marker-assisted selection in wheat

Chapter 7 – Marker-assisted selection in common beans and cassava 89detect the QTL that explain the highestamount of genetic variability, and this hasbeen difficult to achieve in intragene poolcrosses in common beans.However, genetic analysis by markershas been very useful for revealing theinheritance of quantitative traits, especiallyphysiological traits, even when the markersinvolved did not result in application inMAS. Analysis of QTL was applied to roottraits of bean as they relate to absorptionof phosphorus from soil (Liao et al., 2004;Yan et al., 2005; Beebe et al., 2006). Thispermitted associating different physiologicaltraits to P uptake and estimating theirimportance in nutrient acquisition. Oncetraits are better understood, then an appropriateselection strategy can be devised, beit phenotypic or MAS. Thus, markers canbe useful to a breeding programme by elucidatingbasic plant mechanisms even ifthey are not applied directly in selection.Breeding schemes: adaptation toinclude MASThe eventual application of MAS requirescareful prioritization of traits and evenspecific genes for which markers are to besought, in light of the importance of thetrait and genes, and options for phenotypicselection. One should never assume thatMAS is necessarily superior to phenotypicselection, which for some traits may be aseffective and efficient as the use of molecularmarkers. However, if a gene is sufficientlyimportant in a breeding programme todemand that advanced lines have such agene (as in the case of the bgm-1 gene forvirus resistance in Central America), thereis probably some point in the selectionprocess at which MAS would be useful.Also, it is not necessary to select manygenes by MAS for it to be of great value.For example, if a single gene is segregatingand 50 percent of plants lack the gene inadvanced generations, an effective selectionwould eliminate half the population andincrease the subsequent efficiency of thebreeding programme by a factor of 2.Once markers are available, a key issue isdetermining the range of parental genotypeswithin which a marker is polymorphic andtherefore useful for selection. Markers ofgenes that originate from wider crosses (e.g.from different races, gene pools or species)will have a progressively greater chance ofbeing polymorphic among a range of parents(Figure 2) and therefore diagnostic forthe gene of interest. The example of bgm-1is again a good case in point as the resistanceallele and the SR2 marker are bothunique to the Durango gene pool and polymorphicin combinations across otherMesoamerican races as well as the Andeangene pool. In contrast, the ROC11 markerfor the bc-3 gene is only polymorphicacross gene pools and therefore not diagnosticfor the resistant allele.If a breeder has several potential parentsamong which to choose and these arecomparable with regard to other traits,it might be preferable to eliminate thosethat carry a band that would be confusedwith the linked marker and would resultin false positives. Conversely, if more thanone marker is available for a given gene,one might focus on those linked markersthat maintain polymorphism in the greaternumber of combinations. In some combinationsit might be informative to useboth linked markers simultaneously, bothto discern recombinants and to confirmmarkers.Several possible schemes for the introductionof MAS to different breedingschemes are represented in Figure 3. Abreeder must consider at what generationin the breeding programme selection