In selective genotyping, a large number of individuals are phenotyped; however, only individuals with extreme traits are genotyped. This design tends to be more efficient than pure random sampling because phenotypically extreme individuals are likely to be genetically more informative [Huang and Lin, 2007].
Several regression-based methods have been developed for mapping QTLs under selective genotyping. These include the prospective linear regression [Xiong et al.,
2002], the retrospective likelihood approach [Wallace et al., 2006] and the conditional likelihood method [Huang and Lin, 2007]. Tang Y [2010] showed that the prospective, retrospective and conditional likelihoods actually yield identical score tests for association between a quantitative trait and a candidate locus.
