One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction

P. Sae-Lim

Research output: Thesisinternal PhD, WU

Abstract

Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • van Arendonk, Johan, Promotor
  • Komen, Hans, Co-promotor
  • Kause, A., Co-promotor
Award date8 Mar 2012
Place of PublicationS.l.
Publisher
Print ISBNs9789461734648
Publication statusPublished - 2013

Fingerprint

Oncorhynchus mykiss
genotype
breeding
genetic improvement
farmers
fish
markets
macroeconomics
cost benefit analysis
selection index
growth traits
condition factor
fillets
trout
profits and margins
feed conversion
farming systems
heat
body weight
animals

Keywords

  • rainbow trout
  • animal breeding
  • breeding programmes
  • genotype environment interaction
  • optimization
  • traits
  • genetic gain
  • selective breeding
  • simulation
  • fish culture
  • aquaculture

Cite this

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title = "One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction",
abstract = "Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL{\%}), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.",
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author = "P. Sae-Lim",
note = "WU thesis 5424",
year = "2013",
language = "English",
isbn = "9789461734648",
publisher = "s.n.",
school = "Wageningen University",

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TY - THES

T1 - One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction

AU - Sae-Lim, P.

N1 - WU thesis 5424

PY - 2013

Y1 - 2013

N2 - Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

AB - Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

KW - regenboogforel

KW - dierveredeling

KW - veredelingsprogramma's

KW - genotype-milieu interactie

KW - optimalisatie

KW - kenmerken

KW - genetische winst

KW - selectief fokken

KW - simulatie

KW - visteelt

KW - aquacultuur

KW - rainbow trout

KW - animal breeding

KW - breeding programmes

KW - genotype environment interaction

KW - optimization

KW - traits

KW - genetic gain

KW - selective breeding

KW - simulation

KW - fish culture

KW - aquaculture

M3 - internal PhD, WU

SN - 9789461734648

PB - s.n.

CY - S.l.

ER -