title: A method for single nucleotide polymorphism selection for parentage assessment in goats.
abstract: Accurate pedigrees are essential to optimize genetic improvement and conservation of animal genetic resources. In goats, the use of mating groups and kidding management procedures hamper the identification of parentage. Small panels of single nucleotide polymorphisms (SNP) have been proposed in other species to substitute microsatellites for parentage assessment. Using data from the current GoatSNP50 chip, we developed a new 3-step procedure to identify a low-density SNP panel for highly accurate parentage assessment. Methodologies for SNP selection used in other species are less suitable in the goat because of uncertainties in the genome assembly. The procedure developed in this study is based on parent-offspring identification and on estimation of Mendelian errors, followed by canonical discriminant analysis identification and stepwise regression reduction. Starting from a reference sample of 109 Alpine goats with known pedigree relationships, we first identified a panel of 200 SNP that was further reduced to 2 final panels of 130 and 114 SNP with random coincidental match inclusion of 1.51×10(-57) and 2.94×10(-34), respectively. In our reference data set, all panels correctly identified all parent-offspring combinations, revealing a 40% pedigree error rate in the information provided by breeders. All reference trios were confirmed by official tests based on microsatellites. Panels were also tested on Saanen and Teramana breeds. Although the testing on a larger set of breeds in the reference population is still needed to validate these results, our findings suggest that our procedure could identify SNP panels for accurate parentage assessment in goats or in other species with unreliable marker positioning.
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy. Electronic address: andrea.talenti@unimi.it.
authors.forename: A
authors.initials: A
authors.lastname: Talenti
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: E L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: Istituto di Biologia e Biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Chessa
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Frattini
authors.affiliation: Istituto di Biologia e Biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Moretti
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.
authors.forename: B
authors.initials: B
authors.lastname: Coizet
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Nicoloso
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore Via Emilia Parmense, Piacenza, 29122, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Colli
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Pagnacco
authors.affiliation: Fondazione Parco Tecnologico Padano (PTP), Via Einstein, Cascina Codazza, Lodi, 26900, Italy; Istituto di Biologia e Biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Stella
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore Via Emilia Parmense, Piacenza, 29122, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Ajmone-Marsan
authors.affiliation: Dipartimento di Scienze Biomediche Comparate, Università di Teramo, Piazza Aldo Moro 45, Teramo, 64100, Italy; Institute of Animal Production, ul. Sarego 2, Krakow 31-047, Poland.
authors.forename: G
authors.initials: G
authors.lastname: Ptak
authors.affiliation: Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, via Celoria 10, Milano, 20133, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Crepaldi
mesh_terms: D000818:Animals; D001947:Breeding; D006041:Goats / Q000235:genetics*; D018895:Microsatellite Repeats; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide
keywords: goat; parentage analysis; single nucleotide polymorphism