Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
Highlights
IntroductionDoes the number of species undergoing domestication (currently estimated at 598 species; FAO, 2018), where domestication is defined here as the adaptation of an organism from the wild to a captive environment (Price, 1984)
As aquaculture production increases, so does the number of species undergoing domestication, where domestication is defined here as the adaptation of an organism from the wild to a captive environment (Price, 1984)
This study investigated the population genetic structure, evidence for signatures of selection, and genetic diversity related to domestication in the Abbassa Strain (AS) compared to wild Egyptian Nile River O. niloticus populations
Summary
Does the number of species undergoing domestication (currently estimated at 598 species; FAO, 2018), where domestication is defined here as the adaptation of an organism from the wild to a captive environment (Price, 1984). The consequences of inbreeding and genetic drift are widespread and can be observed throughout the genome, whereas selection tends to act differentially across the genome depending on the genetic architecture of the trait (Burke et al, 2005) These micro-evolutionary processes need to be taken into consideration when trying to identify how an organism’s genome is being affected by domestication. Recent advances in high-throughput whole genome sequencing has enabled the cost-effective development of genome-wide markers for many non-model species Such technological developments have enabled researchers to harness increased power in identifying the extent to which genetic processes like selection, genetic drift, and inbreeding affect a genome, and identify specific regions of the genome that have responded to such processes (Carter et al, 2008; Scandura et al, 2011; López et al, 2019). These differences can be used to detect escapees and help estimate their potential impact on local populations
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