marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 333of molecular markers, the many species inaquaculture would make this a costly task(Liu and Cordes, 2004). Hence, a varietyof approaches have been taken to developgenetic markers for aquaculture species.Dominantly-expressed markers havebeen used extensively in aquaculture studies.Amplified fragment length polymorphism(AFLP) markers (Vos et al., 1995) providea cost-effective alternative for specieswhere DNA sequencing is not under wayor when there are restricted resources forQTL mapping. Dominant AFLP markersare preferred over random amplified polymorphicDNA (RAPD) markers becausethey are more reproducible both in otherlines or populations and in other laboratories(e.g. Nichols et al., 2003), and theycan generate hundreds of markers (a singlepolymerase chain reaction commonly generatesover ten markers). Furthermore,heterozygotes can often be distinguishedfrom homozygotes using the fluorescentband intensity (Piepho and Koch, 2000;Jansen et al., 2001).Microsatellite markers are simplesequence repeats (SSRs) arranged in tandemarrays scattered throughout the genome,both within known genes and in anonymousregions. Microsatellite markers areused increasingly in aquaculture species(reviewed by Liu and Cordes, 2004), dueto their elevated polymorphic informationcontent (PIC), co-dominant mode ofexpression, Mendelian inheritance, abundanceand broad distribution throughoutthe genome (Wright and Bentzen, 1994).Microsatellites are generally Type IImarkers, which are associated with genomicregions that have not been annotatedto known genes (O’Brien, 1991). Othermolecular markers can be distinguished asType I markers, which are linked to genes(of known function). Type I markers aremore desirable because they are generallymore conserved across evolutionarilydistant organisms, enabling comparativegenomics, assessment of genome evolutionand candidate gene analysis.Two procedures are used to generatemicrosatellite markers. The first uses agenomic library enriched with microsatellite-bearingsequences to generate clonesthat bear specific SSRs. These clones arethen sequenced to identify microsatellite-bearingsequences and then to designprimers to amplify the regions with specificSSR. Validation is required to studythe level of polymorphism and the numberof null alleles, and to identify any loci thatare duplicates due to any recent evolutionarygenome duplication event givingrise to multiple copies of loci in the haploidgenome (Coulibaly et al., 2005). This isdone by screening a sample of individualsfrom the target population.Many laboratories have been workingon developing expressed sequence tags(ESTs) derived from complementary DNA(cDNA) libraries for a variety of fish andshellfish species (Panitz et al., 2002; Riseet al., 2004a; Hayes et al., 2004; Rexroad etal., 2005; A. Alcivar-Warren, personal communication).EST sequences can be usedfor marker development in species wherethe full genome is not currently beingsequenced. The cDNA libraries are constructedusing messenger RNA (mRNA)that was expressed in different tissues, suchas kidney and gills. The expressed fragmentsof sequence data are not the full sequence ofa known gene, but what was incorporatedinto a mature mRNA molecule.In addition to the library-basedmethod of marker development previouslydescribed, microsatellites can be developedfrom EST databases or from known genesequences. As it is possible to connect the