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

Chontida Phuthaworn; Nguyen Hong Nguyen; Wayne Knibb

doi:10.3390/ jmse11071281

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

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

Chontida Phuthaworn, Nguyen Hong Nguyen and Wayne Knibb

Journal of Marine Science and Engineering, Vol.11(7), pp.1-10

2023

DOI: https://doi.org/10.3390/ jmse11071281

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Abstract

parentage assignment

SNP

selective breeding

banana shrimp

colony

sequoia

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.

Details

Title: Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)
Authors: Chontida Phuthaworn (Corresponding Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Nguyen Hong Nguyen (Corresponding Author) - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
Wayne Knibb (Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
Publication details: Journal of Marine Science and Engineering, Vol.11(7), pp.1-10
Publisher: MDPI AG
Date published: 2023
DOI: 10.3390/ jmse11071281
ISSN: 2077-1312
Copyright note: This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Grant note: Genecology Research Centre 2009/724 / Australian Seafood CRC
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99735294302621
Output Type: Journal article

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