marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 341a combination of genetic mapping (linkageand fine mapping) to localize the QTL toa small region on the chromosome underanalysis, and candidate gene or positionalcloning approaches to identify the geneswithin the QTL region.In some cases, sufficient biochemicalor physiological information is availableto investigate the association between thequantitative expression and the level ofmarker polymorphisms within specificgenes. Nevertheless, this approach requiresa great amount of detailed information inorder to choose which gene explains thegreatest effect and to have sufficient powerto detect the association. This informationis starting to appear in the aquaculture literaturefrom multinational projects suchas the Consortium of Genomic Resourcesfor All Salmonids Project (cGRASP) (Nget al., 2005).QTL mapping in fish using linkage disequilibrium:theoretical and practicalconsiderationsValue of chromosomal manipulationsThe great reproductive flexibility of fishenables different breeding designs to beimplemented relatively easily. Completelyhomozygous fish can be produced inonly one generation using chromosomeset manipulations, without the many generationsof inbreeding needed in othervertebrates. These manipulations enabledoubling of the chromosomal complementof a haploid gamete (Young et al.,1996; Corley-Smith, Lim and Bradhorst,1996). Androgenetic double haploid individualscan be obtained by fertilizing eggsthat were inactivated with gamma radiation,yielding haploid embryos containingonly paternal chromosomes. Alternatively,gynogenetic double haploid individuals canbe obtained by activating the developmentof eggs with ultraviolet-inactivated sperm,yielding haploid embryos containing onlymaternal chromosomes. In each case,diploidy is restored using methods thatsuppress the first mitotic division (Figure 3;Streisinger et al., 1980; Corley-Smith, Limand Bradhorst, 1996; Bijma, van Arendonkand Bovenhuis, 1997; Young et al., 1998).The use of these reproductive manipulationsto provide experimental populationsfor genetic analysis of complex quantitativetraits has been well described (Bongers etal., 1997; Robison, Wheeler and Thorgaard,2001; Tanck et al., 2001).Double haploids from inbred line crossesAfter a second round of uniparental reproduction(Figure 3), a collection of clonal linescan be obtained that collectively is likelyto represent all the genetic variants fromthe base population (Bongers et al., 1997).Crosses of sex-reversed double haploid individualsfrom lines that diverge for the traitsof interest can produce F 1 lines in completelinkage disequilibrium. These F 1 populationscan be used for further experimentationbased on F 2 or backcross designs. Anotherround of androgenesis of F 1 individuals willproduce a population of fully homozygousindividuals. This design will have twice thepower for detecting QTL as the standard F 2design (Martinez, 2003). The standard deviationof QTL position estimates is halved forthe double haploid design. This is due toan increase in the additive genetic variance,which is doubled for the double haploiddesign due to redistribution of the genotypefrequencies in the progeny generation(Falconer and Mackay, 1996).Informative double haploid populationsof this sort have been utilized to performQTL analysis for embryonic developmentrate in rainbow trout (Robison, Wheelerand Sundin, 2001; Martinez et al., 2002;