{"id":10435,"date":"2026-04-09T12:09:48","date_gmt":"2026-04-09T12:09:48","guid":{"rendered":"https:\/\/www.proefschriftmaken.nl\/portfolio\/samuel-bekele-mengistu\/"},"modified":"2026-04-23T07:29:38","modified_gmt":"2026-04-23T07:29:38","slug":"samuel-bekele-mengistu","status":"publish","type":"us_portfolio","link":"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/samuel-bekele-mengistu\/","title":{"rendered":"Samuel Bekele Mengistu"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":8,"featured_media":12680,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"us_portfolio_category":[45],"class_list":["post-10435","us_portfolio","type-us_portfolio","status-publish","has-post-thumbnail","hentry","us_portfolio_category-new-template"],"acf":{"naam_van_het_proefschift":"Closing the yield gap: improving production efficiency in smallholder farms of Nile tilapia through selective breeding","samenvatting":"Er is geen Nederlandse samenvatting beschikbaar. De Engelse samenvatting vind je <a href=\"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/samuel-bekele-mengistu\/\">hier<\/a>.","summary":"Smallholder Nile tilapia farms underperform in terms of feed efficiency, despite the\nuse of genetically improved strains of tilapia such as GIFT. Big differences in\nproductivity among many smallholder tilapia farms are observed leading to a yield\ngap between the best performing and low performing farms. Therefore, the aim of\nthis thesis was to optimise the breeding program of Nile tilapia for a smallholder\nproduction system, thereby contributing to closing the yield gap, the difference\nbetween the best performers and lower ones, is the major concern for small- and\nmedium-scale Nile tilapia farms. The specific objectives were: i) to quantify the\neffects of the most likely environmental and management factors on FCR, mortality\nand growth of Nile tilapia, ii) to investigate the presence of genotype by\nenvironment interaction between selection and production environments, iii) to\nestimate genetic parameters for resilience and iv) to estimate genetic parameters\nfor swimming performance of Nile tilapia (novel trait) and to estimate the genetic\ncorrelation between swimming performance and production traits in aerated and\nnon-aerated ponds.\n\nThe yield gap is affected by differences in growth rate and feed conversion ratio\n(FCR). FCR at the farm level is strongly influenced by survival of fish. Identification\nof the factors that lead to the yield gap is important before any intervention to\nclose the yield gap. In chapter II, we conducted a systematic literature review of\ntwo databases (ASFA and CAB-Abstracts) to quantify the effects of the most likely\nenvironmental factors on FCR, mortality and growth. Results showed that\nincreasing stocking weight (SW) significantly improved both FCR and survival.\nTemperature had the largest effect on FCR followed by dissolved oxygen (DO), pH\nand CP. DO had the largest effect on TGC followed by crude protein (CP) and pH.\nThis study confirms that the optimal rearing temperature for Nile tilapia is between\n27 and 32 . Improving management to optimize DO ( ), stocking density\n\n( ), SW (>10g) and CP ( ) will improve performance and\n\nsurvival in small- and medium-scale tilapia farming. However, it is hard to influence\ntemperature in ponds and cages while DO is largely influenced by aeration. Since\nmany small- and medium-sized farms do not have aeration, these major tilapia\nfarming systems could benefit from genetically improved strains selected for\nresilience to highly fluctuating diurnal temperature and DO levels.\n\nNile tilapia has been selectively bred under optimal dissolved oxygen environment\nbut most smallholder production still takes place in non-aerated ponds which have\nlarge diurnal oxygen fluctuations. In the presence of environmental differences\n\n| 177\n\nSmallholder Nile tilapia farms underperform in terms of feed efficiency, despite the\nuse of genetically improved strains of tilapia such as GIFT. Big differences in\nproductivity among many smallholder tilapia farms are observed leading to a yield\ngap between the best performing and low performing farms. Therefore, the aim of\nthis thesis was to optimise the breeding program of Nile tilapia for a smallholder\nproduction system, thereby contributing to closing the yield gap, the difference\nbetween the best performers and lower ones, is the major concern for small- and\nmedium-scale Nile tilapia farms. The specific objectives were: i) to quantify the\neffects of the most likely environmental and management factors on FCR, mortality\nand growth of Nile tilapia, ii) to investigate the presence of genotype by\nenvironment interaction between selection and production environments, iii) to\nestimate genetic parameters for resilience and iv) to estimate genetic parameters\nfor swimming performance of Nile tilapia (novel trait) and to estimate the genetic\ncorrelation between swimming performance and production traits in aerated and\nnon-aerated ponds.\n\nThe yield gap is affected by differences in growth rate and feed conversion ratio\n(FCR). FCR at the farm level is strongly influenced by survival of fish. Identification\nof the factors that lead to the yield gap is important before any intervention to\nclose the yield gap. In chapter II, we conducted a systematic literature review of\ntwo databases (ASFA and CAB-Abstracts) to quantify the effects of the most likely\nenvironmental factors on FCR, mortality and growth. Results showed that\nincreasing stocking weight (SW) significantly improved both FCR and survival.\nTemperature had the largest effect on FCR followed by dissolved oxygen (DO), pH\nand CP. DO had the largest effect on TGC followed by crude protein (CP) and pH.\nThis study confirms that the optimal rearing temperature for Nile tilapia is between\n27 and 32 . Improving management to optimize DO ( ), stocking density\n\n( ), SW (>10g) and CP ( ) will improve performance and\n\nsurvival in small- and medium-scale tilapia farming. However, it is hard to influence\ntemperature in ponds and cages while DO is largely influenced by aeration. Since\nmany small- and medium-sized farms do not have aeration, these major tilapia\nfarming systems could benefit from genetically improved strains selected for\nresilience to highly fluctuating diurnal temperature and DO levels.\n\nNile tilapia has been selectively bred under optimal dissolved oxygen environment\nbut most smallholder production still takes place in non-aerated ponds which have\nlarge diurnal oxygen fluctuations. In the presence of environmental differences\n\n178 |\n\nbetween production and selection environment, genetic gains achieved in selection and could therefore result in more optimal feeding regimes and less feed waste.\nenvironment may not be fully realized in production environment. Therefore, This would have a favourable effect on the feed efficiency in production units and\nknowledge of GxE interaction is important in designing and optimizing breeding on the environmental impact of fish farming. To improve resilience together with\nprograms. In chapter III, genetic parameters for harvest weight (HW), thermal growth we recommend that fish breeding programs collect repeated records on\ngrowth coefficient (TGC), surface area (SA) and body shape, expressed as ellipticity body weight, preferably in challenging environments.\n(Ec) and their GxE interactions between aerated and non-aerated ponds were\nestimated and the impact of (non-)aeration on genetic parameters were Critical swimming speed (U crit ) another indicator of resilience. We hypothesize that\ninvestigated. The experimental fish were mass-produced using natural group Nile tilapia with high oxygen uptake efficiency (O 2 UE) may perform better under\n\nspawning 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\ngenotyped-by-sequencing (GBS). A genomic relationship matrix was built using potential indicator for O 2 UE. In chapter V, we estimated variance components for\n11,929 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\nimpact on mean HW, genetic variance and genetic coefficient of variation. harvest weight (HW) and daily growth coefficient (DGC) after grow-out in a non-\n-1\nSubstantial 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).\nheritabilities (0.03\u20130.04) 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\nponds, 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\ncoefficients of variation were 20\u201323% lower and heritabilities were 19\u201325% lower absolute U crit and DGC were -0.21 and -0.55 respectively, indicating that fish with\nin 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\nGenetic correlations between ponds for HW, standard length, height, SA and TGC with lower absolute U crit . These results suggest a juvenile trade-off between\nwere 0.81, 0.80, 0.74, 0.78 and 0.78, respectively. In\n, some GxE swimming and growth performance where fish with high U crit early in life show\ninteraction between aerated and non-aerated ponds was found and no-aeration slower growth later under conditions of limited oxygen availability. We conclude\ndecreased 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.\nponds. Breeding programs are recommended to use half sib information from non-\naerated 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\naerated environment either on-station or in farms. family production methods and selection responses to different breeding goals and\nselection indices.\nResilience is an important trait in Nile tilapia. Log-transformed variance of\ndeviations (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\ngenetic 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\nmeasured 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 .\nThe heritability for LnVar was 0.10 in aerated pond and 0.12 in the non-aerated\npond. In aerated ponds the genetic correlation (r g ) of LnVar with harvest weight\n(HW) was 0.36\u00b10.26, and with thermal growth coefficient (TGC) it was 0.47\u00b10.21. In\nthe non-aerated pond, the r g with HW and TGC were close to zero (-0.01\u00b10.29 and-\n0.08\u00b10.22). The genetic correlation for LnVar between both environments was\n0.80. These estimates suggest that selection for HW or TGC in aerated ponds will\nincrease LnVar in both environments. Increased LnVar may decrease resilience and\nthis will be detrimental to performance. Selecting for more resilient fish would lead\nto more constant growth rates, which makes biomass estimation more accurate\n\n| 179\n\nbetween production and selection environment, genetic gains achieved in selection and could therefore result in more optimal feeding regimes and less feed waste.\nenvironment may not be fully realized in production environment. Therefore, This would have a favourable effect on the feed efficiency in production units and\nknowledge of GxE interaction is important in designing and optimizing breeding on the environmental impact of fish farming. To improve resilience together with\nprograms. In chapter III, genetic parameters for harvest weight (HW), thermal growth we recommend that fish breeding programs collect repeated records on\ngrowth coefficient (TGC), surface area (SA) and body shape, expressed as ellipticity body weight, preferably in challenging environments.\n(Ec) and their GxE interactions between aerated and non-aerated ponds were\nestimated and the impact of (non-)aeration on genetic parameters were Critical swimming speed (U crit ) another indicator of resilience. We hypothesize that\ninvestigated. The experimental fish were mass-produced using natural group Nile tilapia with high oxygen uptake efficiency (O 2 UE) may perform better under\n\nspawning 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\ngenotyped-by-sequencing (GBS). A genomic relationship matrix was built using potential indicator for O 2 UE. In chapter V, we estimated variance components for\n11,929 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\nimpact on mean HW, genetic variance and genetic coefficient of variation. harvest weight (HW) and daily growth coefficient (DGC) after grow-out in a non-\n-1\nSubstantial 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).\nheritabilities (0.03\u20130.04) 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\nponds, 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\ncoefficients of variation were 20\u201323% lower and heritabilities were 19\u201325% lower absolute U crit and DGC were -0.21 and -0.55 respectively, indicating that fish with\nin 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\nGenetic correlations between ponds for HW, standard length, height, SA and TGC with lower absolute U crit . These results suggest a juvenile trade-off between\nwere 0.81, 0.80, 0.74, 0.78 and 0.78, respectively. In\n, some GxE swimming and growth performance where fish with high U crit early in life show\ninteraction between aerated and non-aerated ponds was found and no-aeration slower growth later under conditions of limited oxygen availability. We conclude\ndecreased 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.\nponds. Breeding programs are recommended to use half sib information from non-\naerated 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\naerated environment either on-station or in farms. family production methods and selection responses to different breeding goals and\nselection indices.\nResilience is an important trait in Nile tilapia. Log-transformed variance of\ndeviations (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\ngenetic 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\nmeasured 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 .\nThe heritability for LnVar was 0.10 in aerated pond and 0.12 in the non-aerated\npond. In aerated ponds the genetic correlation (r g ) of LnVar with harvest weight\n(HW) was 0.36\u00b10.26, and with thermal growth coefficient (TGC) it was 0.47\u00b10.21. In\nthe non-aerated pond, the r g with HW and TGC were close to zero (-0.01\u00b10.29 and-\n0.08\u00b10.22). The genetic correlation for LnVar between both environments was\n0.80. These estimates suggest that selection for HW or TGC in aerated ponds will\nincrease LnVar in both environments. Increased LnVar may decrease resilience and\nthis will be detrimental to performance. Selecting for more resilient fish would lead\nto more constant growth rates, which makes biomass estimation more accurate","auteur":"Samuel Bekele Mengistu","auteur_slug":"samuel-bekele-mengistu","publicatiedatum":"29 augustus 2022","taal":"EN","url_flipbook":"https:\/\/ebook.proefschriftmaken.nl\/ebook\/samuelbekelemengistu?iframe=true","url_download_pdf":"","url_epub":"","ordernummer":"FTP-202604091205","isbn":"978-94-6447-322-3","doi_nummer":"","naam_universiteit":"Wageningen University","afbeeldingen":12680,"naam_student:":"","binnenwerk":"","universiteit":"Wageningen University","cover":"","afwerking":"","cover_afwerking":"","design":""},"_links":{"self":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10435","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio"}],"about":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/types\/us_portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/comments?post=10435"}],"version-history":[{"count":1,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10435\/revisions"}],"predecessor-version":[{"id":10436,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/10435\/revisions\/10436"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media\/12680"}],"wp:attachment":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media?parent=10435"}],"wp:term":[{"taxonomy":"us_portfolio_category","embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio_category?post=10435"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}