marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 3351999). Although it is possible to use basequality values to discern true allelic variationsfrom sequencing errors, validationis a key step for true positive detection ofSNPs (Marth et al., 1999). This is generallycarried out using a proportion of the SNPsdetected in a sample of individuals from thetarget population. This strategy has beenused recently for SNP detection using ESTsequences from Atlantic salmon (Panitz etal., 2002; Hayes et al., 2004).Linkage mapsA linkage map is an ordered collection ofthe genes and genetic markers occurringalong the lengths of the chromosomes ofa species, with distances between themestimated on the basis of the number ofrecombination events observed in the data.Genetic linkage maps have been publishedfor rainbow trout (Young et al., 1998;Sakamoto et al., 2000; Nichols et al., 2003),channel catfish (Waldbieser et al., 2001),tilapias (Kocher et al., 1998; Lee et al., 2005)and Japanese flounder (Coimbra et al.,2003). References to updated linkage mapsof the major aquaculture species are givenin Table 1. Dense linkage maps includinga relatively large number of markers areunder development.Different patterns of recombinationappear among regions of linkage groups incertain male maps, with markers clusteredin centromeric regions, an extremeexample being Atlantic salmon whererecombination in males is greatly reduced(Moen et al., 2004b). The molecularmechanisms responsible for the differencesin recombination rates between sexes arenot well understood, although studies onmodel organisms such as zebrafish, wheregenomic sequencing is currently underway, may help to clarify this (Singer etal., 2002).Using markers to aidconventional fish and shellfishbreeding programmesMolecular markers may be used in a numberof ways to aid conventional breeding of fishand shellfish species, and some of these aredescribed and exemplified below.Parentage analysisOne of the main constraints facing effectivebreeding programmes for fish and shellfishis that newborn individuals are too small tobe tagged individually. Application of theanimal model approach (i.e. using a statisticalgenetic model to predict individualbreeding values) requires tagging a constantnumber of individuals from each familywith passive integrated transponders (PITtags) when they become sufficiently largeafter a period of individual family rearing.However, this system of early managementcreates common environmental (i.e.tank) effects for full-sib families (Martinez,Neira and Gall, 1999). To address thisissue, mixtures of equal-aged progeny fromdifferent families can be reared communallyto preclude the development of suchfamily-specific environmental effects, andgenetic markers can be used subsequentlyto assign individuals to families after evaluationof individual performance (Doyleand Herbinger, 1994). Thus, the impactof early common environmental effectsis considerably reduced if markers areused for parentage analysis when selectingindividuals for early growth rate traits(Herbinger et al., 1999; Norris, Bradley andCunningham, 2000).The amount of marker data needed toachieve acceptable levels of correct parentageassignment depends on the numberof loci, the number of alleles and the numberof parent-pairs (sires and dams) availablefor reconstructing the pedigree (Jamieson