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Response and inbreeding from a genomic selection experiment in layer chickens.

Wolc A, Zhao HH, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Stricker C, Habier D, Fernando RL, Garrick DJ, Lamont SJ, Dekkers JC - Genet. Sel. Evol. (2015)

Bottom Line: We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year.At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.The results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA. awolc@iastate.edu.

ABSTRACT

Background: Genomic selection (GS) using estimated breeding values (GS-EBV) based on dense marker data is a promising approach for genetic improvement. A simulation study was undertaken to illustrate the opportunities offered by GS for designing breeding programs. It consisted of a selection program for a sex-limited trait in layer chickens, which was developed by deterministic predictions under different scenarios. Later, one of the possible schemes was implemented in a real population of layer chicken.

Methods: In the simulation, the aim was to double the response to selection per year by reducing the generation interval by 50 %, while maintaining the same rate of inbreeding per year. We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year. A multi-trait GS scenario was subsequently implemented in a real population of brown egg laying hens. The population was split into two sub-lines, one was submitted to conventional phenotypic selection, and one was selected based on genomic prediction. At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.

Results: Birds that were selected based on genomic prediction outperformed those that were submitted to conventional selection for most of the 16 traits that were included in the index used for selection. However, although the two programs were designed to achieve the same rate of inbreeding per year, the realized inbreeding per year assessed from pedigree was higher in the genomic selected line than in the conventionally selected line.

Conclusions: The results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

No MeSH data available.


Related in: MedlinePlus

Responses to selection in the experimental breeding program, as deviation of trait means and expressed in genetic standard deviation units. Responses to selection are based on deviations of trait means from trait means at the start of the selection experiment, expressed in genetic standard deviation units of each trait; trait abbreviations: egg weight for first three eggs (eE3), at early (eEW) and late age (lEW), shell color for first three eggs (eC3), at early (eCO) and late age (lCO), albumen height at early age (eAH), yolk weight at early (eYW) and late age (lYW) puncture score at early age (ePS), egg production rates at early (ePD) and late (lPD), egg numbers at early (eEN) and late (lEN) age, body weight at late age (lBW), and age at first egg (eSM)
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Fig3: Responses to selection in the experimental breeding program, as deviation of trait means and expressed in genetic standard deviation units. Responses to selection are based on deviations of trait means from trait means at the start of the selection experiment, expressed in genetic standard deviation units of each trait; trait abbreviations: egg weight for first three eggs (eE3), at early (eEW) and late age (lEW), shell color for first three eggs (eC3), at early (eCO) and late age (lCO), albumen height at early age (eAH), yolk weight at early (eYW) and late age (lYW) puncture score at early age (ePS), egg production rates at early (ePD) and late (lPD), egg numbers at early (eEN) and late (lEN) age, body weight at late age (lBW), and age at first egg (eSM)

Mentions: The standardized responses to selection by the end of the experiment are in Fig. 3. On average, trait means were changed in the desired direction by the end of the experiment for all traits. For most traits, the genomic line significantly outperformed the pedigree line, with a doubled response to selection for some traits, such as EW and YW. Body weight increased for both lines, with a larger response in the genomic line. This reflects selection for a revised objective, i.e., in the past, layer chicken lines were selected for lower BW, while, more recently, selection has aimed at increasing BW at a young age to allow pullets to develop adequately. For egg production rate (ePD and lPD), the pedigree selection line showed a positive response, while the genomic selection line showed a negative response to selection. It should be noted that, for this trait, phenotypes were available for the pedigree selection line at the time of selection but not for the genomic line. However, these results were not supported by the results of egg production measured by egg number (eEN and lEN), for which both lines showed a positive response, with a greater response for the genomic line. This difference in responses in egg production rate versus egg number was explained by both a higher frequency of egg defects in the genomic line (5.7 vs 4.0 %) and earlier age at sexual maturity of birds in the genomic line (141 vs. 145 days).Fig. 3


Response and inbreeding from a genomic selection experiment in layer chickens.

Wolc A, Zhao HH, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Stricker C, Habier D, Fernando RL, Garrick DJ, Lamont SJ, Dekkers JC - Genet. Sel. Evol. (2015)

Responses to selection in the experimental breeding program, as deviation of trait means and expressed in genetic standard deviation units. Responses to selection are based on deviations of trait means from trait means at the start of the selection experiment, expressed in genetic standard deviation units of each trait; trait abbreviations: egg weight for first three eggs (eE3), at early (eEW) and late age (lEW), shell color for first three eggs (eC3), at early (eCO) and late age (lCO), albumen height at early age (eAH), yolk weight at early (eYW) and late age (lYW) puncture score at early age (ePS), egg production rates at early (ePD) and late (lPD), egg numbers at early (eEN) and late (lEN) age, body weight at late age (lBW), and age at first egg (eSM)
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492088&req=5

Fig3: Responses to selection in the experimental breeding program, as deviation of trait means and expressed in genetic standard deviation units. Responses to selection are based on deviations of trait means from trait means at the start of the selection experiment, expressed in genetic standard deviation units of each trait; trait abbreviations: egg weight for first three eggs (eE3), at early (eEW) and late age (lEW), shell color for first three eggs (eC3), at early (eCO) and late age (lCO), albumen height at early age (eAH), yolk weight at early (eYW) and late age (lYW) puncture score at early age (ePS), egg production rates at early (ePD) and late (lPD), egg numbers at early (eEN) and late (lEN) age, body weight at late age (lBW), and age at first egg (eSM)
Mentions: The standardized responses to selection by the end of the experiment are in Fig. 3. On average, trait means were changed in the desired direction by the end of the experiment for all traits. For most traits, the genomic line significantly outperformed the pedigree line, with a doubled response to selection for some traits, such as EW and YW. Body weight increased for both lines, with a larger response in the genomic line. This reflects selection for a revised objective, i.e., in the past, layer chicken lines were selected for lower BW, while, more recently, selection has aimed at increasing BW at a young age to allow pullets to develop adequately. For egg production rate (ePD and lPD), the pedigree selection line showed a positive response, while the genomic selection line showed a negative response to selection. It should be noted that, for this trait, phenotypes were available for the pedigree selection line at the time of selection but not for the genomic line. However, these results were not supported by the results of egg production measured by egg number (eEN and lEN), for which both lines showed a positive response, with a greater response for the genomic line. This difference in responses in egg production rate versus egg number was explained by both a higher frequency of egg defects in the genomic line (5.7 vs 4.0 %) and earlier age at sexual maturity of birds in the genomic line (141 vs. 145 days).Fig. 3

Bottom Line: We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year.At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.The results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011-3150, USA. awolc@iastate.edu.

ABSTRACT

Background: Genomic selection (GS) using estimated breeding values (GS-EBV) based on dense marker data is a promising approach for genetic improvement. A simulation study was undertaken to illustrate the opportunities offered by GS for designing breeding programs. It consisted of a selection program for a sex-limited trait in layer chickens, which was developed by deterministic predictions under different scenarios. Later, one of the possible schemes was implemented in a real population of layer chicken.

Methods: In the simulation, the aim was to double the response to selection per year by reducing the generation interval by 50 %, while maintaining the same rate of inbreeding per year. We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year. A multi-trait GS scenario was subsequently implemented in a real population of brown egg laying hens. The population was split into two sub-lines, one was submitted to conventional phenotypic selection, and one was selected based on genomic prediction. At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.

Results: Birds that were selected based on genomic prediction outperformed those that were submitted to conventional selection for most of the 16 traits that were included in the index used for selection. However, although the two programs were designed to achieve the same rate of inbreeding per year, the realized inbreeding per year assessed from pedigree was higher in the genomic selected line than in the conventionally selected line.

Conclusions: The results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

No MeSH data available.


Related in: MedlinePlus