Samuel Bekele Mengistu

Smallholder Nile tilapia farms underperform in terms of feed efficiency, despite the use of genetically improved strains of tilapia such as GIFT. Big differences in productivity among many smallholder tilapia farms are observed leading to a yield gap between the best performing and low performing farms. Therefore, the aim of this thesis was to optimise the breeding program of Nile tilapia for a smallholder production system, thereby contributing to closing the yield gap, the difference between the best performers and lower ones, is the major concern for small- and medium-scale Nile tilapia farms. The specific objectives were: i) to quantify the effects of the most likely environmental and management factors on FCR, mortality and growth of Nile tilapia, ii) to investigate the presence of genotype by environment interaction between selection and production environments, iii) to estimate genetic parameters for resilience and iv) to estimate genetic parameters for swimming performance of Nile tilapia (novel trait) and to estimate the genetic correlation between swimming performance and production traits in aerated and non-aerated ponds. The yield gap is affected by differences in growth rate and feed conversion ratio (FCR). FCR at the farm level is strongly influenced by survival of fish. Identification of the factors that lead to the yield gap is important before any intervention to close the yield gap. In chapter II, we conducted a systematic literature review of two databases (ASFA and CAB-Abstracts) to quantify the effects of the most likely environmental factors on FCR, mortality and growth. Results showed that increasing stocking weight (SW) significantly improved both FCR and survival. Temperature had the largest effect on FCR followed by dissolved oxygen (DO), pH and CP. DO had the largest effect on TGC followed by crude protein (CP) and pH. This study confirms that the optimal rearing temperature for Nile tilapia is between 27 and 32 . Improving management to optimize DO ( ), stocking density ( ), SW (>10g) and CP ( ) will improve performance and survival in small- and medium-scale tilapia farming. However, it is hard to influence temperature in ponds and cages while DO is largely influenced by aeration. Since many small- and medium-sized farms do not have aeration, these major tilapia farming systems could benefit from genetically improved strains selected for resilience to highly fluctuating diurnal temperature and DO levels. Nile tilapia has been selectively bred under optimal dissolved oxygen environment but most smallholder production still takes place in non-aerated ponds which have large diurnal oxygen fluctuations. In the presence of environmental differences | 177 Smallholder Nile tilapia farms underperform in terms of feed efficiency, despite the use of genetically improved strains of tilapia such as GIFT. Big differences in productivity among many smallholder tilapia farms are observed leading to a yield gap between the best performing and low performing farms. Therefore, the aim of this thesis was to optimise the breeding program of Nile tilapia for a smallholder production system, thereby contributing to closing the yield gap, the difference between the best performers and lower ones, is the major concern for small- and medium-scale Nile tilapia farms. The specific objectives were: i) to quantify the effects of the most likely environmental and management factors on FCR, mortality and growth of Nile tilapia, ii) to investigate the presence of genotype by environment interaction between selection and production environments, iii) to estimate genetic parameters for resilience and iv) to estimate genetic parameters for swimming performance of Nile tilapia (novel trait) and to estimate the genetic correlation between swimming performance and production traits in aerated and non-aerated ponds. The yield gap is affected by differences in growth rate and feed conversion ratio (FCR). FCR at the farm level is strongly influenced by survival of fish. Identification of the factors that lead to the yield gap is important before any intervention to close the yield gap. In chapter II, we conducted a systematic literature review of two databases (ASFA and CAB-Abstracts) to quantify the effects of the most likely environmental factors on FCR, mortality and growth. Results showed that increasing stocking weight (SW) significantly improved both FCR and survival. Temperature had the largest effect on FCR followed by dissolved oxygen (DO), pH and CP. DO had the largest effect on TGC followed by crude protein (CP) and pH. This study confirms that the optimal rearing temperature for Nile tilapia is between 27 and 32 . Improving management to optimize DO ( ), stocking density ( ), SW (>10g) and CP ( ) will improve performance and survival in small- and medium-scale tilapia farming. However, it is hard to influence temperature in ponds and cages while DO is largely influenced by aeration. Since many small- and medium-sized farms do not have aeration, these major tilapia farming systems could benefit from genetically improved strains selected for resilience to highly fluctuating diurnal temperature and DO levels. Nile tilapia has been selectively bred under optimal dissolved oxygen environment but most smallholder production still takes place in non-aerated ponds which have large diurnal oxygen fluctuations. In the presence of environmental differences 178 | between production and selection environment, genetic gains achieved in selection and could therefore result in more optimal feeding regimes and less feed waste. environment may not be fully realized in production environment. Therefore, This would have a favourable effect on the feed efficiency in production units and knowledge of GxE interaction is important in designing and optimizing breeding on the environmental impact of fish farming. To improve resilience together with programs. In chapter III, genetic parameters for harvest weight (HW), thermal growth we recommend that fish breeding programs collect repeated records on growth coefficient (TGC), surface area (SA) and body shape, expressed as ellipticity body weight, preferably in challenging environments. (Ec) and their GxE interactions between aerated and non-aerated ponds were estimated and the impact of (non-)aeration on genetic parameters were Critical swimming speed (U crit ) another indicator of resilience. We hypothesize that investigated. The experimental fish were mass-produced using natural group Nile tilapia with high oxygen uptake efficiency (O 2 UE) may perform better under spawning and nursed in four 30m hapas. Of the stocked fish, 2063 were these conditions than Nile tilapia with low O 2 UE. Critical swimming speed (U crit ) is a genotyped-by-sequencing (GBS). A genomic relationship matrix was built using potential indicator for O 2 UE. In chapter V, we estimated variance components for 11,929 SNPs to estimate G-BLUP parameters. No-aeration had a strong negative U crit and fish size at swim testing, and genetic correlations (r g ) between U crit with impact on mean HW, genetic variance and genetic coefficient of variation. harvest weight (HW) and daily growth coefficient (DGC) after grow-out in a non- -1 Substantial heritabilities (0.14-0.45) were found for HW, TGC, SA and Ec and low aerated pond. Substantial heritability was found for absolute U crit (in ms ; 0.48). heritabilities (0.03–0.04) for survival in aerated and non-aerated ponds. In both The estimated r g between absolute U crit and fish size at testing were all strong and ponds, the environmental effect common to full sibs was not significant. Genetic positive (range 0.72 - 0.83). The estimated r g between absolute U crit and HW, and coefficients of variation were 20–23% lower and heritabilities were 19–25% lower absolute U crit and DGC were -0.21 and -0.55 respectively, indicating that fish with in the non-aerated pond compared to the aerated pond, for HW, TGC and survival. higher absolute U crit had lower growth in the non-aerated pond as compared to fish Genetic correlations between ponds for HW, standard length, height, SA and TGC with lower absolute U crit . These results suggest a juvenile trade-off between were 0.81, 0.80, 0.74, 0.78 and 0.78, respectively. In , some GxE swimming and growth performance where fish with high U crit early in life show interaction between aerated and non-aerated ponds was found and no-aeration slower growth later under conditions of limited oxygen availability. We conclude decreased genetic coefficients of variation and heritabilities compared to aerated that U crit in Nile tilapia is heritable and can be used to predict growth performance. ponds. Breeding programs are recommended to use half sib information from non- aerated farms or to set up a reference population for genomic selection in a non- In Chapter VI, I discussed smallholder Nile tilapia production challenges, different aerated environment either on-station or in farms. family production methods and selection responses to different breeding goals and selection indices. Resilience is an important trait in Nile tilapia. Log-transformed variance of deviations (LnVar) one of the indicators of resilience. In chapter IV, we estimated The results from deterministic simulation showed that HW and LnVar , HW and U crit genetic parameters for resilience in Nile tilapia, using LnVar of body weight in a non-aerated pond can be improved simultaneously by selective breeding in an measured five times during grow-out in either an aerated or a non-aerated pond. aerated pond by placing the right relative weight on LnVar or U crit . The heritability for LnVar was 0.10 in aerated pond and 0.12 in the non-aerated pond. In aerated ponds the genetic correlation (r g ) of LnVar with harvest weight (HW) was 0.36±0.26, and with thermal growth coefficient (TGC) it was 0.47±0.21. In the non-aerated pond, the r g with HW and TGC were close to zero (-0.01±0.29 and- 0.08±0.22). The genetic correlation for LnVar between both environments was 0.80. These estimates suggest that selection for HW or TGC in aerated ponds will increase LnVar in both environments. Increased LnVar may decrease resilience and this will be detrimental to performance. Selecting for more resilient fish would lead to more constant growth rates, which makes biomass estimation more accurate | 179 between production and selection environment, genetic gains achieved in selection and could therefore result in more optimal feeding regimes and less feed waste. environment may not be fully realized in production environment. Therefore, This would have a favourable effect on the feed efficiency in production units and knowledge of GxE interaction is important in designing and optimizing breeding on the environmental impact of fish farming. To improve resilience together with programs. In chapter III, genetic parameters for harvest weight (HW), thermal growth we recommend that fish breeding programs collect repeated records on growth coefficient (TGC), surface area (SA) and body shape, expressed as ellipticity body weight, preferably in challenging environments. (Ec) and their GxE interactions between aerated and non-aerated ponds were estimated and the impact of (non-)aeration on genetic parameters were Critical swimming speed (U crit ) another indicator of resilience. We hypothesize that investigated. The experimental fish were mass-produced using natural group Nile tilapia with high oxygen uptake efficiency (O 2 UE) may perform better under spawning and nursed in four 30m hapas. Of the stocked fish, 2063 were these conditions than Nile tilapia with low O 2 UE. Critical swimming speed (U crit ) is a genotyped-by-sequencing (GBS). A genomic relationship matrix was built using potential indicator for O 2 UE. In chapter V, we estimated variance components for 11,929 SNPs to estimate G-BLUP parameters. No-aeration had a strong negative U crit and fish size at swim testing, and genetic correlations (r g ) between U crit with impact on mean HW, genetic variance and genetic coefficient of variation. harvest weight (HW) and daily growth coefficient (DGC) after grow-out in a non- -1 Substantial heritabilities (0.14-0.45) were found for HW, TGC, SA and Ec and low aerated pond. Substantial heritability was found for absolute U crit (in ms ; 0.48). heritabilities (0.03–0.04) for survival in aerated and non-aerated ponds. In both The estimated r g between absolute U crit and fish size at testing were all strong and ponds, the environmental effect common to full sibs was not significant. Genetic positive (range 0.72 - 0.83). The estimated r g between absolute U crit and HW, and coefficients of variation were 20–23% lower and heritabilities were 19–25% lower absolute U crit and DGC were -0.21 and -0.55 respectively, indicating that fish with in the non-aerated pond compared to the aerated pond, for HW, TGC and survival. higher absolute U crit had lower growth in the non-aerated pond as compared to fish Genetic correlations between ponds for HW, standard length, height, SA and TGC with lower absolute U crit . These results suggest a juvenile trade-off between were 0.81, 0.80, 0.74, 0.78 and 0.78, respectively. In , some GxE swimming and growth performance where fish with high U crit early in life show interaction between aerated and non-aerated ponds was found and no-aeration slower growth later under conditions of limited oxygen availability. We conclude decreased genetic coefficients of variation and heritabilities compared to aerated that U crit in Nile tilapia is heritable and can be used to predict growth performance. ponds. Breeding programs are recommended to use half sib information from non- aerated farms or to set up a reference population for genomic selection in a non- In Chapter VI, I discussed smallholder Nile tilapia production challenges, different aerated environment either on-station or in farms. family production methods and selection responses to different breeding goals and selection indices. Resilience is an important trait in Nile tilapia. Log-transformed variance of deviations (LnVar) one of the indicators of resilience. In chapter IV, we estimated The results from deterministic simulation showed that HW and LnVar , HW and U crit genetic parameters for resilience in Nile tilapia, using LnVar of body weight in a non-aerated pond can be improved simultaneously by selective breeding in an measured five times during grow-out in either an aerated or a non-aerated pond. aerated pond by placing the right relative weight on LnVar or U crit . The heritability for LnVar was 0.10 in aerated pond and 0.12 in the non-aerated pond. In aerated ponds the genetic correlation (r g ) of LnVar with harvest weight (HW) was 0.36±0.26, and with thermal growth coefficient (TGC) it was 0.47±0.21. In the non-aerated pond, the r g with HW and TGC were close to zero (-0.01±0.29 and- 0.08±0.22). The genetic correlation for LnVar between both environments was 0.80. These estimates suggest that selection for HW or TGC in aerated ponds will increase LnVar in both environments. Increased LnVar may decrease resilience and this will be detrimental to performance. Selecting for more resilient fish would lead to more constant growth rates, which makes biomass estimation more accurate