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Estimating the genetic variance of body weight uniformity in a farmed population of Pacific white shrimp

Silvia García-Ballesteros, Ph.D. Beatriz Villanueva, Ph.D. Jesús Fernández, Ph.D. Juan Pablo Gutiérrez, DVM Isabel Cervantes, DVM

Existing genetic variance for weight uniformity suggests possibility for genetic improvement

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Results of this study to estimate the genetic variance for weight uniformity in a farmed L. vannamei population showed that there is genetic variability for the environmental variance of weight at harvest, both in the selection nucleus and in the commercial population, and that response to selection for uniformity in the nucleus can be at least partially transmitted to the commercial population if this trait is included in the breeding program.

Most selective breeding programs for shrimp focus on improving growth traits only, but as growth rate increases and production intensifies, other traits related to the quality and uniformity of the final product gain importance for both consumers and producers, including size uniformity.

Shrimp are graded and classified according to standards that are defined in high-quality marketing evaluations and are mainly determined by their physical characteristics and uniformity of size. In particular, shrimp are graded according to their size and count per unit of weight. Prices between size categories vary widely and a larger number of smaller shrimp per unit weight reduces their price, so increasing the consistency of size within a specific count range can improve profitability.

In addition, large variation in body size can cause competition among shrimp (dominance hierarchies), which negatively affects growth rate, mortality and feed efficiency, and increases the need for management practices such as size grading. Another indirect benefit of improving uniformity is the potential to improve resilience, which is defined as the ability of an animal to maintain performance in spite of environmental perturbations. For all these reasons, and given that weight is genetically highly correlated with size, uniformity of weight is a clear candidate trait to be included in shrimp breeding programs.

Weight uniformity depends on the sensitivity of an individual to macro- and micro-environmental factors. Macroenvironmental factors are measurable factors such as temperature, seasonality, diet and management, whereas microenvironmental factors are non-measurable animal-specific factors within a given macroenvironment. A necessary condition to increase weight uniformity is the existence of genetic variance for response to such microenvironmental factors, such that individuals with genotypes [complete set of genetic material] that make them less sensitive to environmental disturbances will have more homogeneous offspring and show less environmental within-family variance.

In aquaculture selective breeding programs, the breeding nucleus (in which selection is performed) is usually kept separate from the commercial population that is composed of individuals destined for sale in the market. In aquaculture, the macroenvironmental rearing conditions can differ greatly between the nucleus and the commercial population. Thus, if genotype-by-environment interactions exist, genetic improvement achieved in the nucleus may not be fully translated to the commercial population.

This article – summarized and adapted from the original publication [García-Ballesteros, S. et al. 2021. Genetic parameters for uniformity of harvest weight in Pacific white shrimp (Litopenaeus vannamei). Genet Sel Evol 53, 26 (2021)] – reports on a research study to estimate the genetic variance of body weight uniformity in a farmed population of Pacific white shrimp (Litopenaeus vannamei), and to investigate whether selecting for increased weight uniformity in the breeding nucleus leads to improvement of uniformity in the commercial population.

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Study setup

The data used in this study were obtained from CAMANICA S.A., a Nicaragua-based company, carrying out a breeding program in shrimp with discrete generations and selection for shrimp body weight. Once animals reach the appropriate size, random samples of individuals are tagged, with half of them being individually tagged with eye-rings and assigned to the nucleus (N) population and the other half being tagged at the family level with elastomers and assigned to the commercial (C) population.

Within the nucleus, all families are reared in the same tank. However, in the commercial population, three to four ponds that are located in different geographical zones are used per generation, with each family equally represented in each pond. Environmental conditions differ greatly between the nucleus and the commercial populations. Thus, weight in the selection nucleus and weight in the commercial population are considered as two different traits.

The data used here are from three consecutive generations and 425 families. The total number of individuals with phenotypic records for body weight at harvest was 89,643, of which 51,346 belonged to the nucleus and 38,297 belonged to the commercial population. Harvest time was established by estimating the days required to reach an average weight of 15 grams in the nucleus. This time was set for both commercial (all ponds) and for the nucleus environments. However, for management reasons, recording the phenotypes of all shrimp can take a few days. Sex, year and pond were also recorded.

The resulting database had records for body weight on 51,346 shrimp from the selection nucleus and 38,297 shrimp from the commercial population. We used a double hierarchical generalized linear model [used in genetics studies to model quantitative traits (a measurable phenotype – the observable characteristics or traits of an organism – from genetic and environmental factors spread in magnitude in a population rather than none or all) with respect to molecular marker effects (molecules containing genetic information from a sample) to analyze weight uniformity in the two environments. Fixed effects included sex and year for the nucleus data and sex and year-pond combination for the commercial data. Environmental and additive genetic effects were included as random effects.

For detailed information on the study data, parameters evaluated, and analyses, refer to the original publication.

Results and discussion

Although weight uniformity is a very relevant trait with the potential of being included in shrimp breeding programs, there is very little information on the existence of genetic variation for this trait. To our knowledge, ours is the first study that uses a double hierarchical generalized linear model to estimate genetic variance for body weight uniformity in shrimp and constitutes a first step to investigate the possibility of including this trait in the breeding goal. This is important since the weight uniformity evaluated here was individual sensitivity to microenvironmental disturbances.

Estimates of the additive genetic variance, heritability and genetic coefficient of residual variation for weight uniformity that were obtained for this L. vannamei population in the nucleus, in which selection takes place, were all different from 0, which indicates that genetic improvement for this trait is possible. In addition, the genetic correlation of weight uniformity between the nucleus and the commercial population was relatively high, which indicates that improvement obtained in the nucleus would be partially transmitted to the commercial population, with the economic benefits that this would entail.

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Fig. 1: Estimates of heritability (mean and a posteriori standard deviation) of harvest weight for each level of residual systematic effects. Systematic effects were sex and year for the nucleus (a) and sex and year-pond for the commercial population (b).

Results showed that our estimates of the global heritability for body weight at harvest in N and C were within the range of those found in the literature for shrimp. More important is the fact that estimates of the additive genetic variance for uniformity of weight and for the residual heritability were also in the range of those described for shrimp, other aquaculture species and various terrestrial species. This indicates the existence of genetic variation in microenvironmental sensitivity among full-sib families [common parents], which implies that the phenotypes of offspring of different families will be differentially affected by the environment. Thus, our results show that the potential of genetic selection to improve weight uniformity in L. vannamei is similar to that for other species.

To evaluate the potential economic benefit of including weight uniformity in the breeding goal, correlations with other traits that are currently in the breeding goal, such as body weight, must be estimated. The ideal scenario would be the existence of a negative genetic correlation between weight and its variability because it would facilitate selection for higher weight and more uniformity. In aquaculture, estimates of the genetic correlation between weight and its variability vary largely in the literature. Our estimate was not significantly different from 0, which indicates that it may not be difficult to improve weight and weight uniformity simultaneously through a selection index. This would require the economic value for uniformity to be determined, which is unknown at this point.

It is very important that genetic improvements made in the nucleus are transferred to the commercial population that is composed of individuals for sale in the market. Thus, a high genetic correlation between the nucleus and commercial environments for traits that are selected for in the nucleus is desirable. This is not always the case because, although conditions are intended to be similar in the two environments, this is not usually feasible. Particularly in aquaculture species, some environmental factors are more important than others in affecting the re-ranking of individuals based on their estimated breeding values.

In our study, estimates of the genetic correlation between environments N and C were for weight and for weight uniformity were within the range reported for weight in other aquaculture species. Our estimate of the genetic correlation of weight between environments was lower than what has been reported for shrimp by some researchers, but within the range reported by others. Our study provides, for the first time, an estimate of the genetic correlation of weight uniformity between different environments for shrimp, and it is similar to what has been reported for trout.

Many studies have shown that the proportion of phenotypic variance [variability in phenotypes in a population, including height, weight, body shape and others] due to common environmental effects, although significantly different from 0 in shrimp and other aquaculture species, is of low magnitude. Some studies have suggested that common environmental effects are difficult to separate from family genetic effects. The few studies that have included common environmental effects for weight uniformity did not achieve significant estimates.

Perspectives

Our results show that genetic variability for the environmental variance of weight at harvest exists in shrimp, both in the selection nucleus and in the commercial population. The genetic variation for these traits (uniformity measured in the nucleus and in the commercial population) was large enough to conclude that response to selection could be obtained if these traits were included in the breeding program.

Including weight uniformity should not decrease weight since the genetic correlation between the two traits was not significantly different from zero. Further investigation is necessary to determine what is the best combination of these traits to reach the greatest economic benefit. Based on the genetic correlation of weight uniformity between the two environments estimated here, selection in the nucleus will be transmitted to the commercial population.


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