Parentage assessment with 200 single nucleotide polymorphisms on 15 Italian goat breeds

Abstract

In this study we describe a panel of 200 SNPs for parentage testing in goat, optimized on 15 Italian breeds. Data on 350 goats genotyped with the Illumina 50K SNP array were provided by the Italian Goat Consortium (IGC). Animals belong to 15 breeds/populations farmed in North (Saanen, Alpine, Valdostana, Orobica, Bionda dell\u2019Adamello and Valpassiria), Center (Teramana and Grigia Ciociara), South Italy and Islands (Aspromontana, Nicastrese, Girgentana, Argentata dell\u2019Etna, Maltese, Maltese Sarda e Sarda). Quality editing excluded 2,211 SNPs with minor allele frequency <1%, genotype call rate <95% and individual call rate <90%. Genomic Parentage (GP) and Mendelian Errors (ME) were assessed on the 350 goats using the remaining 51,136 markers. Pairs of individuals were classified as Parent-Offspring (PO) when ME<1000 and GP 650.4. A total of 34 PO were identified out of 61,075 pairwise comparisons. We developed a novel method based on multivariate discriminant analysis and stepwise regression for choosing the best SNPs for parentage testing. Following ISAG standards for parentage testing in cattle, we identified a 200 SNP subset suitable to parentage testing in goat based on pairwise ME calculation. We considered PO all pairs of animals sharing 641 ME, doubtful all pairs sharing 2-3 ME and unrelated all pairs sharing >3 ME. The sensibility, specificity and accuracy (false negative, false positive and true assignment ratio, respectively) of the panel were assessed. In addition, we estimated the probability of single parental exclusion (Pe) and the probability of a random coincidental match inclusion (Pi) for each breed. The parentage panel showed good assessment power, with high specificity (0.9705882), sensibility (1.0) and accuracy (0.9999836). Pe values ranged from a minimum of 0.9999995 for Teramana to a maximum of 1.0 for Alpine. Pi values ranged from 8.49 X 10-78 for Alpine to 1.21 X 10-61 for Teramana. Pe for single SNP ranged from 0.0677\ub10.0592 to 0.1085\ub10.0506 (mean\ub1SD) for Teramana and Alpine, respectively. This is the first SNP panel available for parentage testing in goat. Our results suggest that genomic research can help solve practical problems in breeding, such as pedigree registration errors. In this context, cost-effective parentage testing would help goat breeders in the management of consanguinity