Parentage control of pigs based on SNP data

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00027014%3A_____%2F23%3A10005838" target="_blank" >RIV/00027014:_____/23:10005838 - isvavai.cz</a>

Result on the web

<a href="https://vuzv.cz/_privat/23105.pdf" target="_blank" >https://vuzv.cz/_privat/23105.pdf</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Parentage control of pigs based on SNP data

Original language description

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(R) Genomic ProfilerTM GGP Porcine 50K). From all of the SNP 32898 were shared between these chips. The GenCall score (GC GREATER-THAN OR EQUAL TO70 and GREATER-THAN OR EQUAL TO80), minor allele frequency (30%LESS-THAN OR EQUAL TOpMLESS-THAN OR EQUAL TO50%) and known position of each SNP locus on all autosomes were considered. The evaluation was done separately for each breed. Panels consisting of 435 (GCGREATER-THAN OR EQUAL TO70) and 240 (GCGREATER-THAN OR EQUAL TO80) 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). The study was supported by Czech Republic project QK1910217 and MZE-RO0723 - V02.

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

40203 - Husbandry

Project

<a href="/en/project/QK1910217" target="_blank" >QK1910217: Creation of a reference population and development of methods for estimating genomic breeding values of pig traits included into the Czech National Breeding Program.</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů