Evaluation of marker-assisted selection through computer simulation

Computer simulation was used to evaluate responses to marker-assisted selection (MAS) and to compare MAS responses with those typical of phenotypic recurrent selection (PRS) in an allogamous annual crop species such as maize (Zea mays L.). Relative to PRS, MAS produced rapid responses early in the selection process; however, the rate of these responses diminished greatly within three to five cycles. The gains from MAS ranged from 44.7 to 99.5% of the maximum potential, depending on the genetic model considered. Linkage distance between markers and quantitative trait loci (QTLs) was the factor which most limited the responses from MAS. When averaged across all models considered, flanking QTLs within two marker loci produced 38% more gain than did selection based on single markers if markers were loosely-linked to a QTL (20% recombination). Flanking markers were much less advantageous when markers were closely-linked to a QTL (5% recombination), producing an advantage over single markers of only 11%. Markers were most effective in fully exploiting the genetic potential when fewer QTLs controlled the trait. Large QTL numbers exacerbated the problem of marker-QTL recombination by requiring more generations for fixation. In annual crop species, MAS may offer a primary advantage of enabling two selection cycles per year versus the 2 years per cycle required by most PRS schemes for the evaluation of testcross progeny. MAS thus appears to allow very rapid gains for the first 2-3 years of recurrent selection, after which time conventional methods might replace MAS to achieve further responses.