Genomic Prediction for Whole Weight, Body Shape, Meat Yield, and Color Traits in the Portuguese Oyster Crassostrea angulata

Abstract

Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, Crassostrea angulata. The study consisted of 647 oysters: 188 oysters from 57 full-sib families from the first generation and 459 oysters from 33 full-sib families from the second generation. The number per family ranged from two to eight oysters for the first and 12–15 oysters for the second generation. After quality control, a set of 13,048 markers were analyzed to estimate the genetic parameters (heritability and genetic correlation) and predictive accuracy of the genomic selection for these traits. The multi-locus mixed model analysis indicated high estimates of heritability for meat yield traits: 0.43 for soft tissue weight and 0.77 for condition index. The estimated genomic heritabilities were 0.45 for whole weight, 0.24 for cup ratio, and 0.33 for fan ratio and ranged from 0.14 to 0.54 for color traits. The genetic correlations among whole weight, meat yield, and body shape traits were favorably positive, suggesting that the selection for whole weight would have beneficial effects on meat yield and body shape traits. Of paramount importance is the fact that the genomic prediction showed moderate to high accuracy for the traits studied (0.38–0.92). Therefore, there are good prospects to improve whole weight, meat yield, body shape, and color traits using genomic information. A multi-trait selection program using the genomic information can boost the genetic gain and minimize inbreeding in the long-term for this population.

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

“…shell height, shell width and shell length). The estimation of heritability for total weight (herein referred to as TW) was similar to those reported for nine-month-old Portuguese oysters (ℎ 2 = 0.45) and a two-year old Pacific oyster strain (ℎ 2 = 0.42) (Vu et al 2021b;Xu et al 2017). Total weight, as measured in this study, is a composite phenotype made up of the animal's shell and soft tissue weights, in addition to the weight of any pallial fluid -thus is not a direct reflection of meat yield.…”

“…Total weight, as measured in this study, is a composite phenotype made up of the animal’s shell and soft tissue weights, in addition to the weight of any pallial fluid - thus is not a direct reflection of meat yield. Nevertheless, in C. angulata , a positive genetic correlation (0.63) has been found between TW and soft tissue weight (Vu et al 2021b), suggesting that selecting for TW - a trait easier to measure - could lead to improvements in meat yields. Such indirect improvements of correlated traits have been reported in a Portuguese oyster line selected only for harvest weight.…”

“…angulata, a positive genetic correlation (0.63) has been found between TW and soft tissue weight (Vu et al 2021b), suggesting that selecting for TW -a trait easier to measure -could lead to improvements in meat yields. Such indirect improvements of correlated traits have been reported in a Portuguese oyster line selected only for harvest weight.…”

“…salmonids, Nile tilapia, tropical shrimp) (Lillehammer et al 2020; Boudry et al 2021; Zenger et al 2019). Studies into the feasibility of applying genomic selection schemes in oyster breeding programmes have shown that for growth (Vu et al 2021b; Gutierrez et al 2018), edibility (Vu et al 2021b), low salinity tolerance (McCarty et al 2021), and disease resistance traits (Vu et al 2021b; Gutierrez et al 2020), greater genetic gains could be achieved through GS compared to traditional breeding. Nevertheless, the practical application of GS as a selection strategy will likely depend on how cost-effective it is compared to pedigree-based methods.…”

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

“…However, commercial application to aquaculture production is largely limited to the major finfish and crustacean species (e.g., salmonids, Nile tilapia, shrimp) ( Zenger et al, 2019 ; Lillehammer et al, 2020 ; Boudry et al, 2021 ). Studies into the feasibility of applying genomic selection schemes in oyster breeding programmes have shown that for growth ( Gutierrez et al, 2018 ; Vu et al, 2021b ), edibility ( Vu et al, 2021a ), and disease resistance traits ( Gutierrez et al, 2020 ; Vu et al, 2021a ), greater genetic gains could be achieved through GS compared to traditional breeding. Nevertheless, the practical application of GS as a selection strategy will likely depend on how cost-effective it is compared to pedigree-based methods.…”