marker-assisted selection in wheat - ictsd

Chapter 16 – Possibilities for marker-assisted selection in aquaculture breeding schemes 321their phenotypic values and the batch sizevaried from 50 to all (1 000, 5 000 or 10 000)candidates. Relatively small batches of fishwere genotyped at any one time to minimizegenotyping costs. Thereafter, BLUPbreeding values (Henderson, 1984) wereestimated and the optimum contributions ofthe candidates calculated using the methodof Meuwissen (1997). If the constraint onthe rate of inbreeding could not be achieved,another batch of fish was genotyped andincluded in the total number of candidates.Results showed that with a batch size of100, 76–92 percent of the genetic gain wasachieved compared with schemes where all1 000, 5 000 or 10 000 fish were genotypedto provide candidates for the optimum contributionselection algorithm. Hence, highgenetic gain was achieved at a fixed rate ofinbreeding with low genotyping costs.The main practical advantage of thesemarker-assisted breeding schemes is thatexpenses associated with separate rearingof full-sib families are not incurred, whichdecreases start-up and operational costs forthe breeding scheme. The most importanttrait at the start of a breeding programmeis probably growth, which can easily bemeasured on the candidate. Use of theoptimum contribution selection algorithmkeeps the rate of inbreeding under control,which is especially important in breedingprogrammes for aquaculture species whereselection intensity can be very high due tothe large family sizes. In combination withBLUP estimated breeding values, whichhave a high within-family correlation suchthat individuals with the highest breedingvalues will tend to come from only a fewfamilies, high rates of inbreeding can result(Sonesson, Gjerde and Meuwissen, 2005).However, there remain unsolved issueswith the combined optimum contributionand walk-back selection method:• Biased BLUP breeding values lead toa reduction in accuracy of selection,because not all selection candidates areincluded in the estimation of breedingvalues.• Low and unequal survival of families maylead to reduced genetic variation and thusincreased rate of inbreeding. However,the optimum contribution selection willcorrect for some of this loss by selectingfrom more families to keep the geneticbase broader than when selecting onlyfor the BLUP estimated breeding values.One option for reducing this problem ofunequal and low survival is to pool anequal number of individuals from eachfamily after the main period of earlymortality is over. In general, it is possibleto use more parents in these programmescompared with conventional familybasedselection programmes, which couldcompensate for some of the loss of familiescontributing to the next generation dueto low and unequal survival.• Multitrait selection is probably the largestpractical problem to solve. One alternativecould be to base the pre-selection ononly one or two traits that are inexpensiveto measure on the candidate. Techniquesfor measuring more traits on live selectioncandidates are steadily evolving (e.g.fat content in Atlantic salmon, Solberg etal., 2003), such that the sib-testing systemmight be unnecessary for these traits inthe future.Introgression schemesMany fish breeding schemes have beenstarted with a relatively narrow geneticbase, selecting for only one or two traits inrelatively few animals. However, becauseall farmed aquatic species still have wildancestors, introgression of genes (i.e. identifiedgenes or QTL) from these wild