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CROP BREEDING & GENETICS

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

^a Marker-assisted Rice Breeding Research Team, National Institute of Crop Science, Tsukuba 305-8518, Japan
^b Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-0901, Japan
^c Dep. of Biotechnology, Kyoto Sangyo Univ., Kyoto 603-8555, Japan

^* Corresponding author (yonezaw{at}cc.kyoto-su.ac.jp).

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.

Abbreviations: AF, gene assemblage first • BF, backcross first • MDP, marker data points • MDP-AL, number of marker data points when both target genes and background markers are subject to molecular selection • MDP-BG, number of marker data points when phenotypic selection is used for target genes • PFR, probability of full recovery • PMT, probability of missing any target gene • RPG, rate of recovery of recurrent parent genome • RPG-DC, rate of recovery of background markers for loci located on different chromosomes as target genes • RPG-SC, rate of recovery of background markers for loci located on the same chromosome as target genes