Marker-assisted Backcross Breeding: A Case- Study in Genotype Building Theory

Introduction I wish here to provide an overview of some past and more recent results on marker-assisted backcross breeding theory, and discuss the general consequences for marker-assisted selection and genotype building. Backcross breeding (MAB) is a well-known procedure for the introgression of a target gene from a donor line into the genomic background of a recipient line. The objective is to reduce the donor genome content (DGC) of the progenies by repeated back-crosses to the recipient line. Genotype building (GB) terms here the use of markers to design new genotypes combining favourable alleles previously detected at a (possibly large) number of loci, in (possibly many) different parental lines. Here, the genomic background in which those alleles are combined cannot, in general, be controlled because the genes are too numerous. The theory in this domain remains largely unexplored, and few results are available. For example, de Koning and Weller (1994), and Dekkers and van Arendonk (1998) have considered the optimization of marker-assisted selection for identified quantitative trait loci (QTL) plus a possible ‘polygenic’ background controlling the rest of the genetic variation not explained by the identified QTL. These analyses are restricted to one or two identified QTL. Also, van Berloo and Stam (1998) and Charmet et al. (1999) have considered a larger set of identified QTL, each controlled by flanking markers, and studied selection of recombinant inbred lines or doubled haploids based on flanking markers to produce the best hybrid. This analysis is restricted to selection among inbreds for one or two generations only. Hospital et al. (2000) studied selection on marker pairs flanking 50 QTL identified in an F2 population. With a ‘QTL complementation strategy’ selection of 3-5 individuals among a total of 200 for 10 generations increases the frequency of favourable alleles at the 50 QTL up to 100% when markers are located exactly on the QTL, but only to 92% when marker-QTL distance is 5 cM. The authors conclude that the efficiency of marker-based selection is bounded by the recombinations taking place between the markers and the QTL. Hence, one has to accelerate the response to selection to fix favourable QTL alleles before marker-QTL linkage disequilibrium vanishes. The main limitation identified is the fact that selected individuals are mated at random: the authors suggest that pairwise matings should increase the efficiency of selection. But, the theory in this domain remains unexplored. Marker-assisted backcross is of great practical interest in applied breeding schemes either to manipulate ‘classical’ genes between elite lines or from genetic resources, or to manipulate transgenic constructions. From a theoretical standpoint, it is a ‘simple’ example of marker-based selection: in general, only two alleles are segregating, and the gametic phase is known because only one chromosome of each pair is issued from effective recombination (the chromosome from the gamete produced by the backcrossed parent). It is then also an