Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean
| Autor: | Pariset, L, Joost, S, Marsan, P. A, Valentini, A, Abo, Shehada, Jamil, M, A. T, Angiolillo, Baret, A, Baumung, P, R, Beja, Pereira, Bertaglia, A, Bordonaro, M, Bruford, S, Caloz, M, Canali, R, Canon, G, Cappuccio, J, Carta, I, Cicogna, A, Crepaldi, M, Dalamitra, P, Krugmann, S, Petrit, D, Popielarczyk, D, Susana, D, D'Urso, D, G, Barody, El, M. A. A, England, Erhardt, P, Ertugrul, G, O, Eva, Maria, Eveline, P, I. A, Ewa, Fadlaoui, S, Fornarelli, A, Garcia, F, Georgoudis, D, Gesine, A, Giovenzana, L, Gutscher, S, Hewitt, K, Hoda, G, Horst, A, Istvan, B, Juma, A, Joost, G, Jones, S, Karetsou, S, Kliambas, K, Koban, G, Kutita, E, Lazlo, O, Lenstra, F, J. A, Ligda, Lipsky, C, Luikart, S, Marie, Louise, Marilli, G, Marletta, M, Milanesi, D, Negrini, E, Nijman, R, I. J., Obexer, Ruff, Papachristoforou, G, Pariset, C, Pellecchia, L, Peter, M, Perez, C, Pietrolà, T, E, Pilla, Fabio, Roman, F, Roosen, N, Scarpa, J, Sechi, R, Taberlet, T, Taylor, P, Togan, M, Trommetter, I, Van, M, Lisette, C, Vlaic, M, Wiskin, A, Zundel, L, Angiolillo, Antonella |
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| Předmět: |
Genetics
Genetics (clinical) lcsh:QH426-470 Population Single-nucleotide polymorphism Genomics Biology Mediterranean Basin Polymorphism Single Nucleotide SNP markers Animals Genetics(clinical) FST Selection Genetic education Allele frequency Selection (genetic algorithm) GOAT BREEDS education.field_of_study Natural selection Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO Mediterranean Region Goats Nucleotide polymorphisms lcsh:Genetics Genetics Population Outlier Razze caprine Polimorfismi nucleotidici Research Article |
| Zdroj: | BMC Genetics, Vol 10, Iss 1, p 7 (2009) BMC Genetics |
| Popis: | Background In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring. Results The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the identification of the same three loci involved in milk and meat quality data by using the two methods, while the FST based method identified 3 more loci as under selection sweep in the breeds examined. Conclusion Data appear congruent by using the two methods for FST values exceeding the 99% confidence limits. The methods of FST and SAM can independently detect signatures of selection and therefore can reduce the probability of finding false positives if employed together. The outlier loci identified in this study could indicate adaptive variation in the analysed species, characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade, that implies plasticity in adapting to new environments. |
| Databáze: | OpenAIRE |
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