marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 337text of fish breeding is also discussed bySonesson (this volume).For most breeding programmes, physicaltagging will prove efficient both ineconomic and biological terms to achieveacceptable rates of genetic gain, while minimizingrates of inbreeding. Genetic markertechnology can still be costly for routineassignment of parentage, althoughthese costs can be reduced using multiplexpolymerase chain reaction (PCR)technology (Paterson, Piertney and Knox,2004; Taris, Baron and Sharbel, 2005) inwhich more than one marker can be genotypedsimultaneously in a single gel laneor capillary. This is especially the casewhen only DNA markers are used withoutphysical tagging, as individuals must be retypedwhen records for multiple traits areincluded in the selection criteria (Gjerde,Villaneuva and Bentsen, 2002).It is expected that rates of genetic gainfor economic traits will not be affected significantlywhen common environmentaleffects are present. This is because, in manyspecies of cultured salmonids, the commonenvironmental effect decreases considerably,from about 20 percent for alevin weight to5 percent for body weight at harvest, whichis the trait with most impact on profit(Herbinger et al., 1999; Henryon et al.,2002; Kause et al., 2005). Hence, commonenvironmental effects should not decreasethe rates of genetic gain for traits measuredat harvest when physical tagging is used.Furthermore, multistage selection offers thepossibility of first selecting individuals on awithin-family basis directly from tanks (fortraits influenced by common environmentaleffects), and then selecting at a second stagefor traits measured at harvest (Martinez,2006a). This alternative would either maintainrates of gain while decreasing the costsassociated with tagging, or even increaserates of gain, when recording from tanks(within families) can be carried out relativelyinexpensively (Martinez, 2006a).The sample size (i.e. the numbers ofindividuals and markers required forreconstructing the pedigree of a populationaccurately) is a practical issue, asnot all individuals in a population can begenotyped for all markers available. Suchissues arise in species where physical taggingis not possible or not economicallysound, as in nucleus populations withoutelectronic tagging (e.g. when recovering aback-up population for nucleus breedingprogrammes) or when disease challenges(e.g. for infectious pancreatic necrotic virus[IPNV]) are carried out early in the lifecycle (Martinez et al., in preparation). Smallsample sizes, together with sperm competition(Withler and Beacham, 1994), matingpreference (as in Artemia; G. Gajardo, personalcommunication) and other biologicalfactors after fertilization can increase thevariance of family size, thereby decreasingthe effective population size to unsustainablelevels (Brown, Woolliams andMcAndrew, 2005).Another problem arises in practicewhen selection is carried out before genotypingwith markers. In this case, BLUPof breeding values is likely to be biasedbecause not all phenotypic informationis used when predicting breeding values.The magnitude of re-ranking is dependenton the amount of information from afamily within the selected group. In theseinstances, the mixed model equations needto be modified to account for such selecteddata (Morton and Howarth, 2005).Establishing breeding programmesusing molecular informationThe choices made at the founding of abreeding programme have a critical