Comparison of Selection Strategies for Marker-Assisted Backcrossing of a Gene

for manipulating QTL in foreground selection. Further, they investigated the combination of foreground and Marker-assisted selection can accelerate recovery of the recurrent background selection in QTL introgression. Openshaw parent genome (RPG) in backcross breeding. In this study, we used et al. (1994) determined the population size and marker computer simulations to compare selection strategies with regard to (i) the proportion of the RPG recovered and (ii) the number of marker density required in background selection. They recomdata points (MDP) required in a backcross program designed for mended the use of four markers per chromosome (of introgression of one target allele from a donor line into a recipient 200-cM length) and a selection strategy for proximal line. Simulations were performed with a published maize (Zea mays recombinants of the target allele. L.) genetic map consisting of 80 markers. Selection for the target Although efficient PCR-based DNA markers such as allele was based on phenotypic evaluation. In comparison to a constant simple sequence repeats and amplified fragment length population size across all generations, increasing population sizes from polymorphisms are available (Ribaut et al., 1997), their generation BC1 to BC3 reduced the number of required MDP by as use in background selection is restricted by the large much as 50% without affecting the proportion of the RPG. A fournumber of required MDP. In this study, we investigate stage selection approach, emphasizing in the first generations selection strategies for reducing the total number of MDP needed for recombinants on the carrier chromosome of the target allele, reduced the required number of MDP by as much as 75% in compariin background selection. Our research objectives were son to a selection index taking into account all markers across the to (i) determine the number of MDP required in backgenome. Adopting the above principles for the design of markerground selection, (ii) investigate the effects of varying assisted backcross programs resulted in substantial savings in the population sizes from early to late backcross generations number of MDP required. on the level of RPG and the MDP required, and (iii) compare a two-stage selection procedure, consisting of one foreground and one background selection step, with T backcross procedure is used in plant breeding alternative selection procedures consisting of one foreto transfer favorable alleles from a donor genotype, ground selection step and two or three background sewhich has mostly poor agronomic properties, into a relection steps. cipient elite genotype (Allard, 1960, p. 150). Marker assays can be of advantage in backcross breeding for METHODS foreground selection and background selection (HospiGenetic Map tal and Charcosset, 1997). In the first approach, the presence of a target allele in an individual is diagnosed Our simulations were based on a published linkage map of by monitoring the genotype at flanking markers for maize (Schön et al., 1994) constructed from a population of 380 F2 individuals derived from the cross of two flint inbred alleles of the donor parent. This is a powerful tool for lines. The total map length was 1612 cM. On the basis of manipulation of oligogenic traits under numerous situaprevious investigations (Openshaw et al., 1994; Visscher et tions in plant breeding (for review see Melchinger, al., 1996; Frisch et al., 1998), an average marker density of 1990), but also for manipulation of quantitative trait loci about 20 cM is sufficient to warrant a good coverage of the (QTL) (Stuber, 1995). The second approach, devised by genome in marker-assisted selection programs. Hence, 80 of Tanksley et al. (1989), accelerates recovery of the RPG. the 89 polymorphic restriction fragment length polymorphism Individuals are selected which are homozygous for the markers used by Schön et al. (1994) were chosen to obtain alleles of the recurrent parent at a large number of an average marker density of 20 cM. Markers umc128, umc5, marker loci covering the entire genome. Markerumc175, bn16.06, umc54, umc51, umc110, bnl7.61, and bnl9.44 assisted background selection has meanwhile been eswere tightly linked to other markers and, therefore, excluded from the present study. There were two larger gaps on this tablished as a standard tool in plant breeding (see, e.g., map: one 90-cM marker interval on Chromosome 3 and one Ragot et al., 1995). 89-cM marker interval on Chromosome 9. The target locus Computer simulations have proved to be a powerful was assumed to be located on Chromosome 5, 30 cM from the tool for investigating the design and efficiency of telomere. In our simulations, the entire map was additionally marker-assisted selection programs (for review see covered with equally spaced (1 cM) background loci to moniVisscher et al., 1996). These authors studied markertor the parental origin of the whole genome. assisted QTL introgression in an animal breeding context, using an infinitesimal model to explain differences Algorithm among breeds. Hospital and Charcosset (1997) deterSoftware PLABSIM (Frisch et al., 1999b), a computer promined the optimal position and number of marker loci gram written in C11, was used to simulate the recombination process during meiosis. Crossover events were generated by Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany. Received 24 Abbreviations: BCt, tth backcross generation; cM, centimorgan; MDP, Nov. 1998. *Corresponding author ([email protected]). marker data points; QTL, quantitative trait locus; RPG, recurrent parent genome. Published in Crop Sci. 39:1295–1301 (1999).