A novel breeding design to produce genetically protected homogenous fish populations for on-growing (original) (raw)
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Aquaculture, 2014
When setting up a breeding program for fish, an optimal breeding scheme is sought, and especially the number of families to use is a pivot parameter in this regard. This simulation study tests a range of probable number of families, with the use of two different methods for implementation of optimum contribution procedures in fish: one based on individual quotas and one with family quotas. Schemes are compared at the same prescribed rate of inbreeding. The breeding goal consisted of two correlated traits, one that could be measured on all selection candidates, the second only on full-sibs. The number of families ranged from 50 to 400, whereas the number of offspring per full-sib family was fixed at 50. Average genetic gain for generations 5 to 15 was used for comparing the schemes, and the rate of inbreeding per generation was restricted to 1%. The individual-based method gave the overall highest genetic gain, but the superiority for this method was most evident for the breeding schemes with a high number of families. The biggest difference between the two methods tested stems from the fact that the family-based method furnished a relatively larger proportion of the gain on the first trait; measurable only on the informants. For the individual-based method, this trait had negative or almost no gain when the genetic correlation was negative. The study also showed that although the total gain did not differ too much, the choice of method could highly influence the specific gain in each of the two traits. It is concluded that for the parameters and assumptions used in this study, the optimal number of families for both methods are likely to be around 200 to 300 if economic considerations are also included.
The rates of genetic gain and inbreeding were examined in alternative breeding designs of rainbow trout with different mating ratios, variable number of individuals measured and different number of traits included in a selection index in a closed nucleusbreeding scheme. Three body weight records during growth at the nucleus central station and body weight before marketing at a separate sea station (the breeding objective) were assumed to be recorded, and the genetic parameters were obtained from the actual Finnish breeding program. The rates of genetic gain were determined using the prediction error variance-covariance matrix of the traits included into the best linear prediction of breeding values. The rates of inbreeding were calculated using a first-order approximation, by empirically obtaining the probabilities of co-selection of relatives. The analysis showed that the rate of genetic gain can be improved as much as 20% by changing the mating ratios from the traditional nested designs (e.g., ratio of sires to dams 1M : 3F) to factorial mating (e.g., 3M : 5F). This enhance in genetic gain is mainly due to an increase in the selection intensity of females, which is constant in the nested designs with a fixed number of full-sib family tanks for a given family size. The rates of inbreeding appear to be higher for factorial than for nested designs, although, at the same rate of inbreeding, factorial designs present equal or higher rates of genetic gain compared to nested designs. The accuracy of the breeding values differ only little among the different mating ratios explored, whereas the inclusion of information from relatives at the sea station in the selection index increased the accuracy, and thus, the genetic gain.
Selective breeding in fish and conservation of genetic resources for aquaculture
Reproduction in Domestic Animals
To satisfy increasing demands for fish as food, progress must occur towards greater aquaculture productivity whilst retaining the wild and farmed genetic resources that underpin global fish production. We review the main selection methods that have been developed for genetic improvement in aquaculture, and discuss their virtues and shortcomings. Examples of the application of mass, cohort, within family, and combined between-family and within-family selection are given. In addition, we review the manner in which fish genetic resources can be lost at the intra-specific, species and ecosystem levels and discuss options to best prevent this. We illustrate that fundamental principles of genetic management are common in the implementation of both selective breeding and conservation programmes, and should be emphasized in capacity development efforts. We highlight the value of applied genetics approaches for increasing aquaculture productivity and the conservation of fish genetic resources.
Aquaculture, 2006
In selection programs, the aim is to produce genetic progress but also to preserve genetic variability. We investigated a simple way to preserve the genetic variability i.e. the choice of appropriate mating schemes, when pedigrees are unknown. We used computer simulations to compare the ability of different mating systems to preserve genetic variability in populations undergoing selection. The model used for data simulation was a simple polygenic additive model which did not take into account maternal effect, inbreeding depression and unbalanced family sizes. The mating systems considered were full factorial, partial factorial, nested and single pair matings. The evolution of additive genetic variability was studied at two different levels of heritability (0.1; 0.5), two different population sizes (1000 or 5000 animals), 30 generations of selection and different combinations of number of sires/number of dams. Results showed that the various mating designs did differ in terms of long-term genetic variability and genetic response. For the same selection pressure, designs which created the highest number of families were the most efficient. Thus, factorial designs were the most efficient and single pair designs were the least efficient. However, differences between full factorial and partial factorial designs were small. When possible, partial factorial mating (FS) designs seemed to be a good compromise to achieve high genetic responses while preserving genetic variability. Further studies dealing with effect of inbreeding depression, maternal effects or unbalanced family sizes should complete our present results. D
Aquaculture, 2011
The aim of this paper was to develop and test different methods of applying optimum contribution (OC) to control the rate of inbreeding in various practical breeding schemes for fish, where there is a limitation on the number of full-sib families that can be managed. A simulation study using an infinitesimal genetic model was used to compare the performance of four different ways of implementing OC together with a method commonly used today for controlling inbreeding in fish populations. Breeding programs of different sizes were studied, with the number of families ranging from 40 to 200, and the number of offspring per family ranging from 8 to 200. Heritabilities of 0.1, 0.25 and 0.5 were assumed, and the rate of inbreeding per generation (ΔF) was restricted to 0.005. Average genetic gain (ΔG) for generations 5-15 was used to compare the different schemes. The genetic gain obtained with OC methods were up to 13% higher than for the method commonly used today. The results show although conventional methods of inbreeding control may work in many situations, OC procedures are beneficial and practically possible to implement. Therefore it is concluded that OC procedures should be implemented in aquaculture breeding programs.
Improving uniformity of growth by mating and selection strategies in rainbow trout
Abstract Text: Minimal variation in fish growth increases profit of fish farming and improves fish welfare. Uniformity can be increased by reducing additive genetic and residual variation. We first present a mating strategy to create a production stock that has only 38% of the original genetic variance, and assuming heritability of 0.26 for body weight of rainbow trout, 84% of the original phenotypic variance. An experimental test confirmed that phenotypic variance can be indeed reduced to 80% of the variation in the original breeding programme. Secondly, genetic CV for residual variation in body weight was notable (37%). Hence, one generation of sib selection for reduced residual variation is expected to reduce phenotypic variance to 87-89% of the original phenotypic variance. Both methods aid to produce more uniform populations for on-growing, while simultaneously maintaining genetic variation in the nucleus. Keywords: additive genetic variance heterogeneity of residual variance r...
Aquaculture, 2018
Marker-based parentage assignment provides the opportunity to investigate factors of efficiency for mixed-family designs and factorial mating. In such designs, family size is both uncontrolled and small, which may be thought to limit the accuracy of estimated breeding values (EBVs). The objective of this work was to estimate the accuracy of EBVs of growth and quality traits in a large factorial mating design and in commercial breeding conditions. An expected six hundred full-sib families of rainbow trout Oncorhynchus mykiss (2042 fish in total) were produced by ten factorial matings of six dams with ten sires. Fish were phenotyped for body weight, carcass yield, fillet yield, fillet fat content and fillet colour, and family information was recovered using microsatellite markers. The accuracy of EBVs was estimated using or removing individual performance to mimic combined family selection (with individual phenotype) or sib selection (without individual phenotype). The traits investigated had medium to high heritability (0.17-0.58). High to very high accuracy (0.630-0.817) was estimated for combined family selection. The accuracy of sib selection (not using individual phenotype) was 18-22% lower (0.542-0.638), but remained in the upper range reported for such traits. This level of accuracy was higher than those reported in conventional breeding programs using separate family rearing. This was true even for families with a very low number of full-sibs. Individual EBV accuracy was more closely linked to the total number of full-and half-sibs of each fish than to its number of full-sibs. We hypothesize that this was due to the factorial mating, which led to a high number of the genetic ties between sibs. Highlights ► This work reports for the first time accuracies of EBV in a mixed family breeding design assisted by DNA-parentage assignment for growth and quality traits (0.6-0.8). ► Theses accuracies were higher than those reported in classical family-based breeding program and similar or higher than reported by simulation for genomic selection ► The factorial mating is proposed as the factor that allow such interesting advantage ► This result confirms the potential interest to use such design to initiate domestication and selective breeding program
Livestock Science, 2012
Application of DNA parentage assignment for commercial selection in aquaculture is still rare. An experiment was performed to quantify and to minimize maternal effects on growth in rainbow trout. Six hundred families were reared until 198 day post fertilization (dpf) according to two different procedures. In the first procedure (NORM), all families were pooled at eyed stage. In the second procedure (MIN), where maternal effects due to differences in egg size were expected to be minimal, the spawns were divided into sub-groups with similar mean egg weight at eyed stage. These subgroups were then pooled when they achieved the same mean body length (147 dpf). Genetic parameters were estimated for body weight, body length and condition factor at 198 dpf, with 2964 fish assigned to their parents using microsatellites. Significant maternal effects were observed in the NORM group for body weight and body length (m²=0.08±0.03). The heritability of body weight was 0.16±0.07 in the NORM group and 0.36±0.06 in the MIN group, in which maternal effects were not significant. It is concluded that, when eggs of different females are mixed at eyed stage, maternal effects persist at least until 198 dpf. The proposed procedure efficiently limits maternal effects, substantially increasing the heritability for growth, and therefore the expected selection response.