Abstract
Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP arrays for Pacific oyster (Crassostrea gigas) raises the opportunity to test genomic selection strategies for polygenic traits. In this study, a population of 820 oysters (comprising 23 full-sibling families) were genotyped using a medium density SNP array (23 K informative SNPs), and the genetic architecture of growth-related traits [shell height (SH), shell length (SL), and wet weight (WW)] was evaluated. Heritability was estimated to be moderate for the three traits (0.26 ± 0.06 for SH, 0.23 ± 0.06 for SL and 0.35 ± 0.05 for WW), and results of a GWAS indicated that the underlying genetic architecture was polygenic. Genomic prediction approaches were used to estimate breeding values for growth, and compared to pedigree based approaches. The accuracy of the genomic prediction models (GBLUP) outperformed the traditional pedigree approach (PBLUP) by ∼25% for SL and WW, and ∼30% for SH. Further, reduction in SNP marker density had little impact on prediction accuracy, even when density was reduced to a few hundred SNPs. These results suggest that the use of genomic selection in oyster breeding could offer benefits for the selection of breeding candidates to improve complex economic traits at relatively modest cost.
Highlights
Pacific oyster (Crassostrea gigas) is the most cultivated oyster species worldwide and has been introduced to many countries for aquaculture production (Troost, 2010)
There was no evidence of genetic correlation between the traits of survival and the growth-related traits, which is consistent with the findings of Dégremont et al (2007)
While this fixed effect was not significant, these early life differences may have impacted on the results, since genotype by environment interaction has been shown to be important for growth traits in Pacific oyster (Langdon et al, 2003; Dégremont et al, 2007)
Summary
Pacific oyster (Crassostrea gigas) is the most cultivated oyster species worldwide and has been introduced to many countries for aquaculture production (Troost, 2010). Substantial effort has been put toward the development of genomic resources for Pacific oyster, which include a reference genome assembly (Zhang et al, 2012), genetic marker databases including microsatellites (Li et al, 2003; Sekino et al, 2003) and SNPs (Sauvage et al, 2007; Fleury et al, 2009; Wang J. et al, 2015) and low density linkage maps, containing both microsatellites and SNPs (Hubert and Hedgecock, 2004; Hedgecock et al, 2015). A high density linkage map containing ∼20 K SNPs has recently been created and aligned with the physical reference genome assembly (Gutierrez et al, 2018)
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