Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree
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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2021, Aquaculture ReportsCitation Excerpt :Most farmed aquatic species are either still sourced from the wild or in the early stages of domestication, suggesting a substantial potential for genetic improvement in aquatic productions (Gjedrem and Rye, 2018). Molluscan shellfish have traditionally been a major product of world aquaculture, and many selective breeding programs for oyster (Langdon et al., 2003), clam (Zhao et al., 2012), scallop (Zheng et al., 2012), and mussel (Nguyen et al., 2014) species have been initiated worldwide. For selective breeding to be effective, there must be additive genetic variation present in the current population.