Development of SNP parentage assignment in the Portuguese oyster Crassostrea angulata

Vu, Sang V.; Premachandra, H.K.A.; O’Connor, Wayne A.; Nguyen, Ngoc T. H.; Dove, Michael; Vu, In Van; Le, Tuan Son; Vendrami, David L. J.; Knibb, Wayne

doi:10.1016/j.aqrep.2021.100615

Cited by 4 publications

(2 citation statements)

References 35 publications

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“…It could imply that the low MAF could still be used for sibship assignment, provided that there were sufficient numbers of SNPs. This was similarly suggested by the previous studies in Portuguese oysters (18 sires, 15 dams), wherein 1352 SNPs (minimum MAF = 0.1) were as informative as 400 SNPs (minimum MAF ≥ 0.3) for parentage assignment, with an accuracy higher than 98% [34].…”

Section: Maf and Snp Number For Sibship Assignmentsupporting

confidence: 81%

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Phuthaworn

Nguyen

Knibb

2023

JMSE

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Pedigrees are essential components in selective breeding programs to manage genetic diversity and obtain accurate genetic parameter estimates to ensure long-term response to selection in captive populations. High throughput and cost-effective sequencing technologies has offered opportunities of using single nucleotide polymorphisms (SNPs) to resolve penaeid shrimp pedigrees from mass spawning cohorts and communal rearing. Effects of SNPs for sibship assignment were investigated on 546 shrimp using two software programs, Colony and Sequoia. Assignment rates and accuracies using SNP subsets with six different minor allele frequencies (MAFs), four sets of SNPs, and five genotyping error rates were compared to the microsatellite-based pedigree established in a previous study. High MAFs and numbers of SNPs contributed to significant increases in assignment rates and accuracies, whereas genotyping error rates showed negligible impacts on assignment results. Sibship assignments achieved rates and accuracies of 98% and 83%, respectively, with a minimum number of 91 SNPs (average MAF ≥ 0.14), and the two different programs exhibited similar resulting patterns for different SNP subsets. High consistencies between SNP-based and microsatellite-based pedigrees showed that accurate pedigrees could be achieved by using SNPs and thus contribute to the long-term response to selection in farmed banana shrimp.

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Section: Maf and Snp Number For Sibship Assignmentsupporting

confidence: 81%

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Phuthaworn

Nguyen

Knibb

2023

JMSE

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“…The number per family ranged from two to eight oysters for the first and 12-15 oysters for the second generation. Most of the oysters from the second generation were progeny of the first generation of oysters (Vu et al, 2021b). All tissue samples were preserved in 80% ethanol, stored at −80 • C, and sent to Diversity Array Technology Pty.…”

Section: Oyster Samplesmentioning

confidence: 99%

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

Knibb

Gondro

et al. 2021

Front. Genet.

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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.

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High macro-collinearity between Crassostrea angulata and C. gigas genomes was revealed by comparative genetic mapping with transferable EST-SNP markers

Wang

Zhang

et al. 2021

Aquaculture

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Development of SNP parentage assignment in the Portuguese oyster Crassostrea angulata

Cited by 4 publications

References 35 publications

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

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

High macro-collinearity between Crassostrea angulata and C. gigas genomes was revealed by comparative genetic mapping with transferable EST-SNP markers

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