title: Efficiency of genomic selection in an established commercial layer breeding program.
abstract: BACKGROUND
  In breeding programs for layers, selection of hens and cocks is based on recording phenotypic data from hens in different housing systems. Genomic information can provide additional information for selection and/or allow for a strong reduction in the generation interval. In this study, a typical conventional layer breeding program using a four-line cross was modeled and the expected genetic progress was derived deterministically with the software ZPLAN+. This non-genomic reference scenario was compared to two genomic breeding programs to determine the best strategy for implementing genomic information in layer breeding programs.
  
  
  RESULTS
  In scenario I, genomic information was used in addition to all other information available in the conventional breeding program, so the generation interval was the same as in the reference scenario, i.e. 14.5 months. Here, we assumed that either only young cocks or young cocks and hens were genotyped as selection candidates. In scenario II, we assumed that breeders of both sexes were used at the biologically earliest possible age, so that at the time of selection only performance data of the parent generation and genomic information of the selection candidates were available. In this case, the generation interval was reduced to eight months. In both scenarios, the number of genotyped male selection candidates was varied between 800 and 4800 males and two sizes of the calibration set (500 or 2000 animals) were considered. All genomic scenarios increased the expected genetic gain and the economic profit of the breeding program. In scenario II, the increase was much more pronounced and even in the most conservative implementation led to a 60% improvement in genetic gain and economic profit. This increase was in all cases associated with higher breeding costs.
  
  
  CONCLUSIONS
  While genomic selection is shown to have the potential to improve genetic gain in layer breeding programs, its implementation remains a business decision of the breeding company; the possible extra profit for the breeding company depends on whether the customers of breeding stock are willing to pay more for improved genetic quality.
authors.affiliation: Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany. fsitzen@gwdg.de
authors.forename: Florian
authors.initials: F
authors.lastname: Sitzenstock
authors.forename: Florence
authors.initials: F
authors.lastname: Ytournel
authors.forename: Ahmad R
authors.initials: AR
authors.lastname: Sharifi
authors.forename: David
authors.initials: D
authors.lastname: Cavero
authors.forename: Helge
authors.initials: H
authors.lastname: Täubert
authors.forename: Rudolf
authors.initials: R
authors.lastname: Preisinger
authors.forename: Henner
authors.initials: H
authors.lastname: Simianer
mesh_terms: D000818:Animals; D001947:Breeding / Q000191:economics / Q000379:methods; D002645:Chickens / Q000235:genetics; D003362:Cost-Benefit Analysis; D005260:Female; D016678:Genome; D023281:Genomics / Q000191:economics / Q000379:methods; D006824:Hybridization, Genetic; D008297:Male; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D012984:Software
references.citation: PLoS One. 2008;3(10):e3395
references.pmid: 18852893
references.citation: Br Poult Sci. 1999 May;40(2):203-8
references.pmid: 10465386
references.citation: Genome Res. 2009 Mar;19(3):510-9
references.pmid: 19088305
references.citation: J Dairy Sci. 2009 Jan;92(1):382-91
references.pmid: 19109296
references.citation: Genetics. 2009 May;182(1):343-53
references.pmid: 19299339
references.citation: J Anim Sci. 2012 Dec;90(13):4681-9
references.pmid: 23087087
references.citation: Genetica. 2009 Jun;136(2):245-57
references.pmid: 18704696
references.citation: Genetics. 2010 Jul;185(3):1021-31
references.pmid: 20407128
references.citation: Poult Sci. 2006 Dec;85(12):2079-96
references.pmid: 17135661
references.citation: Genomics. 2005 Aug;86(2):225-32
references.pmid: 15916878
references.citation: Nature. 2004 Dec 9;432(7018):717-22
references.pmid: 15592405
references.citation: J Anim Breed Genet. 2006 Aug;123(4):218-23
references.pmid: 16882088
references.citation: Virus Genes. 2010 Jun;40(3):410-20
references.pmid: 20229182
references.citation: J Dairy Sci. 2011 Jul;94(7):3679-86
references.pmid: 21700057
references.citation: J Anim Breed Genet. 2007 Dec;124(6):331-41
references.pmid: 18076470
references.citation: Genet Sel Evol. 2011 Jan 21;43:5
references.pmid: 21255418
references.citation: Poult Sci. 2011 Jan;90(1):241-50
references.pmid: 21177466
references.citation: BMC Genomics. 2011 May 31;12(1):274
references.pmid: 21627800