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

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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

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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