marker-assisted selection in wheat

Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 353erode the initial LD and therefore it isexpected that accuracy of estimating thebreeding value of many haplotypes willdecay (Zhang and Smith, 1992), the extentof the erosion being dependent on severalpopulation parameters (Meuwissen,Hayes and Goddard, 2001). In practice, theresponse to selection obtained needs to beverified in each generation; thus, re-estimationcan be used based on a random sampleof individuals from the population.One possible caveat is that by assuminga certain mode of gene action (i.e. onlyadditive effects), there may in fact be a morecomplicated genetic architecture influencingquantitative traits. For example, whenestimating dominance and epistasis with thesame data, more haplotype effects need tobe estimated. Therefore, it is likely that theaccuracy of individual effects will decrease.Another potential complication that ariseswhen the true model involves non-additiveeffects is that assignment of potential matesneeds to be optimized to increase the meanphenotype of the population simultaneouslythrough heterosis arising from combinationof different QTL alleles. In the long term,the frequency of homozygotes that areidentical-by-descent will increase withinthe population as a whole; consequently,methods are required to constrain the ratesof inbreeding to obtain similar changes ofthe population mean across generations.Furthermore, expression of differentcombinations of alleles after selection willrequire re-estimation of between-haplotypeeffects in each generation.ConclusionQTL mapping and MAS are not as welladvanced in aquaculture species as interrestrial plants and animals. However,the merger between genetics and genomicsis expected to be a fertile area of researchin the coming years due to the plethora ofinformation that is currently being gatheredby many laboratories around the world.It is through these research efforts thatvariations affecting complex traits in fishand shellfish species may be detected andused for increasing the usefulness of MASschemes. In the final analysis, however, allthese techniques must be cost-effective ifthey are to be profitable in actual breedingprogrammes.AcknowledgementsI am indebted for comments from Mr EricHallerman who greatly helped clarify themanuscript. This chapter has been fundedpartially by: INNOVA-Corporación deFomento de la Producción (CORFO)(05CT6 PP-10) on “Using functionalgenomics for understanding disease resistancein salmon” from the Governmentof Chile; Vicerrectoria de Investigaciony Creación, Universidad de Chile hatchproject 03/03312; and Fondo de Cienciias yTecnologia (FONDECYT) 1061190.ReferencesAnderson, E.C. & Thompson, E.A. 2002. A model-based method for identifying specieshybrids using multilocus genetic data. Genetics 160: 1217–1229.Arkush, K.D., Giese, A.R., Mendonca, H.L., McBride, A.M., Marty, G.D. & Hedrick, P.W. 2002.Resistance to three pathogens in the endangered winter-run Chinook salmon (Oncorhynchustshawytscha): effects of inbreeding and major histocompatibility complex genotypes. Can. J.Fisheries and Aquatic Sci. 59: 966–975.