We studied the efficiency of recurrent selection based solely on marker genotypes (marker-based
selection), in order to increase favourable allele frequency at 50 previously detected quantitative
trait loci (QTLs). Two selection procedures were investigated, using computer simulations: (1)
Truncation Selection (MTS), in which individuals are ranked based on marker score, and best
individuals are selected for recombination; and (2) QTL Complementation Selection (QCS), in
which individuals are selected such that their QTL composition complements those individuals
already selected. Provided QTL locations are accurate, marker-based selection with a population
size of 200 was very effective in rapidly increasing frequencies of favourable QTL alleles. QCS
methods were more effective than MTS for improving the mean frequency and fixation of
favourable QTL alleles. Marker-based selection was not very sensitive to a reduction in population
size, and appears valuable to optimize the use of molecular markers in recurrent selection
programmes.
Simulation of QTL by sequencing for agronomic quantitative trait loci detection in small to medium population size in soybean