Rates of inbreeding using DNA fingerprinting in aquaculture breeding programs at various broodstock fitness levels — a simulation study

Abstract

A simulation study was used to examine the potential use of DNA fingerprinting (DNA tagging) as a tool to avoid excessive inbreeding by identifying suitable candidate breeders in genetic selection programs. ‘Broodstock fitness’ (the ability of broodstock to survive from harvest and reproduce) needs to be considered in designing breeding programs using DNA tagging. In this study, reduced broodstock fitness increased inbreeding exponentially. The level of inbreeding was also dependent on the intraclass correlation (t), selection intensity, number of individuals DNA tagged (NDNA), number of families maintained (Nf) and the number of candidate breeders retained per sex/family at harvest (C). With a broodstock fitness of 0.90, DNA tagging could theoretically achieve a selection intensity, in terms of the total phenotypic variance, of 2.90 standard deviations with 800 000 graded at harvest, while maintaining an inbreeding rate of 1.0% per generation (NDNA = 800, Nf = 30, C = 4, t = 0.3). In practice, the numbers required could be achieved by growing families in individual facilities (e.g. sea cages for barramundi or ponds for prawns). When mechanical grading is not possible, the selection pool may be limited to a level where physical tagging is feasible. In this case, there was no advantage in selection response using DNA tagging compared with physical tags. DNA tagging as a selection tool may be more feasible when broodstock fitness is above 0.6, and may fill a niche where industry infrastructure is not large enough to support separate rearing of families or where physical tagging is not economically viable or suitable. DNA tagging may also be useful as a means of recovering families in backup facilities where families have been pooled to reduce infrastructure costs. Due to the random nature of DNA sampling, not all families may be recovered and a reduction in selection pressure may facilitate family recovery.

Genetic parameter estimates for growth-related traits of blunt snout bream (Megalobrama amblycephala) using microsatellite-based pedigree

“…By communally rearing offspring immediately after hatching and using microsatellite‐based pedigree, it will be possible to greatly reduce the environmental component of phenotypic variation among families, thereby giving greater accuracy for the estimation of genetic parameters (Couch ). The communal rearing approach also reduces the number of rearing units necessary for production of families and increases the number of families or groups that can be compared per unit cost (Macbeth ).…”

“…As molecular markers (e.g. microsatellites) can be used to determine the parentage of each communally reared individual, communal rearing techniques have been widely applied to selective breeding programme in aquaculture (Vandeputte, Kocour, Mauger, Dupont‐Nivet, De Guerry, Rodina, Gela, Vallod, Chevassus & Linhart ; Saillant, Dupont‐Nivet, Haffray & Chatain ; Gray, Joyce & Wertheimer ), which can reduce the cost of culture facilities and increase the number of families or groups used for breeding programmes (Macbeth ). In addition, the environmental component of phenotypic variation among families can be largely minimized, unmasking additive genetic contributions to commercially important performance traits (Couch ).…”

Evaluation of 1-stage and 2-stage selection in yellow perch I: Genetic and phenotypic parameters for body weight of F1 fish reared in ponds using microsatellite parentage assignment1

“…Correlation coefficients (CC) of mean family BW and family length for yellow perch between any 2 ponds at yr 1 and their significance levels Using molecular markers to establish pedigrees allows for the use of communal rearing in selective breeding programs. This technique can reduce the number of rearing units necessary for production of families and increase the number of families or groups that can be compared (McGinty, 1987;Macbeth, 2005). Communal rearing has the additional importance of largely minimizing the environmental component of phenotypic variation among families and unmasking additive genetic contributions to commercially important performance traits (Couch, 2006).…”

“…Thanks to the advent of molecular markers (e.g., RFLP, amplified fragment-length polymorphism, microsatellites, SNP) that can be used to determine the parentage of each communally reared individual (Vandeputte et al, 2004;Couch, 2006;Saillant et al, 2006;Castro et al, 2008;Dupont-Nivet et al, 2008;Gray et al, 2008), a communal rearing technique (i.e., rearing all families in the same environment) can be applied to selective breeding in aquaculture. The communal rearing technique can reduce the costs of culture facilities and increase the number of families or groups used for breeding programs (McGinty, 1987;Macbeth, 2005). Additionally, the environmental component of phenotypic variation among families can be largely minimized, unmasking additive genetic contributions to commercially important performance traits (Couch, 2006).…”