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

Agustin Barria Gonzalez, Carolina Penaloza, Athina Papadopoulou, M. Mahmuddin, Andrea Wilson, J. Benzie, Ross Houston, Pam Wiener

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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 programmes 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 was able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (FST) 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.
Original languageEnglish
Pages (from-to)1-16
Number of pages16
JournalEvolutionary Applications
Issue number6
Early online date12 Jun 2023
Publication statusPublished - Jun 2023

Keywords / Materials (for Non-textual outputs)

  • aquaculture
  • GIFT
  • Nile tilapia
  • Poolseq
  • population genomics
  • SNP array


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