marker-assisted selection in wheat

72Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishFigure 2Examples of autoradiograms showing the segregation of 2 SSR triplexes observed amongBC 4 plants and used for the targeted genotyping of specific regions along chromosomes c5and c25 (a subset of around 15 BC 4 plants from the 450 plants analysed is shown)c5BNL3995CIR034CIR301CIR034CIR301BNL3995CIR280ac25CIR109CIR109BNL1047aBNL1047aCIR280a(Lander et al., 1987). The MapMaker“group” (using a logarithm of the oddsratio [LOD] of 5.0 and 30 as a maximalrecombination frequency), “order” and“sequence” commands were used in eachcase. After aligning the BC 1 and BC 2 mapsusing common loci, a consensus frameworkBC 1 /BC 2 map was constructed bysimple extrapolation of the positions of theadditional BC 2 loci on the BC 1 map usedas a backbone map. The allelic constitutionthroughout the 26 chromosomes of allBC 1-4 individuals was displayed graphicallyusing Graphical GenoTyping software (R.van Berloo, Laboratory of Plant Breeding,Wageningen, Netherlands) and representedalong the consensus BC 1 map data.QTL analysesThe combined marker and phenotypic datathen served for three (BC 1 , BC 2 and BC 2 S 1 )separate QTL analyses of fibre qualitycomponents. The association betweenphenotype and marker genotype was investigatedthrough simple marker analysis(SMA), interval mapping (IM) and compositeinterval mapping (CIM) using thecomputer software QTL Cartographer 1.13(Basten, Weir and Beng, 1999) as describedin Lacape et al. (2005). In each data set(trait, generation), permutation-basedthresholds were considered at a 5 percentrisk at the genome level. Interval methodsrelied on the positions of the loci on theconsensus BC 1 map. Molecular data offurther generations (BC 3 and BC 4 ) werealso combined with phenotypic measurementsfor conducting the SMA option ofQTL Cartographer. Cotton fibre propertieswere considered from a product transformationperspective, meaning thatdecreases the in fibre fineness and yellow-