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Fulltext Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

Peñaloza C, Robledo D, Barría A, Trịnh TQ, Mahmuddin M, Wiener P, et al.

G3 (Bethesda), 2020 08 05;10(8):2777-2785.
PMID: 32532799 DOI: 10.1534/g3.120.401343

Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.
Fulltext Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

Barría A, Benzie JAH, Houston RD, De Koning DJ, de Verdal H

Front Genet, 2021;12:737906.
PMID: 34616434 DOI: 10.3389/fgene.2021.737906

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.
Fulltext Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations

Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl-Wilson A, Benzie JAH, et al.

Evol Appl, 2023 Jun;16(6):1220-1235.
PMID: 37360025 DOI: 10.1111/eva.13560

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.
Fulltext Correction to: A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Barría A, Trịnh TQ, Mahmuddin M, Peñaloza C, Papadopoulou A, Gervais O, et al.

Heredity (Edinb), 2021 Sep;127(3):344.
PMID: 34408297 DOI: 10.1038/s41437-021-00461-6
Fulltext A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Barría A, Trịnh TQ, Mahmuddin M, Peñaloza C, Papadopoulou A, Gervais O, et al.

Heredity (Edinb), 2021 Sep;127(3):334-343.
PMID: 34262170 DOI: 10.1038/s41437-021-00447-4

Enhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E-10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.
Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus

Etherington GJ, Nash W, Ciezarek A, Mehta TK, Barria A, Peñaloza C, et al.

BMC Genomics, 2022 Dec 15;23(1):832.
PMID: 36522771 DOI: 10.1186/s12864-022-09065-8

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.