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Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
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Etherington GJ, Nash W, Ciezarek A, Mehta TK, Barria A, Peñaloza C, Khan MGQ, Durrant A, Forrester N, Fraser F, Irish N, Kaithakottil GG, Lipscombe J, Trong T, Watkins C, Swarbreck D, Angiolini E, Cnaani A, Gharbi K, Houston RD, Benzie JAH, Haerty W. Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics 2022; 23:832. [PMID: 36522771 PMCID: PMC9756657 DOI: 10.1186/s12864-022-09065-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND 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. 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 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.
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Affiliation(s)
- G J Etherington
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - W Nash
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - A Ciezarek
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - T K Mehta
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - A Barria
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - C Peñaloza
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - M G Q Khan
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - A Durrant
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - N Forrester
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - F Fraser
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - N Irish
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - G G Kaithakottil
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - J Lipscombe
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - T Trong
- WorldFish, 10670, Penang, Malaysia
| | - C Watkins
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - D Swarbreck
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - E Angiolini
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - A Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization - Volcani Institute, Rishon LeTsiyon, Israel
| | - K Gharbi
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK
| | - R D Houston
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- Benchmark Genetics, 1 Pioneer Building, Edinburgh Technopole, Penicuik, EH26 0GB, UK
| | | | - W Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Barría A, Benzie JAH, Houston RD, De Koning DJ, de Verdal H. Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia ( Oreochromis niloticus) Population. Front Genet 2021; 12:737906. [PMID: 34616434 PMCID: PMC8488396 DOI: 10.3389/fgene.2021.737906] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; -0.60 and -0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - John A. H. Benzie
- WorldFish, Bayan Lepas, Malaysia
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hugues de Verdal
- CIRAD, UMR ISEM, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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