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Prospects for inferring pairwise relationships with single nucleotide polymorphisms
Author(s) -
Glaubitz Jeffrey C.,
Rhodes O. Eugene,
Dewoody J. Andrew
Publication year - 2003
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1046/j.1365-294x.2003.01790.x
Subject(s) - microsatellite , biology , single nucleotide polymorphism , pedigree chart , genetics , pairwise comparison , identification (biology) , computational biology , linkage (software) , evolutionary biology , allele , computer science , genotype , artificial intelligence , gene , botany
An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full‐sibs from half‐sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al . (1996). We have explored a ‘best case scenario’ in which 100 independently segregating SNPs are available. For discrimination among single‐generation relationships or for the identification of parent–offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16–20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future.