TY - JOUR
T1 - Functional SNP panel for parentage assessment and assignment in worldwide goat breeds
AU - Talenti, Andrea
AU - Palhière, Isabelle
AU - Tortereau, Flavie
AU - Pagnacco, Giulio
AU - Stella, Alessandra
AU - Nicolazzi, Ezequiel L
AU - Crepaldi, Paola
AU - Tosser-Klopp, Gwenola
AU - AdaptMap consortium
AU - Mwacharo, JM
PY - 2018/11/19
Y1 - 2018/11/19
N2 - 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.
AB - 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.
KW - Animals
KW - Breeding/methods
KW - Female
KW - Gene Frequency
KW - Goats/genetics
KW - Linkage Disequilibrium
KW - Male
KW - Polymorphism, Single Nucleotide
KW - Sex Determination Processes
U2 - 10.1186/s12711-018-0423-9
DO - 10.1186/s12711-018-0423-9
M3 - Article
C2 - 30449282
SN - 0999-193X
VL - 50
JO - Genetics Selection Evolution
JF - Genetics Selection Evolution
IS - 1
M1 - 55
ER -