Optimization of the Marker‐based Procedures for Pyramiding Genes from Multiple Donor Lines: III. Multiple‐Gene Assemblage Using Background Marker Selection

Constructing high‐degree gene‐pyramided lines has important practical implications; such lines could be used for multiple purposes, for example, as a high‐powered breeding stock line, a material line for characterizing multigene interactions, or a market variety as it stands. Effectiveness of two typical marker‐based schemes for constructing such lines, named AF (gene assemblage first) and BF (backcross first), is discussed. In AF, target genes of all donor parents are assembled onto the genome of a plant first, followed by backcross generations for the recovery of recipient parent genome. In BF, backcross is performed first separately for each donor, followed by generations of crossing for the assemblage of target genes. Our stochastic calculations show that BF is superior to AF when molecular selection is used for both target genes and background markers; with the same number of generations (time) and cost of genotyping, BF produces a much higher recovery of recurrent parent genome than AF. The superiority of BF weakens somewhat when target genes are selected by phenotype; AF is superior when assembling three or more unlinked target genes, or could be a choice of the breeder when assembling three or more linked genes. Otherwise, BF is superior. To minimize cost, genotyping and selection for background markers should be performed stepwise in each generation, that is, in three or four stages starting from markers closely linked with target genes to unlinked ones.