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Talenti A, Palhière I, Tortereau F, Pagnacco G, Stella A, Nicolazzi EL, Crepaldi P, Tosser-Klopp G. Functional SNP panel for parentage assessment and assignment in worldwide goat breeds. Genet Sel Evol 2018; 50:55. [PMID: 30449282 PMCID: PMC6240953 DOI: 10.1186/s12711-018-0423-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 10/15/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs. RESULTS Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires. CONCLUSIONS In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Flavie Tortereau
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
| | - Ezequiel L. Nicolazzi
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - AdaptMap Consortium
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, 26900 Lodi, Italy
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