marker-assisted selection in wheat - ictsd

170Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishpair that each individual carries. An individualwith genotype MmQq could havethe following two haplotypes: MQ/mq,where the / separates the two homologouschromosomes. Alternatively, it could carrythe haplotypes Mq/mQ. This alternativearrangement of linked alleles on homologouschromosomes is referred to as themarker-QTL linkage phase. The arrangementof alleles in haplotypes is importantbecause progeny inherit one of the twohaplotypes that a parent carries, barringrecombination.The presence of linkage equilibrium(LE) or disequilibrium relates to the relativefrequencies of alternative haplotypes inthe population. In a population that is inlinkage equilibrium, alleles at two loci arerandomly assorted into haplotypes. In otherwords, chromosomes or haplotypes thatcarry marker allele M are no more likelyto carry QTL allele Q than chromosomesthat carry marker allele m. In technicalterms, the frequency of the MQ haplotypesis equal to the product of the populationallele frequency of M and the frequencyof Q. Thus, if a marker and QTL are inlinkage equilibrium, there is no value inknowing an individual’s marker genotypebecause it provides no information on QTLgenotype. If the marker and QTL arein linkage disequilibrium, however, therewill be a difference in the probability ofcarrying Q between chromosomes thatcarry M and m marker alleles and, therefore,a difference in mean phenotype betweenmarker genotypes would also be expected.The main factors that create LD in apopulation are mutation, selection, drift(inbreeding), and migration or crossing. SeeGoddard and Meuwissen (2005) for furtherbackground on these topics. The mainfactor that breaks down LD is recombination,which can rearrange haplotypes thatDisequilibriumFigure 1Break-up of LD over generationsLD is continuously eroded byrecombination10.90.80.70.60.50.40.30.20.100r=.5r=.2r=.1r=.05Generationr=.01rM Qexist within a parent in every generation.Figure 1 shows the effect of recombination(r) on the decay of LD over generations.The rate of decay depends on the rate ofrecombination between the loci. For tightlylinked loci, any LD that has been createdwill persist over many generations but, forloosely linked loci (r > 0.1), LD will declinerapidly over generations.Population-wide versus within-family LDAlthough a marker and a linked QTL maybe in LE across the population, LD willalways exist within a family, even betweenloosely linked loci. Consider a double heterozygoussire with haplotypes MQ/mq(Figure 2). The genotype of this sire isidentical to that of an F 1 cross betweeninbred lines. This sire will produce fourtypes of gametes: non-recombinants MQand mq and recombinants Mq and mQ.As non-recombinants will have higher frequency,depending on the recombinationrate between the marker and QTL, thissire will produce gametes that will be inLD. Furthermore, this LD will extendover a larger distance (Figure 1), becauseit has undergone only one generation ofrecombination. This specific type of LD,mqr=.0015 10 15 20 25