Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity

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.

Miller, Joshua M.Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA. (författare)
Kardos, MartyUppsala universitet,Evolutionsbiologi(Swepub:uu)marka787 (författare)
Uppsala universitetEvolutionsbiologi (creator_code:org_t)

Ingår i:Journal of Heredity: Oxford University Press (OUP)107:2, s. 193-1950022-15031465-7333

Av författaren/redakt...: Shafer, Aaron B. ...; Miller, Joshua M ...; Kardos, Marty

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