Parentage control of pigs based on SNP data

ŽÁKOVÁ, Eliška, KRUPOVÁ, Zuzana; KRUPA, Emil, STIBAL, J. a VRTKOVÁ, I. ., 2023 Parentage control of pigs based on SNP data. In Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science. Wageningen, The Netherlands: Wageningen Academic Publishers, s. 214. ISSN
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Genotyping of animals included in the national breeding programme CzePig has been applied for genomic evaluation and pedigree assessment. To determine accurate animal evaluation and selection the parentage test is necessary. Therefore, the presented study was aimed to employ the pig genomic data for definition of SNP panel that could be used for routine parentage control. Samples were taken from the animals that were parents of the next generation of breeding animals or that had sufficient performance data records in the studbook database. From the 1489 animal samples, 68% belongs to maternal and 17% to sire breeds and 15% were of the endangered Prestice black-pied breed. In 869 and 221 animals one and both parents were genotyped, respectively. The ratio of the evaluated samples by sex was 55:45 for sows and boars. Three SNP chips were used for genotyping (Illumina, Inc. Porcine SNP60v2 and PorcineSNP60 BeadChip and GeneSeek® Genomic Profiler™ GGP Porcine 50K). From all of the SNP 32898 were shared between these chips. The GenCall score (GC ≥70 and ≥80), minor allele frequency (30%≤pM≤50%) and known position of each SNP locus on all autosomes were considered. The evaluation was done separately for each breed. Panels consisting of 435 (GC≥70) and 240 (GC≥80) SNP loci were selected for routine parentage control. The SNPs have to be known for more than 95% of animals. Subsequently, the genotype of an individual was compared with one or with both of parents. Only 3.6% of samples were assessed as incorrect (unreliable sample or pedigree error). These may be refined in the future as data increases. Simultaneously, the panels will be continuously reassessed due to upcoming samples (especially of sire breeds).

ProjektVytvoření referenční populace a vývoj postupů pro odhad genomických plemenných hodnot znaků prasat zařazených do Českého národního šlechtitelského programu, Dlouhodobý koncepční rozvoj výzkumné organizace
OdděleníGenetika a šlechtění hospodářských zvířat