More on the efficiency of marker-assisted selection

Computer simulations were used to study the efficiency of marker-assisted selection (MAS) based on an index combining the phenotypic value and the molecular score of individuals. The molecular score is computed from the effects attributed to markers by multiple regression of phenotype on marker genotype. The results show that in the first generation the ratio RE of the expected efficiency of MAS over the expected efficiency of purely phenotypic selection generally increases when considering: (1) larger population sizes, (2) lower heritability values of the trait, and (3) a higher type-I error risk of the regression. This is consistent with previously published results. However, at low heritabilities our results point out that response to MAS is more variable than response to phenotypic selection. Hence, when the difference of genetic gains is considered instead of their ratio, RE, the heritability values corresponding to maximal advantage of using MAS rather than phenotypic selection are still low, but higher than predicted based on RE. The study over several successive generations of the rate of fixation of QTLs shows that the higher efficiency of MAS on QTLs with large effects in early generations is balanced by a higher rate of fixation of unfavourable alleles at QTLs with small effects in later generations. This explains why MAS may become less efficient than phenotypic selection in the long term. MAS efficiency therefore depends on the genetic determinism of the trait. Finally, we investigate a modified MAS method involving an alternation of selection on markers with and without phenotypic evaluation. Our results indicate that such a selection method could at low cost, provide an important increase in the genetic gain per unit of time in practical breeding programs.