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

Abstract

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.