'apparent': a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information

BMC Bioinformatics
Arthur T O Melo, Iago Hale

Abstract

The accurate determination of parent-progeny relationships within both in situ natural populations and ex situ genetic resource collections can greatly enhance plant breeding/domestication efforts and support plant genetic resource conservation strategies. Although a range of parentage analysis tools are available, none are designed to infer such relationships using genome-wide single nucleotide polymorphism (SNP) data in the complete absence of guiding information, such as generational groups, partial pedigrees, or genders. The R package ('apparent') developed and presented here addresses this gap. 'apparent' adopts a novel strategy of parentage analysis based on a test of genetic identity between a theoretically expected progeny (EPij), whose genotypic state can be inferred at all homozygous loci for a pair of putative parents (i and j), and all potential offspring (POk), represented by the k individuals of a given germplasm collection. Using the Gower Dissimilarity metric (GD), genetic identity between EPij and POk is taken as evidence that individuals i and j are the true parents of offspring k. Significance of a given triad (parental pairij + offspringk) is evaluated relative to the distribution of all GDij|k values for th...Continue Reading

References

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Citations

Dec 29, 2020·Plant Communications·Mitchell B Cruzan, Elizabeth C Hendrickson

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Methods Mentioned

BETA
genotyping

Software Mentioned

ParentOffspring
MasterBayes
Cervus
MaxIdent
R
Solomon
hsphase
R package
Windows

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