Inbreeding and effective population size in a coho salmon (Oncorhynchus kisutch) breeding nucleus in Chile (original) (raw)
Related papers
Canadian Journal of Fisheries and Aquatic Sciences, 2004
Chilean salmon culture is based on a high degree of artificial selection, which has had the tendency to increase the inbreeding (F). Three types of nonrandom mating were evaluated to control the inbreeding in two best linear unbiased prediction selected coho salmon (Oncorhynchus kisutch) populations (even and odd). These included compensatory mating on the basis of breeding values (C), modified compensatory mating (C1) based on the family mean of breeding values, and mating that minimized the mean co-ancestry of the group selected (MC scheme). In the odd population, the MC scheme (F = 2.0%) reduced the increase in inbreeding of the next generation by 50% and 46% when compared with random mating of selected individuals with sib mating restricted (F = 3.9%) and with C (F = 3.7%), respectively. In the even population, the MC scheme reduced the increase in inbreeding by 14% compared with C1 (9.7 versus 11.2). In both populations, the MC scheme also reduced variance in inbreeding (even, 59%; odd, 39%). Thus, the MC scheme was more efficient in reducing the increase and variance of inbreeding, thus limiting the expression of inbreeding depression. Although the MC scheme was more time consuming, we recommend this scheme to carry out crosses in each generation.
An analytical investigation of the dynamics of inbreeding in multi-generation supportive breeding
2002
Supportive breeding is being increasingly used as a measure to reduce the short-term probability of extinction of populations with highly reduced abundance relative to historical levels. In this paper, we provide a conceptual framework and analytical tools to compute changes in inbreeding coefficient (F) in the case of supportive breeding over any number of generations. The dynamics of inbreeding coefficients were investigated by means of a system of recurrence equations. We focussed on quantifying the dynamics of F for specific combinations of parameter values in terms of the effects of captive population census size, refreshment rate of breeders in captivity, scale of supplementation program, and migration rate. We observed that supplementation did not always result in substantial inbreeding increment and several conditions lowered overall inbreeding relative to control situations without supplementation. The census size of captive populations was the single most important controllable parameter determining the genetic consequences of supportive breeding. While the proportion of captive breeders brought into captivity from the wild bore a complex relationship to inbreeding coefficient dynamics, the results indicated that managers should generally aim at high refreshment rates (that is, large proportions of their captive stock originating from the wild). This is especially important when a small captive population is expected to contribute large numbers of breeders to the supplemented population. The analysis also showed how supplemented populations connected to a large metapopulation through gene flow recover from the genetic risks of inbreeding due to supportive breeding program more quickly than isolated populations. The results of this study join those of an increasing number of investigations showing that supportive breeding does not always increase inbreeding, and may even decrease it in several circumstances. However, supportive breeding systems are complex, and results such as presented here should not be used in isolation, but in consideration of other issues such as the consequences on long-term fitness of wild individuals.
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, 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
Open-nucleus breeding strategies compared with population-wide positive assortative mating
Theoretical and Applied Genetics, 2004
This study compares population-wide positive assortative mating (PAM) with open-nucleus breeding with an elite and main population when more effort is allocated to parents of the elite. A companion study showed that PAM is advantageous when testing effort is independent of parental value. In the present study, unbalanced testing was imposed by varying the number of crosses or the number of genotypes per cross. These unbalanced alternatives are compared with PAM, where the testing effort was varied so that better parents were mated more frequently. More effort allocated to parents of higher rank increased the additive effect and the additive variance and only slightly altered the group coancestry and inbreeding in the breeding population (BP) compared with completely balanced scenarios. Of particular interest to the breeder, large enhancement of the additive variance in the BP contributed to higher gains in the production population (PP). These simulations demonstrate that populationwide PAM leads to higher genetic gains compared with open-nucleus alternatives at any desired target level of diversity in the PP. This is true for both balanced (part I) and unbalanced distribution of testing effort (part II).
Aquaculture, 2004
Levels of inbreeding and inbreeding depression were studied in two populations of Coho salmon (Oncorhynchus kisutch) in Chile. The two populations, termed even year, and odd year were artificially selected by weight at harvest over four generations, using the best linear unbiased prediction (BLUP) of breeding values. Also, general linear models (GLM) were used to analyze the effects of inbreeding on reproductive traits of the females and on survival of the progeny. The selection resulted in 56 -76% of the parents of the base population not contributing with descendents in the fourth generation. The inbreeding rate was greater in the even population (DF=2.45% per generation) than the odd population (DF=1.10% per generation) as a direct consequence of the smaller number of founder individuals in the former population (Ne=61 and 106, respectively). The level of inbreeding in the last generation was 9.5% (S.D.=2.7, range 5 -19%) for year-class 2000 and 4.3% (S.D.=2.6, range 1 -12%) for year-class 2001. Significant inbreeding depression was estimated for the gonadosomatic index (À5.3% per each 10% increase in inbreeding) in population year 2000, and for body length at spawning (À1.56%) in population year 2001. The inbreeding did not significantly reduce other traits such as weight body at spawning, weight of the gonad, number of green eggs, or relative fecundity. No significant inbreeding depression was observed in either population regarding the survival of eggs in the 0044-8486/$ -see front matter D Aquaculture 234 (2004) 111 -122 eyed stage. Given the deleterious effects of inbreeding on reproductive traits, salmon selection programs should employ methods which limit the rate of increase of this factor. D
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.
Minimizing inbreeding by managing genetic contributions across generations
Genetics, 2003
Here we present the strategy that achieves the lowest possible rate of inbreeding (⌬F) for a population with unequal numbers of sires and dams with random mating. This new strategy results in a ⌬F as much as 10% lower than previously achieved. A simple and efficient approach to reducing inbreeding in small populations with sexes of unequal census number is to impose a breeding structure where parental success is controlled in each generation. This approach led to the development of strategies for selecting replacements each generation that were based upon parentage, e.g., a son replacing its sire. This study extends these strategies to a multigeneration round robin scheme where genetic contributions of ancestors to descendants are managed to remove all uncertainties about breeding roles over generations; i.e., male descendants are distributed as equally as possible among dams. In doing so, the sampling variance of genetic contributions within each breeding category is eliminated and consequently ⌬F is minimized. Using the concept of long-term genetic contributions, the asymptotic ⌬F of the new strategy for random mating, M sires and d dams per sire, is φ/(12M), where φ ϭ [1 ϩ 2(1 ⁄ 4) d ]. Predictions were validated using Monte Carlo simulations. The scheme was shown to achieve the lowest possible ⌬F using pedigree alone and showed that further reductions in ⌬F below that obtained from random mating arise from preferential mating of relatives and not from their avoidance. MATERIALS AND METHODS Notation: See Table 1 for a description of the main nota-1