Software

SEEKPARENTF90 A tool from the BLUPF90 family programs for parentage validation and discovery using genomic information

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Abstract

Parentage verification among animals is relevant from a genetic-improvement perspective, since pedigree errors have a negative effect on the estimation of genetic parameters and prediction of breeding values thus affecting the rate of genetic progress. Moreover, in genomic evaluation model as in ssGBLUP, having genealogical and genomic information inconsistency could lead to numerical instabilities. Default behaviour of BLUPF90 programs requires to detect and correct parent-progeny mismatches and a general rule is applied masking progeny genotype to be excluded from analysis. However, this is not always optimal and tools for handling parentage inconsistences are necessary. As more genomic data has been available with different commercial arrays of different density having a tool to perform data verification as part of periodically quality control is essential. The aim of this work is to describe the seekparentf90 tool, a program for parentage verification and discovery using SNP genomic information. It detects parent-offspring incompatibilities based on count of conflicts (opposite homozygous). The tool is command-line program that needs at least: a pedigree file and marker file with SNP coded as 0,1,2 and 5 for missing calls. Identifications of individuals in both files support alphanumeric codes with not need of an extra tool for renumbering. Extra arguments could be used to select specific individuals to perform the verification, to include/exclude list of SNPs or chromosomes, include sex and year of birth from pedigree files (useful for discovery), detect duplicate samples, change default thresholds of conflicts for verification/discovery, including those recommended by the ICAR guidelines for parentage verification and discovery in cattle, however the program could be used in other animal or plant species using SNP panels. As many arrays densities are available, versatility and efficient use of all SNP information is supported allowing users to use raw SNP data from different arrays without any pre-filtering or subset of SNP, then the program will select for each verification SNPs in common based on arrays of individuals involved, and then chose the appropriate rule (e.g. ICAR rules for 200 SNP or > 200 SNP). Seekparentf90 is being used for more than 60 arrays involving chip densities from 100 SNP up to 700k SNP. Best practices for use the seekparentf90 usually involves running it on the full pedigree file and marker data, prior to imputation of markers and/or to analyses programs (blupf90+, gibbsf90+, etc.) using clean pedigree files created by seekparentf90. Also, the tool was designed for daily use, e.g. for genetic evaluation centers, to perform quality control of new genomic samples. In summary seekparentf90 is a simple tool for detection of mendelian inconsistences, discovery parents and perform other quality control of genotype samples.

Keywords: 2026

How to Cite:

Aguilar, I., Bermann, M., Legarra, A., Lourenco, D., Misztal, I. & Tsuruta, S., (2026) “SEEKPARENTF90 A tool from the BLUPF90 family programs for parentage validation and discovery using genomic information”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287225. doi: https://doi.org/10.31274/wcgalp.24239

Rights: 1