Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species.
aquaculture
bivalve
fish
genomic prediction
imputation
selective breeding
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2023
2023
Historique:
received:
26
03
2023
accepted:
26
04
2023
medline:
30
5
2023
pubmed:
30
5
2023
entrez:
30
5
2023
Statut:
epublish
Résumé
Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of selection candidates. However, it is not widely implemented in most aquaculture species, and remains expensive due to high genotyping costs. Genotype imputation is a promising strategy that can reduce genotyping costs and facilitate the broader uptake of genomic selection in aquaculture breeding programmes. Genotype imputation can predict ungenotyped SNPs in populations genotyped at a low-density (LD), using a reference population genotyped at a high-density (HD). In this study, we used datasets of four aquaculture species (Atlantic salmon, turbot, common carp and Pacific oyster), phenotyped for different traits, to investigate the efficacy of genotype imputation for cost-effective genomic selection. The four datasets had been genotyped at HD, and eight LD panels (300-6,000 SNPs) were generated
Identifiants
pubmed: 37252666
doi: 10.3389/fgene.2023.1194266
pii: 1194266
pmc: PMC10213886
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1194266Informations de copyright
Copyright © 2023 Kriaridou, Tsairidou, Fraslin, Gorjanc, Looseley, Johnston, Houston and Robledo.
Déclaration de conflit d'intérêts
Authors ML and IJ were employed by Xelect Ltd., and author RH was employed by Benchmark Genetics. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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