title: Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity.
abstract: Cross-species application of single-nucleotide polymorphism (SNP) chips is a valid, relatively cost-effective alternative to the high-throughput sequencing methods generally required to obtain a genome-wide sampling of polymorphisms. Kharzinova et al. (2015) examined the applicability of SNP chips developed in domestic bovids (cattle and sheep) to a semi-wild cervid (reindeer). The ancestors of bovids and cervids diverged between 20 and 30 million years ago (Hassanin and Douzery 2003; Bibi et al. 2013). Empirical work has shown that for a SNP chip developed in a bovid and applied to a cervid species, approximately 50% genotype success with 1% of the loci being polymorphic is expected (Miller et al. 2012). The genotyping of Kharzinova et al. (2015) follows this pattern; however, these data are not appropriate for identifying runs of homozygosity (ROH) and can be problematic for estimating linkage disequilibrium (LD) and we caution readers in this regard.
authors.affiliation: From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller). aaron.shafer@ebc.uu.se.
authors.forename: Aaron B A
authors.initials: AB
authors.lastname: Shafer
authors.affiliation: From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller).
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Miller
authors.affiliation: From the Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, SE-75236 Uppsala, Sweden (Shafer and Kardos); and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT (Miller).
authors.forename: Marty
authors.initials: M
authors.lastname: Kardos
mesh_terms: D000818:Animals; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012053:Reindeer / Q000235:genetics*