marker-assisted selection in wheat - ictsd

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 331IntroductionThe main goals of fish and shellfish breedingprogrammes are to increase the profitabilityand sustainability of productionenterprises, while maintaining genetic variabilityin the cultured stock. Traditionally,selective breeding has targeted traits suchas body weight that can be easily improvedusing mass selection. Relatively few studieshave analysed other traits that are economicallyimportant. However, disease resistanceand carcass quality are traits that are difficultto measure on candidates for selection,but have major effects on the productionefficiency and profitability of many speciesin aquaculture.When developing efficient breedingprogrammes, pedigree information isrequired to maximize effective populationsizes and to use information from relativesto increase the accuracy of predictingbreeding values for all traits included inthe breeding objective. In most commercialapplications, pedigree information islacking; therefore, markers can be used toinfer relatedness between individuals, withor without parental information. Severalissues need to be considered on a case-bycasebasis when applying such molecularinformation for increasing the profitabilityof breeding programmes in practice.For traits that are difficult to measureon candidates for selection, prediction ofbreeding value has to rely on measurementson relatives. Under these circumstances,the accuracy of predicted breeding values(and thus, response) is lower than whenrecords are obtained directly on candidatesfor selection. In addition, there is anincreased probability of co-selecting relatives.It is especially for these traits thatmolecular markers that directly affect orare linked to quantitative trait loci (QTL)have been regarded as useful for markerassistedselection (MAS) or gene-assistedselection (GAS) programmes.This chapter begins by discussing thestatus of “conventional” breeding programmes,the challenges involved whenstarting such programmes for new speciesand the possibilities of incorporatingmarker information in “conventional” programmes.An outline is then provided ofthe molecular markers developed for aquaculturespecies and of their use for geneticanalysis. The main features of designs forQTL mapping, including the use of chromosomalmanipulations, are described,followed by a discussion of the prospectsand challenges of GAS or MAS for diseaseor carcass traits. Finally, new genomic toolsare considered briefly.Breeding programmes andresponse to selectionManagement of modern breeding programmesin aquaculture requires usingpedigree information to carry out soundand efficient statistical evaluations (usingbest linear unbiased prediction [BLUP]methodology). This approach enablesbreeders to maximize genetic gain whilelimiting rates of inbreeding to acceptablelevels (Meuwissen, 1997; Toro and Mäki-Tanila, 1999).Most of the genetic improvement infish and shellfish species to date has beenmade through the use of traditional selectivebreeding (reviewed by Hulata, 2001).Well-designed breeding programmes haveshown substantial response to selectionfor body weight, e.g. Atlantic salmon, 10–14 percent (Gjøen and Bentsen, 1997). Inrainbow trout, rates of genetic gain variedfrom 8 percent for indirect selection forbody weight at sea (Kause et al., 2005)to 13 percent for direct selection (Gjerde,1986). The response to selection was about