marker-assisted selection in wheat

338Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishbearing on its ultimate success. Criteria forchoosing individuals that will be foundersshould be essentially the same as those usedwhen the selection response is optimizedunder restricted co-ancestry when pedigreeinformation is available (Meuwissen,1997; Toro and Mäki-Tanila, 1999). Thus,it is necessary to avoid matings betweenclose relatives for managing existing quantitativegenetic variation at the start of theprogramme. Experiments with the planktonicmicrocrustacean Daphnia spp. haveshown that neutral genetic variation giveslittle indication of the levels of quantitativegenetic variation available for selection(Pfrender et al., 2000). However, increasingthe population size at the beginning of thebreeding programme will diminish the subsequenteffect of random genetic drift, andtherefore larger founding populations willhave an increased likelihood of showingresponse to selection. Lack of adequatebase populations is the main reason for thelack of selection response observed in somespecies of fish (Gjedrem, 2000).The effective population size (N e )required for setting up a breeding programmedepends on the policy regardingrisk management (Brown, Woolliams andMcAndrew, 2005), but to prevent declinein fitness, some authors have recommendedN e values ranging from 31 to 250, which interms of rates of inbreeding should be lessthan 2 percent (Meuwissen and Woolliams,1994). Due to the large family sizes possiblefor many fish and shellfish species, breedingprogrammes that fail to control the geneticcontributions of parents in every generationare expected to incur relatively high rates ofinbreeding (Meuwissen, 1997). The situationis even more extreme when selection isbased on a complex breeding objective thatincludes information from relatives andmany traits jointly (Martinez, 2006b).Fish within commercial productionpopulations generally are not taggedindividually and pedigree information istherefore lacking. Genetic markers allow theestimation of pairwise relatedness betweenindividuals or sib-ship reconstructioneven with unknown ancestors (Toro andMäki-Tanila, 1999; Thomas and Hill,2000; Toro, Barragán and Óvilo, 2002;Wang, 2004; Fernandez and Toro, 2006).There is a plethora of estimators forcalculating pairwise relatedness (Quellerand Goodnight, 1989; Lynch and Ritland,1999). The efficiency of inferring pairwiserelatedness using markers without parentalinformation is affected by assuming knownallele frequencies in the base populationand unlinked loci in Hardy-Weinbergequilibrium. Furthermore, pair-wisemethods can lead to inconsistent assignationsbetween triplets of individuals because theyuse information from only two individualsat a time (Fernandez and Toro, 2006). Inaddition, it is difficult to set thresholds forclaiming different types of relatedness inthe data (Thomas and Hill, 2000; Norris,Bradley and Cunningham, 2000). On theother hand, sib-ship reconstruction methodsdo not attempt to calculate co-ancestry;rather, they attempt to reconstruct full- orhalf-sib or other family groups (Thomasand Hill, 2000; Emery, Boyle and Noble,2001; Smith, Herbinger and Merry, 2001).Such reconstructions of full- or half-sibfamilies or even other groups of relativesappear robust to lack of knowledge of basepopulation allele frequencies (Thomas andHill, 2000; Fernandez and Toro, 2006).Marker information can be used to inferrelatedness between individuals available ascandidate broodstock to generate the firstgeneration of offspring in the breeding programme,and thereby avoid mating amongclose relatives. This approach uses molec-