Abstract
Since the middle of the 1990s, parentage assignment using microsatellite markers has been introduced as a tool in aquaculture breeding. It now allows close to 100% assignment success, and offered new ways to develop aquaculture breeding using mixed family designs in commercial conditions. Its main achievements are the knowledge and control of family representation and inbreeding, especially in mass spawning species, above all the capacity to estimate reliable genetic parameters in any species and rearing system with no prior investment in structures, and the development of new breeding programs in many species. Parentage assignment should not be seen as a way to replace physical tagging, but as a new way to conceive breeding programs, which have to be optimized with its specific constraints, one of the most important being to well define the number of individuals to genotype to limit costs, maximize genetic gain while minimizing inbreeding. The recent possible shift to (for the moment) more costly single nucleotide polymorphism markers should benefit from future developments in genomics and marker-assisted selection to combine parentage assignment and indirect prediction of breeding values.
Highlights
Aquaculture is the fastest growing animal production worldwide, and provides half of the fish for human consumption worldwide (FAO, 2014). Such an important sector would be expected to use the best knowledge-based improvement methods, amongst which selective breeding is of paramount importance
There may be several reasons for this, but one clear technical weakness of aquaculture regarding the development of optimized selective breeding schemes is the fact that pedigree information is difficult and costly to obtain
Effective to obtain genetic gain, this method is very limiting for studying genetic variation as: (1) it provides results only after a minimum of two generations, (2) it requires the maintenance of at least two fish lines, selected/control or divergent lines, (3) it limits the evaluation of genetic variation to one trait only, and (4) the precision of realized heritability estimates is low in reasonably-sized two generation experiments (Nicholas, 1980)
Summary
Aquaculture is the fastest growing animal production worldwide, and provides half of the fish for human consumption worldwide (FAO, 2014). The second option to solve the pedigree problem is to use separate rearing of families until a size where tagging is possible, as in the Norwegian salmon breeding program, the first family-based selective breeding program in aquaculture, started in 1972 (Gjedrem, 2010). This was successfully extended to major aquaculture species such as salmonids, tilapias, oyster, or shrimps (Krishna et al, 2011; Thodesen et al, 2011; Gjedrem, 2012; Gjedrem et al, 2012; Zak et al, 2014). Mating designs are constrained to those where the number of families produced is low for a given number of parents tested, like single pair mating www.frontiersin.org
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