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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.

Abstract Nile tilapia is predominantly produced in smallholder ponds without aeration. We hypothesize that Nile tilapia with high oxygen uptake efficiency (O2UE) may perform better under these conditions than Nile tilapia with low O2UE. Critical swimming speed (U crit, in cm s−1) is a potential indicator for O2UE. Our objectives were to estimate variance components for U crit and fish size at swim testing early in life, and genetic correlations (r g ) between U crit with harvest weight (HW) and daily growth coefficient (DGC) later after grow-out in a non-aerated pond. Substantial heritability was found for absolute U crit (0.48). The estimated r g between absolute U crit and fish size at testing were all strong and positive (range 0.72–0.83). The estimated r g between absolute U crit and HW, and absolute U crit and DGC were − 0.21 and − 0.63 respectively, indicating that fish with higher absolute U crit had lower growth in the non-aerated pond as compared to fish with lower absolute U crit. These results suggest a juvenile trade-off between swimming and growth performance where fish with high U crit early in life show slower growth later under conditions of limited oxygen availability. We conclude that U crit in Nile tilapia is heritable and can be used to predict growth performance.

The performance of two strains of Nile tilapia (the Nyakabera and Lake Kivu) fed a commercial feed or either a fishmeal-based or a fishmeal-free feed formulated using local ingredients was evaluated for 99 days in Bukavu, eastern highlands of the DR Congo (Experiment 1). Strain × feed interaction was significant (p < 0.05) for final body weight (FBW) and condition factor (CF). Growth of both strains was best with the commercial feed. Fish-meal free formulated feed resulted in similar or better fish growth than a local fishmeal-based formulated feed depending on the strains. Lake Kivu strain had significantly (p < 0.05) higher FBW when fed the commercial and fishmeal-free feeds than the Nyakabera strain, but when fed the fishmeal-based feed the difference was not significant. The performance of the other three Nile tilapia strains (the GIFT-Congo Futur, GIFT-RATALBI and Tihange strains) fed a single commercial feed was evaluated for 84 days in Kinshasa, western lowlands of the DRC (Experiment 2). Male GIFT-Congo Futur and GIFT-RATALBI did not differ significantly (p > 0.05) in FBW and CF, but both performed better than the Tihange. FBW of the female GIFT-Congo Futur was significantly higher than that of the other two strains, while CF was not significantly (p > 0.05) different among strains in females.

Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the Genetically Improved Farmed Tilapia (GIFT) strain and the Cirad strain were entered into the study (128 GIFT and 109 Cirad). The GIFT strain were reared over three consecutive periods of 7 days each under different feeding, recording, and rearing scenarios (i) in groups fed an optimal ration (g100) or (ii) fed a 50% restricted ration (g50) both with video records of all meals and (iii) reared in isolation and fed a 50% restrictive ration. The Cirad strain were tested similarly but only for scenarios (i) and (iii). All fish were fed twice daily with a calculated ration. Correlations showed the same trends for the GIFT and the Cirad strains. For the GIFT strain, correlations were positive and significant for BWG and FI measured in scenarios (i) and (ii), 0.49 and 0.63, respectively, and FI measured in scenarios (i) and (iii) (0.50) but not for BWG measured in scenarios (i) and (iii) (0.29, NS). The phenotypic correlation estimated for FCR between scenarios (i) and (ii) with fish fed an optimal or a 50% restricted ration was low and not significant (0.22). Feed Conversion Ratio for GIFT fish reared in groups or in isolation and fed with a restricted ration [scenarios (ii) and (iii)] were not significantly correlated either. Social interactions between fish, potentially impacting their efficiency, may explain the results. Therefore, selective breeding programs seeking to improve feed efficiency will need to carefully plan the feeding rate and the rearing system used to estimate FCR in order to optimize selection for the targeted production system.

Feed conversion ratio (FCR), the ratio between feed intake and body weight gain, is of major interest for improving aquaculture sustainability through reduced feed costs and environmental impacts. Demonstrating whether FCR measured in juvenile fish is an accurate predictor of their performance during the whole rearing period is critical to developing genetic improvement programs for this trait. This is especially true for estimates obtained in individually reared fish, for which this has high implications regarding the size of the necessary rearing structures. We obtained individual FCR from 30 male Nile tilapia Oreochromis niloticus from the GIFT strain individually reared in a recirculating system, from 36 to 260 g mean weight. They were fed twice a day and uneaten pellets were counted every day to determine the feed intake of each fish. Individual growth was monitored every week. Feed conversion ratio was estimated over two-week periods and over the whole rearing period (210 days). Phenotypic correlations between the two-week FCRs and global FCR estimations were mostly significant (ranged from 0.38 to 0.64). A significant phenotypic correlation between growth and FCR was also found: faster-growing fish had a better (lower) FCR. Individual breeding values for global FCR were estimated using FCR phenotypes from the present study and previously published heritabilities for FCR in Nile tilapia. Potential estimated genetic gain for global FCR was 2.2% per generation with 50% selection intensity. When selecting fish on their FCR from only a two-week period, approximately 50% of the reference genetic gain could be obtained with the same selection intensity. FCR measured during a two-week period at juvenile stage could be a moderately accurate approximation of the whole rearing period FCR, and could be used as a lower cost criterion to select for FCR in future genetic improvement programs using individual rearing of fish.