marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 343populations: full-sib mating, hierarchicalmating, or double haploid designs. Thisanalysis suggested that the use of doublehaploids appeared to be of benefit whendetecting QTL, particularly when both thevariance of the QTL and of the polygeniceffects was small. Furthermore, given therelatively large size of full-sib families infish, there appeared to be little advantageof hierarchical mating over full-sib matingdesigns for detecting QTL, the optimumfamily size depending on the size of theQTL and the population structure usedfor mapping (Martinez, Hill and Knott,2002). The gain in power of the double haploiddesign comes from the increase in thevariance of the Mendelian sampling termwithin families, which is effectively doubledfor traits that are explained by additiveeffects (Falconer and Mackay, 1996).As experimental settings constrain thetotal number of individuals genotyped,designs aimed at QTL mapping shouldinclude a small number of families of relativelylarge size in order to maximizethe likelihood of detecting the QTL. Thisis because most of the information formapping QTL uses linkage informationthat comes from within-family segregation(Muranty, 1996; Xu and Gessler, 1998).However, increasing power comes at theexpense of reducing the accuracy of estimatingthe additive genetic variance forpolygenic effects. A QTL mapping methodhas been developed for double haploids,which efficiently accommodates all theuncertainties that pertain to outbred populations,such as unknown linkage phasesand differing levels of marker informativeness,using the identical-by-descentvariance component method (see below;Martinez, 2003). Also, it is possible to combinedouble haploids and outbred relativesin the same family. Simulations of differingamounts of marker information and heritabilityfor the QTL were used to comparethe empirical power of the double haploidand full-sib designs. While the power ofthe full-sib design was lower than that fordouble haploids, QTL position estimatesfor double haploids had large confidenceintervals (about 30 cM as compared with 40cM for full-sibs; Martinez, 2003).The double haploid design was usedfor mapping QTL for stress response incommon carp using single marker analysis(Tanck et al., 2001). The authors foundonly suggestive evidence for QTL, which isnot surprising due to limited genome coveragefor markers used in the analysis.Published results have shown that doublehaploid lines are a useful resource for QTLdetection studies. However, double haploidlines are difficult to develop due to theexpression of deleterious recessive alleles(McCune et al., 2002) and the low survivalfollowing shocks applied to restore diploidyto the haploid embryo. As the rate of malerecombination is depressed, the precisionof mapping QTL in androgenetic families islower than that obtained using recombinationevents from females. Another practicalmatter is the labour needed for developinga clonal line, as at least two generations arerequired (Figure 3). This delay can be quiteexpensive and time-consuming for specieswith a long generation interval, such assalmon or trout (two to four years).Aspects of QTL mapping in outbredpopulations of fishInbred line crosses are ideal for mappingQTL because they are expected to be completelyinformative for both markers andQTL, providing that the inbred lines arefixed for alternative alleles. Outbred populationsare not completely informative forboth QTL and markers; thus, experimental