Enhancing backcross programs through increased recombination

Elise Tourrette,Olivier C Martin,Matthieu Falque

doi:10.1186/s12711-021-00619-0

Abstract

BackgroundIntrogression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters.ResultsIn this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental.ConclusionsDepending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.

Highlights

Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines by introducing alleles from exotic material
Based on our investigation of how successful such backcross programs are according to population size or position of the target locus, we find that modifying the recombination rate is generally quite advantageous if it changes the region that contains the target locus from cold to warm with respect to recombination
Using modeling and simulations, we investigated the effects of increasing recombination rate and/or modifying the shapes of recombination landscapes on a program that introgresses the allele of a donor parent at a target locus into a recurrent parent by successive backcrosses

Summary

Introduction

Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). Breeding schemes that are based on recurrent backcrossing result in the introgression of an allele from a donor parent at a target locus into the genetic background of a recurrent parent. The proportion of the donor genome will decrease less for the chromosome that carries the target locus (carrier chromosome) than for the others. This is the so-called linkage drag problem [4,5,6]. It is possible to accelerate the return to the recurrent genome and to reduce the linkage drag by exploiting markers both in the genetic background and close to the target locus [7,8,9,10]. It is possible to obtain crossovers that flank closely the target locus (on both sides) if a sufficient number of generations is used, essentially independently of the presence of crossover interference

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