Comparing genomic signatures of selection between the Abbassa Strain and eight wild populations of Nile tilapia (Oreochromis niloticus) in Egypt

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

Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima)

Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G × E effects) among populations in this region. Global F(st) values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise F(st) comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAF(avg) = 0.144, H(o) = 0.238 and MAF(avg) = 0.232, H(o) = 0.369, respectively) compared to Aru (MAF(avg) = 0.292, H(o) = 0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and F(st) analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure

Pipette and paper: combining molecular and genealogical methods to assess a Nile tilapia (Oreochromis niloticus) breeding program

[Extract] Aquaculture selective breeding programs employ a closed nucleus mating strategy whereby animals displaying sought-after characteristics are mated to produce next generation offspring with increased pre-valence of desirable phenotypes. Offspring exhibiting high genetic merit for favorable traits are then usually chosen as candidate parents for the subsequent breeding cycle. The selective breeding process is replicated each succeeding generation in order to accumulate genetic gain within the breeding population. The long term success of these closed breeding systems is dependent on a number of factors: including, the heritability of a trait, the intensity of selection, the additive genetic variance observed in the founding population, and the amount of additive genetic variance maintained over subsequent generations (Falconer et al., 1996; Loughnan et al., 2016). If breeding practices are not properly managed, the number of animals with high relatedness will increase (Gjedrem and Baranski, 2009b), leading to a substantial loss of genetic diversity over subsequent generations (Pante et al.,2001). The maintenance of genetic diversity is critical to accommodate current and future changes in production environments, and if left unchecked, it can lead to inbreeding through increased homozygosity and deleterious fitness consequences associated with inbreeding depression (Pante et al., 2001). This loss of genetic diversity can also hamper progress within the selective breeding program as it limits the amount of genetic variance available for selection (Falconer, 1960)

The GIFT that keeps on giving? A genetic audit of the Fijian Genetically Improved Farmed Tilapia (GIFT) broodstock nucleus 20 years after introduction

The Genetically Improved Farmed Tilapia (GIFT) strain of Nile tilapia is a valuable global freshwater aquaculture commodity, forming the basis of the Fiji Islands' largest freshwater aquaculture industry. Unfortunately, recent negative stock performance has been reported by farmers, possibly indicating reduced genetic diversity and inbreeding in the primary broodstock nucleus. Using high-resolution genome-wide markers (5208 SNPs), 282 individuals from three Fijian broodstock ponds were analysed and compared against two reference strains of Nile tilapia: 9th generation GIFT fish from the WorldFish Center, Malaysia, and 11th generation fish from the Abbassa Selection Line, Eygpt, (n = 94 respectively for each strain). Genetic data were used to evaluate levels of genetic diversity, inbreeding, relatedness and genetic structure; and assess the viability of the Fijian nucleus for future seed production. Results revealed only mild declines in the Fijian GIFT nucleus genetic diversity compared to both reference strains, since introduction 20 years ago. Average observed and expected heterozygosities were largely comparable for all sample groups, except for one Fijian pond which showed a heterozygote deficit (Ho = 0.2025, Hn.b. = 0.2320). One of the three Fijian ponds sampled exhibited reduced effective population size; (NeLD = 3.2 [95% C.I. = 3.2–3.2], cf. 23.3[23.2–23.3] and 31.5[31.4–31.6]), however allelic diversity remained high (A = 1.953, cf. 1.765–1.770). Fish sampled from this pond also showed a loss of rare alleles (Ar = 0.1542, cf. 0.4063–0.4065) and displayed genetic sub-structuring, possibly as a result of wild O. niloticus entering the broodstock nucleus. Analyses of genetic structure and relatedness revealed admixture of founding individuals, likely due to a combination of stock management practices and past pond flooding events. These findings suggest that the Fijian GIFT nucleus has retained much of the genetic diversity from its source population. It is recommended that the nucleus culture performance (fecundity, growth and survival) be evaluated through a phenotypic audit, to determine if valuable high-performing alleles have been lost. Over the longer term, stock management guidelines and genetic monitoring of the broodstock nucleus at regular intervals are proposed, to minimise further erosion of valuable genetic diversity. These results have important implications for stock management practices by demonstrating the importance of monitoring, and undertaking genetic assessments of broodstock nuclei after initial introduction, to ensure that genetic quality and performance is maintained over subsequent generations