Effect of different mating designs on inbreeding, genetic variance and response to selection when applying individual selection in fish breeding programs (original) (raw)
Related papers
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.
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.
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
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.
Aquaculture, 2016
In this simulation study, the effect of the mating scheme on genetic gain and inbreeding has been explored for aquaculture selection programs where tank effects and large family sizes are common. Different selection methods were investigated (individual, family, sib, combined and within-family selection). Our results suggest that under family and sib selection, genetic gain was increased with assortative mating in comparison to random mating. The advantage of assortative mating increased when common environmental effects were present. Contrarily, a decrease in genetic gain was observed with disassortative mating, except for the case of within-family selection. The advantage of assortative mating over random mating was due to the increase in the betweenfamily component of the additive genetic variance that was exacerbated with the presence of common environmental effects. Under family and sib selection, the join effect of assortative mating and common environmental effects produced an increase in genetic gain of around 80 and 40% at early generations, and around 10 and 60% at later generations, respectively. Inbreeding was low under family selection for all mating schemes but much higher under sib selection when assortative mating was performed. In fact, the inbreeding coefficient after 10 generations of selection was 300% higher when assortative matings were performed under sib selection, compared to random matings. This was due to the fact that under sib selection, matings were based on family means, leading to an increased frequency of within-family matings. To our knowledge, this is the first study that investigates the effect of the mating scheme on genetic gain and inbreeding in an aquaculture context where family sizes are large and tank effects are present, and shows that assortative mating can substantially enhance the response to selection, particularly when family selection methods are applied. Statement of relevance: Our article complies with the Policy Statement for submission of manuscripts to the Genetics Section, as it provides insight into the issue of breeding programs. Here, we have connected previous work in the field to address new questions, focusing on how the mating scheme may affect both genetic gain and inbreeding in aquaculture selection programs, where family sizes are typically large and tank effects are usually present. In fish species, it is possible to consider different mating schemes because fecundity is high and because in vitro fertilization is often possible. A particular problem in aquaculture breeding programs is the impossibility of tagging physically newborn individuals. Given this, a common practice in aquaculture is to rear families in separate tanks until the fish are large enough to be individually tagged. This introduces an environmental effect common to the members of the same family (tank effect) which can lead to a reduction of the response to selection that needs to be considered. We studied here the efficiency of different selection methods in terms of genetic gain and inbreeding and investigated the effect of the mating scheme to optimize breeding programs in aquaculture when tank effects are present. We have shown that assortative mating can substantially enhance the response to selection, particularly when family selection methods are applied and tank effects are present. To our knowledge, the effect of the mating scheme in an aquaculture context has never been addressed before. Our results suggest that assortative mating in the presence of common environmental variance may be considered in selection programs in aquaculture. Our conclusions will help breeders make optimal mating choices.
Designing aquaculture mass selection programs to avoid high inbreeding rates
Aquaculture, 2002
A series of replicated stochastic simulations was carried out to determine the effect of the Ž . Ž number of breeders selected 4-100 pairs , the number of progeny tested 5-150 progeny per . Ž . pair and the magnitude of the heritability 0.1-0.4 on the rate of inbreeding, and the response to selection through 15 generations of mass selection. It was found that to keep inbreeding rates low Ž . about 1% per generation , a minimum of 50 pairs of breeders should be selected and the number of progeny tested should be restricted and standardized to not less than 30-50 progeny per pair.
A novel breeding design to produce genetically protected homogenous fish populations for on-growing
Aquaculture Research, 2013
We present a novel KING breeding design to produce genetically protected homogeneous fish material for commercial producers from a breeding nucleus. KING F2-production population is established from the nucleus, first through full-sib mating within two unrelated high-quality families to produce inbred F1-progeny and then resolving the inbreeding in F2 through mating of the unrelated F1-individuals. Owing to a small number of founders and the inbred F1-parents, the remaining additive genetic variance is 37.5% of the original. This restricts the use of F2-progeny to establish new breeding programmes, thereby protecting the genetic material of the nucleus. The theoretical calculations show that a concomitant decrease of phenotypic variance is possible. However, the reduction is considerable only for traits with high heritability (h 2 > 0.50). The method was tested with rainbow trout. The results revealed that the mean body weight of the KINGprogeny was similar, but, surprisingly, phenotypic variation (especially due to residual variance) was higher compared with either their outbred control group or the nucleus breeding population. Although further evaluation of this breeding design is needed, the results suggest that while genetic protection is achieved, the efficiency of the method to reduce phenotypic variation is limited for economically important traits with lowto-moderate heritability.