Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree

doi:10.1016/j.aquaculture.2013.11.021

Aquaculture

Volumes 420–421, 15 January 2014, Pages 295-301

https://doi.org/10.1016/j.aquaculture.2013.11.021 Get rights and content

Highlights

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We reported the first SNP panel developed de novo for the blue mussel.
•
Estimates of heritabilities have increased compared to the first generation.
•
Realised selection response were positive and up to 10%.

Abstract

In this study, we estimated genetic parameters and realised response to selection in the second generation of a breeding programme of the blue mussel (Mytilus galloprovincialis). A total of 77 full-sib families were produced and reared communally after the fertilisation stage. To assist the reconstruction of a pedigree from these families, a panel of single nucleotide polymorphisms (SNPs) was developed de novo from genomic sequences. A total of 227 out of 432 SNPs were validated. We used only SNPs with polymorphic information content greater than or equal to 0.10 (i.e. 179 SNPs) for family identification. The Bayesian approach using Cervus-type model could assign 92.5% of offspring to the intended parent pairs, which is a significant improvement compared to previously used microsatellites. Likely as a result of both improved parentage assignment and greater depth of pedigree, estimates of heritability of economic traits increased compared to that reported in the first generation. In the second generation, estimates for heritability of total weight (TW), shape (SH), meat yield as ratio between meat weight and total weight (MY1), and meat yield as ratio between meat weight and the sum of meat weight and shell weight (MY2) were 0.35 ± 0.09, 0.64 ± 0.10, 0.23 ± 0.08 and 0.46 ± 0.10, respectively. Realised selection response (compared to wild–wild matings) from the selection decisions in the first generation of the breeding programme were positive and up to 10%, indicating that further genetic gains can be achieved through this family-based breeding programme.

Introduction

The blue mussel, Mytilus galloprovincialis, is recognised as an important aquaculture species in many countries, including Australia. In Victoria (Australia), the traditional farming method relying on collection of natural spat has shifted towards the use of hatchery-produced seed since the success of the artificial propagation of the species in 2008 (Ingram et al., 2013, Jahangard et al., 2010). As a result, annual production of mussel culture in Victoria increased from 449 t in 2008/09 to 951 t in 2010/11 (Ingram et al., 2013).

The success of hatchery production of the blue mussel, M. galloprovincialis, in 2008 enabled the establishment of a family-based selective breeding programme for the species, based on a founder population of 74 full-sib families (Nguyen et al., 2011). These mussels were reared communally and microsatellite markers were used to identify families in order to improve the accuracy in estimation of genetic parameters. A total of 48 individuals (G₁) from each sex were selected from the first generation based on their breeding values for total weight, shape and meat yield as broodstock for the second generation (G₂).

Although microsatellites were proven to be useful in family identification in blue mussel, the resolution was low (62.6% of mussels could be assigned to single families) (Nguyen et al., 2011). With recent advances in genome sequencing, coupled with significant reduction in associated costs, we aimed to develop a panel of single nucleotide polymorphisms (SNPs) for blue mussel. This panel of SNPs was tested for efficiency in family identification for the G₂ mussels in this study.

The aim of the present study were three-fold: 1) to develop a SNP panel for parentage assignment in blue mussel using the Illumina sequencing technology; 2) to estimate genetic parameters for total weight, shape and meat yield in the G₂ population, the results from which will be used to select mussels to generate the third generation (G₃), and 3) to estimate selection response, by comparing the performance of these traits in the offspring generated by the selected line with those from non-selected parents.

Section snippets

Mussel spawning and culture

The design of the current experiment is schematically illustrated in Fig. 1. A total of 77 families were generated in June 2010, including 43 families of G₁ ♂ × G₁ ♀ (SS), 5 families of G₁ ♂ × wild ♀ (SW), 5 families of wild ♂ × G₁ ♀ (WS), and 24 families of wild ♂ × wild ♀ (WW). Wild broodstock were included in the experiment to introduce new genetic material into the selected line, and for comparison with families generated from the selected G₁ individuals. Due to the fact that blue mussel in

SNP validation and genotyping

GeneSeek designed a number of multiplexes from these 1248 sequences and the first nine multiplexes (48 SNPs each) were used to assay 432 SNPs. Out of these, 38 SNPs failed to PCR. The remaining 384 SNPs were scored for 3711 samples (including 40 replicates of the sequenced mussel) with an average call rate of 0.915.

We found 125 homozygous loci when examining the 40 replicates of the sequenced mussel. We also found 23 loci which showed missing data in eight replicates or more. In the remaining

Discussion

This study reports the estimates of genetic and phenotypic parameters as well as selection response in the second generation of a blue mussel breeding programme in Victoria, Australia. We developed a panel of SNPs using genomic sequences generated by the massive-parallel sequencing technology, which was more effective in family identification than previously used microsatellites in this population. Estimates of heritability for all traits were greater compared to that in the first generation.

Conclusions

We report genetic parameters and response to selection in the second generation of the Australian blue mussel breeding programme which was established in 2008. We successfully developed a SNP panel de novo from genomic sequence data that can be effectively used for reconstruction of pedigree. Success rate in parentage assignment using this SNP panel was much higher compared to that resulting from previously developed microsatellites. As a result, estimates of heritability for economic traits in

Acknowledgements

This study was funded by Fisheries Victoria, Department of Environment and Primary Industries, Victoria (DEPI) with support from the Victorian mussel farming industry through the Victorian Shellfish Hatchery Pty Ltd. (VSH) (Queenscliff, Victoria). We thank Nathan O'Mahony (FV), Samad Jahangard (FV) and Mike Williams (VSH) for activities associated with mussel husbandry and assisting with sample collection throughout the project. Dr. Steve Petrovski is acknowledged for his kind assistance in

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Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree

Highlights

Abstract

Introduction

Section snippets

Mussel spawning and culture

SNP validation and genotyping

Discussion

Conclusions

Acknowledgements

J. Mol. Biol.

Aquaculture

Aquaculture

Aquaculture

Aquaculture

Aquaculture

Aquaculture

Aquaculture

Aquaculture

J. Dairy Sci.

Heritability of body size in the Chilean blue mussel (Mytilus chilensis Hupé 1854): effects of environment and ageing

Aquac. Res.

Personalized copy number and segmental duplication maps using next-generation sequencing

Nat. Genet.

Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3′UTR-primed SNP detection approach

BMC Genomics

Introduction to Quantitative Genetics

ASReml User Guide Release 1.0.

Genetic improvement of cold-water fish species

Aquac. Res.

Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework