NDLI: First-degree relationships and genotyping errors deciphered by a high-density SNP array in a Duroc × Iberian pig cross

Content Provider	Springer Nature : BioMed Central
Author	Gomez-Raya, L. Gómez Izquierdo, E. de Mercado de la Peña, E. Garcia-Ruiz, F. Rauw, W.M.
Abstract	Background Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent–offspring relationships cannot be homozygous for alternative alleles (genetic exclusion). Methods Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of Single Nucleotide Polymorphisms (SNPs) do not share at least one allele. An Expectation–Maximization algorithm is applied to estimate parentage. In addition, genotyping errors are estimated in true parent–offspring relationships. Samples from nine candidate Duroc sires and 55 Iberian dams producing 214 Duroc × Iberian barrows were typed for the HD porcine Affymetrix array. Results We were able to establish paternity and maternity of 75 and 85 piglets, respectively. Rate of rejection in true parent–offspring relationships was estimated as 0.000735. This is a lower bound of the genotyping error since rate of rejection depends on allele frequencies. After accounting for allele frequencies, our estimate of the genotyping error is 0.6%. A total of 7,744 SNPs were rejected in five or more true parent–offspring relationships facilitating identification of “problematic” SNPs with inconsistent inheritance in multiple parent–offspring relationships. Conclusions This study shows that animal experiments and routine genotyping in genomic selection allow to establish or to verify first-degree relationships as well as to estimate genotyping errors for each batch of animals or experiment.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-022-01025-1.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-022-01025-1
Journal	BMC Genomic Data
Issue Number	1
Volume Number	23
Language	English
Publisher	BioMed Central
Publisher Date	2022-02-17
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Single Nucleotide Polymorphism Genotyping errors Paternity test HD SNP array Pig
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

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