Selective genotyping with a main trait and a correlated trait

In some instances of quantitative trait loci (QTL) mapping, a correlated trait may be available for which measurement is less costly or more convenient than direct measurement of the trait of main interest. In this paper we consider ways of combining phenotyping for a main trait and a correlated trait to maximize power within the overall framework of a selective genotyping design. Four schemes are compared: (1) Selection for the main trait only (2) Selection for the correlated trait only (3) Two-stage selection (4) Three-stage selection. Optimum proportion selected for the two traits were obtained for the various schemes, and power parameters compared, according to the correlation r, between the two traits, and the proportion of the population, Q, phenotyped for the main trait. The schemes were compared under two sets of assumptions: (1) Total population size and proportion that can be phenotyped for the main trait are fixed, and (2) Total costs are fixed, with relative cost, c′, of rearing and phenotyping for the correlated trait as compared to the main trait. Under (1), the multi-stage schemes are very advantageous when r is high, and Q is low. Under (2), the single-stage schemes were always superior to the multi-stage schemes; Scheme 1 being preferred when r²/c′ < 1.0, and Scheme 2 when r²/c′ > 1.0.