggest that selection can play a significant role in shaping selection signatures in local turkey populations and could provide a basis for identifying gene mutations that may be beneficial in adaptation to climate change. Our results will be useful in developing and implementing conservation and selection plans for Italian turkey populations. |
| format | Article |
| id | doaj-art-02318396b8e04055a3906003031288e8 |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-02318396b8e04055a3906003031288e82025-01-22T05:40:25ZengElsevierPoultry Science0032-57912025-01-011041104543Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populationsMedhat S. Saleh0Vincenzo Landi1Martijn F.L. Derks2Gerardo Centoducati3Martien A.M. Groenen4Pasquale De Palo5Elena Ciani6Maria G. Strillacci7Alessandro Bagnato8Nicola Pugliese9Elena Circella10Antonio Camarda11Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy; Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, Wageningen, 6700 AH, the Netherlands; Department of Animal Production, Faculty of Agriculture, Benha University, Benha 13736, EgyptDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy; Corresponding author.Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, Wageningen, 6700 AH, the NetherlandsDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, ItalyAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, Wageningen, 6700 AH, the NetherlandsDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, ItalyDepartment of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Bari, ItalyDepartment of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, ItalyDepartment of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, ItalyDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, ItalyDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, ItalyDepartment of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, ItalyItalian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. We used new data from 73 WGS samples (12X) representing five turkey populations, together with previous data from 107 birds genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array from 11 populations. The PCA and Admixture show a relatively strong isolation effect between the populations. Moreover, the values of genomic inbreeding based on ROH (FROH) showed marked differences among populations and ranged from 0.096 to 0.643. Selective sweeps were identified using the integrated haplotype score (iHS) within the local group, the commercial line, and the Narragansett breed, resulting in the identification of 20, 19, and 27 regions with a total of 73, 48, and 90 candidate genes, respectively. Some of these genes such as FAM107B, MSTN, PDZRN4, HSF2 and GJA1 are associated with heat stress, growth, and carcass traits. We conclude that our results improve our understanding of the genomic architecture of the Italian turkey populations. The findings of iHS suggest that selection can play a significant role in shaping selection signatures in local turkey populations and could provide a basis for identifying gene mutations that may be beneficial in adaptation to climate change. Our results will be useful in developing and implementing conservation and selection plans for Italian turkey populations.http://www.sciencedirect.com/science/article/pii/S0032579124011210Genome-wide scanGenetic diversityPopulation structureSelection signatureTurkey |
| spellingShingle | Medhat S. Saleh Vincenzo Landi Martijn F.L. Derks Gerardo Centoducati Martien A.M. Groenen Pasquale De Palo Elena Ciani Maria G. Strillacci Alessandro Bagnato Nicola Pugliese Elena Circella Antonio Camarda Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations Poultry Science Genome-wide scan Genetic diversity Population structure Selection signature Turkey |
| title | Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations |
| title_full | Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations |
| title_fullStr | Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations |
| title_full_unstemmed | Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations |
| title_short | Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations |
| title_sort | genome wide analyses of genomic diversity population structure and selection signatures in italian turkey populations |
| topic | Genome-wide scan Genetic diversity Population structure Selection signature Turkey |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124011210 |
| work_keys_str_mv | AT medhatssaleh genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT vincenzolandi genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT martijnflderks genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT gerardocentoducati genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT martienamgroenen genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT pasqualedepalo genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT elenaciani genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT mariagstrillacci genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT alessandrobagnato genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT nicolapugliese genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT elenacircella genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations AT antoniocamarda genomewideanalysesofgenomicdiversitypopulationstructureandselectionsignaturesinitalianturkeypopulations |