marker-assisted selection in wheat - ictsd

330Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishSummaryThe main goals of breeding programmes for fish and shellfish are to increase the profitabilityand sustainability of aquaculture. Traditionally, these have been carried outsuccessfully using pedigree information by selecting individuals based on breeding valuespredicted for traits measured on candidates using an “animal model”. This methodologyassumes that phenotypes are explained by a large number of genes with small effectsand random environmental deviations. However, information on individual genes withmedium or large effects cannot be used in this manner. In selective breeding programmesusing pedigree information, molecular markers have been used primarily for parentageassignment when tagging individual fish is difficult and to avoid causing common environmentaleffects from rearing families in separate tanks. The use of these techniques in suchconventional breeding programmes is discussed in detail.Exploiting the great biological diversity of many fish and shellfish species, differentexperimental designs may use either chromosomal manipulations or large family sizesto increase the likelihood of finding the loci affecting quantitative traits, the so-calledQTL, by screening the segregation of molecular markers. Using information on identifiedloci in breeding schemes in aquaculture is expected to be cost-effective compared withtraditional breeding methods only when the accuracy of predicting breeding values israther low, e.g. for traits with low heritability such as disease resistance or carcass quality.One of the problems facing aquaculture is that some of the resources required to locateQTL accurately, such as dense linkage maps, are not yet available for the many species.Recently, however, information from expressed sequence tag (EST) databases has beenused for developing molecular markers such as microsatellites and single nucleotidepolymorphisms (SNPs). Marker-assisted selection (MAS) or genome-wide marker-assistedselection (G-MAS) using linkage disequilibrium within families or across populations arenot widely used in aquaculture, but their application in actual breeding programmes isexpected to be a fertile area of research. This chapter describes how genomic tools can beused jointly with pedigree-based breeding strategies and the potential and real value ofmolecular markers in fish and shellfish breeding schemes.