Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area
Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale ge...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-04-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731121000343 |
| _version_ | 1819010383643410432 |
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| author | I. Baazaoui S. Bedhiaf-Romdhani S. Mastrangelo E. Ciani |
| author_facet | I. Baazaoui S. Bedhiaf-Romdhani S. Mastrangelo E. Ciani |
| author_sort | I. Baazaoui |
| collection | DOAJ |
| description | Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58–49.61 Mbp). These results were confirmed using FST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds. |
| first_indexed | 2024-12-21T01:11:24Z |
| format | Article |
| id | doaj.art-b8b509cf64ea442890cbd931cd07566b |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-12-21T01:11:24Z |
| publishDate | 2021-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-b8b509cf64ea442890cbd931cd07566b2022-12-21T19:20:55ZengElsevierAnimal1751-73112021-04-01154100193Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid areaI. Baazaoui0S. Bedhiaf-Romdhani1S. Mastrangelo2E. Ciani3Faculty of Sciences of Bizerte, University of Carthage, 7021 Zarzouna, Bizerte, TunisiaInstitut National de la Recherche Agronomique de Tunisie, Laboratoire des Productions Animales et Fourragères, Université de Carthage, 2049 Ariana, Tunisie.; Corresponding author.Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy.Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70121 Bari, ItalyUnder a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58–49.61 Mbp). These results were confirmed using FST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.http://www.sciencedirect.com/science/article/pii/S1751731121000343Fat tailGenetic structureLocal sheepRuns of homozygositySelection signature |
| spellingShingle | I. Baazaoui S. Bedhiaf-Romdhani S. Mastrangelo E. Ciani Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area Animal Fat tail Genetic structure Local sheep Runs of homozygosity Selection signature |
| title | Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area |
| title_full | Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area |
| title_fullStr | Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area |
| title_full_unstemmed | Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area |
| title_short | Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area |
| title_sort | genome wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi arid area |
| topic | Fat tail Genetic structure Local sheep Runs of homozygosity Selection signature |
| url | http://www.sciencedirect.com/science/article/pii/S1751731121000343 |
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