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. 2018 Nov 19;50(1):55.
doi: 10.1186/s12711-018-0423-9.

Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Andrea Talenti  1 , Isabelle Palhière  2 , Flavie Tortereau  2 , Giulio Pagnacco  1 , Alessandra Stella  3 , Ezequiel L Nicolazzi  3 , Paola Crepaldi  4 , Gwenola Tosser-Klopp  2 ; AdaptMap Consortium
Affiliations

Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Andrea Talenti et al. Genet Sel Evol. .

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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Figures

Fig. 1
Fig. 1
Linkage disequilibrium between the 195 SNPs of the reduced panel, calculated as R2 values for each pair of SNPs (blue dots). In red, we report the LD decay as the average in the following windows: 10–100 kb, 100–250 kb, 250 kb–1 Mb and then every 1 Mb
See this image and copyright information in PMC

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