Elsevier

Aquaculture

Volume 490, 1 March 2018, Pages 350-354
Aquaculture

Short communication
Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss

https://doi.org/10.1016/j.aquaculture.2018.03.003Get rights and content

Highlights

  • This work reports for the first time accuracies of EBV in a mixed family breeding design for growth and quality traits.

  • They were higher (0.6–0.8) than reported in classical family-based programs or for 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.

Abstract

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.

These results highlight the possibility of introducing precise estimated breeding values for quality traits into combined or sib selection in breeding programs when using mixed families from factorial designs and marker-based parentage assignment in aquaculture species.

Introduction

Less than 10% of world aquaculture production benefits from genetically improved seed. When it does, this comes mostly from conventional family-based breeding programs (Gjedrem et al., 2012), using families reared separately until tagging and Best Linear Unbiased Prediction, or BLUP (Henderson, 1984). One of the major reasons for this limited development is the high cost of these programs, which require both initial investment in numerous family tanks (>100) and highly trained staff using very good traceability and rearing practices to limit both pedigree errors and initial tank effect. This is a serious obstacle for small and medium enterprises (SMEs) and for the initiation of selective breeding in new aquaculture species.

Alternative breeding schemes using marker-based parentage assignment and combining mass selection on traits measurable in candidates (such as growth) and sib selection on lethal traits (quality, disease resistance, etc.) have not been greatly studied so far (Vandeputte and Haffray, 2014). This kind of breeding scheme limits both tank effect and initial investment, as all families can be reared together in just one tank. The use of common garden rearing and molecular pedigrees also relieves constraints on family number, allowing the production of more families for a fixed number of parents (e.g., by the use of factorial mating designs). This increases the potential for between-family selection intensity at a given level of inbreeding (Dupont-Nivet et al., 2006; Sorensen et al., 2005).

The relative efficiency of breeding programs can be assessed by the accuracy (r) of the estimated breeding values (EBVs). This accuracy is the correlation between the true breeding value (TBV) and the EBV, and can be derived from mixed-model equations (Van Van Vleck, 1993).

In aquaculture, there are few reports on the accuracy of EBVs for production traits, with only two references available on conventional breeding schemes with initially separated families (Gonzalez-Pena et al., 2016; Kause et al., 2007) and one on a mixed families scheme (Blonk et al., 2010). One problem with the mixed-families design, using a posteriori parentage assignment, is that the number of sibs per family is variable and unpredictable. In addition, as factorial designs generate very high numbers of families, they can result in very low numbers of fish recorded from each family. Small and variable family sizes could be seen as unfavourable to the accuracy of breeding values.

The aim of the present work was to estimate the accuracy of EBVs for different traits (growth, carcass traits and fillet quality) in a factorial mating design in rainbow trout Oncorhynchus mykiss using a posteriori parentage assignment. Genetic parameters, EBVs and r were estimated within a single generation using performances collected from a random sample of 2000 offspring. Both univariate and multivariate models were investigated as the literature mostly reports evaluations or simulations with univariate models, but breeding programs generally rely on multivariate models. The accuracy of sib selection was compared with combined family selection for each trait and with univariate or multivariate models using a leave-one-out (LOO) procedure, where the phenotype of any given individual was either used (combined selection) or not (sib selection).

These estimates of accuracy in a mixed-family design in aquaculture are expected to support the introduction of combined family or sib-based selection on quality traits in mass selection programs initially designed to improve growth.

Section snippets

Management and phenotyping of animals

The measured traits and rearing environments were indexed according to the ATOL (Animal Trait Ontology for Livestock) and EOL (Environment Ontology for Livestock) ontologies available on the ATOL (http://www.atol-ontology.com/index.php/en/les-ontologies-en/visualisation-en) website.

The offspring sample had already been used to estimate genetic parameters and design predictors for quality traits in previous studies (Haffray et al., 2012a; Haffray et al., 2013) and was established from a

Results

Basic statistics for all traits measured at slaughter are given in Table 1.

DNA parentage assignment success was 99.5%. All parents were represented in the progeny. The observed number of full-sib families was 559 (93.1% of the expected 600). The average full-sib family size was 3.5 ± 2.2 and varied from 0 to 13. Paternal (or maternal) half-sib family size varied from 8 to 45 (from 12 to 61).

Heritability at processing for the traits previously published (BW, Carc%, Fil%) for this experiment (

Discussion

We estimated genetic parameters and breeding accuracies for individual and sib evaluated traits (growth and quality traits) in a mixed-family factorial mating design. Intermediate to high accuracy of EBVs was estimated even with a low number of full-sibs per family (3.3 on average) for combined family selection and sib-based selection.

Heritability estimates for BW, Fil% and Carc% (already published in Haffray et al., 2012a) and for new traits (Fat% and a*) were in the upper range of previous

Conclusions and perspectives for application

This study is the first of its kind estimating genetic parameters, EBVs and r of growth, processing traits and fillet quality in a mixed-family rearing design. The accuracy of EBVs was high, at least equivalent with those simulated in conventional (using separate families) breeding programs, and superior to those estimated from conventional breeding program data. This provides new insights for starting selection programs combining mass selection for growth and sib-based selection on quality

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

PH managed the project, estimated the heritabilities and r and wrote the manuscript, FE estimated accuracy of EBVs and set up the LOO procedure, JB managed the data collection on a* colour and Fat%, HC supervised the estimation of genetic parameters and of EBV accuracy, MDN and MV supervised the genetic data treatment and the writing of the manuscript. All authors contributed to designing the study, interpreting the results, revising the manuscript and read and approved the final manuscript.

Acknowledgements

The authors are indebted to Cyrilles Deshayes and Marine Levadoux from the French Interprofessional Committee for Aquaculture Products (CIPA) for their support and management of the project and the staff of INRA, IFREMER and French breeding companies who are members of SYSAAF (Aqualande, Viviers de France, Font Rome Pisciculture and Les Fils de Charles Murgat) for their participation in the fish rearing and data collection. This work was supported by the French National Interprofessional Office

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