Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.

Animals Cichlids / genetics Tilapia / genetics Genomics Aquaculture Chromosomes / genetics

Aquaculture Introgression Reference genome Tilapia

Journal

BMC genomics

ISSN: 1471-2164

Titre abrégé: BMC Genomics

Pays: England

ID NLM: 100965258

Informations de publication

Date de publication:
15 Dec 2022

Historique:

received: 10 05 2022

accepted: 05 12 2022

entrez: 15 12 2022

pubmed: 16 12 2022

medline: 20 12 2022

Statut: epublish

Résumé

The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

Sections du résumé

BACKGROUND BACKGROUND

RESULTS RESULTS

Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.

CONCLUSION CONCLUSIONS

Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

Identifiants

DOI: 10.1186/s12864-022-09065-8 PMID: 36522771 PMC: PMC9756657

pubmed: 36522771

doi: 10.1186/s12864-022-09065-8

pii: 10.1186/s12864-022-09065-8

pmc: PMC9756657

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

832

Informations de copyright

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