marker-assisted selection in wheat - ictsd

172Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishbecause it has undergone only one generationof recombination in the F 2 (Figure 1).Thus, although these markers may be inLE with QTL within the parental breeds,they will be in partial LD with the QTLin the crossbred population if the markerand QTL differ in frequency between thebreeds. This population-wide LD enablesdetection of QTL that differ between theparental breeds based on a genome scanwith only a limited number of markersspread over the genome (~ every 15 to20 cM). This approach has formed the basisfor the extensive use of F 2 or backcrossesbetween breeds or lines for QTL detection,in particular in pigs, poultry and beef cattle(see Andersson, 2001 for a review). Theextensive LD enables detection of QTLthat are some distance from the markersbut also limits the accuracy (map resolution)with which the position of the QTLcan be determined.More extensive population-wide LD isalso expected to exist in synthetic lines,i.e. lines that were created from a cross inrecent history. These can be set up on anexperimental basis through advanced intercrosslines (Darvasi and Soller, 1995) orbe available as commercial breeding lines.Depending on the number of generationssince the cross, the extent of LD will haveeroded over generations and will, therefore,span shorter distances than in F 2 populations(Figure 1). This will require a moredense marker map to scan the genome withequivalent power as in an F 2 but will enablemore precise positioning of the QTL.QTL detection using LE markers inoutbred populationsAs linkage phases between the markerand QTL can differ from family to family,use of within-family LD for QTL detectionrequires QTL effects to be fitted on awithin-family basis, rather than across thepopulation. Similar to F 2 or backcrosses,the extent of within-family LD is extensiveand, thus, genome-wide coverage is providedby a limited number of markers butsignificant markers may be some distancefrom the QTL, resulting in poor map resolution.Thus, LE markers can be readilydetected on a genome-wide basis usinglarge half-sib families, requiring only sparsemarker maps (~15 to 20 cM spacing). Manyexamples of successful applications of thismethodology for detection of QTL regionsare available in the literature, in particularfor dairy cattle, utilizing the large paternalhalf-sib structures that are available throughextensive use of artificial insemination (seeWeller, Chapter 12).QTL detection using LE markers canalso be applied to extended pedigrees bymodelling the co-segregation of markersand QTL (Fernando and Grossman, 1989).These approaches use statistical modelsthat are described further in the sectionon genetic evaluation using LE markers.Depending on the number of generationswith phenotypes and marker genotypesthat are included in the analysis, map resolutionwill be better than with analysis ofhalf-sib families because multiple rounds ofrecombination are included in the data set.QTL detection using LD markers inoutbred populationsThe amount and extent of LD that existsin the populations that are used for geneticimprovement are the net result of all forcesthat create and break down LD and are,therefore, the result of the breeding andselection history of each population, alongwith random sampling. On this basis, populationsthat have been closed for manygenerations are expected to be in linkageequilibrium, except for closely linked loci.