Evaluation of approaches for identifying population informative markers from high density SNP Chips

A 95% assignment success rate for the 384 individually genotyped animals was achieved with < 80, < 100, < 140 and < 200 SNP markers (with increasing stringency threshold levels) across all the examined methods for marker selection. No further gain in power of assignment was achieved by sampling in excess of 200 SNP markers. The marker selection method that required the lowest number of SNP markers to verify the animal's breed origin was Wright's FST (60 to 140 SNPs depending on the chosen degree of confidence). Certain breeds required fewer markers (< 100) to achieve 100% assignment success. In contrast, closely related breeds require more markers (~200) to achieve > 95% assignment success. The power of assignment success, and therefore the number of SNP markers required, is dependent on the levels of genetic heterogeneity and pool of samples considered.While all SNP selection methods produced marker panels capable of breed identification, the power of assignment varied markedly among analysis methods. Thus, with effective exploration of available high density genetic markers, a diagnostic panel of highly informative markers can be produced.The identification and verification of the origin of individuals is useful in a variety of biological contexts and the practical applications of individual assignment protocols are extensive [1-3]. Topical issues in population, conservation and evolutionary biology can benefit from the inference of ancestry of individuals. In an applied context, genetic identification can shed light on issues such as the contribution of source populations in mixed fisheries [3,4], meat traceability or brand authentication [5], translocated or migrant individuals [6], structure and levels of discrimination amongst populations [7,8], anthropological forensic investigations [2] and tracking the trade routes of illegally poached animals [3].Where there is sufficient genetic heterogeneity amongst populations genetic markers can be used to identify and