title: Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values.
abstract: BACKGROUND
  Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs.
  
  
  METHODS
  Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection.
  
  
  RESULTS
  All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively.
  
  
  CONCLUSIONS
  Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space.
authors.affiliation: Sheep Cooperative Research Centre, Armidale, 2351, Australia. tgranle2@une.edu.au.|School of Environmental and Rural Science, University of New England, Armidale, 2351, Australia. tgranle2@une.edu.au.
authors.forename: Tom
authors.initials: T
authors.lastname: Granleese
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, 2351, Australia. sam.clark@une.edu.au.
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Clark
authors.affiliation: Sheep Cooperative Research Centre, Armidale, 2351, Australia. Andrew.Swan@une.edu.au.|Animal Genetics and Breeding Unit, Armidale, 2351, Australia. Andrew.Swan@une.edu.au.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Swan
authors.affiliation: Sheep Cooperative Research Centre, Armidale, 2351, Australia. jvanderw@une.edu.au.|School of Environmental and Rural Science, University of New England, Armidale, 2351, Australia. jvanderw@une.edu.au.
authors.forename: Julius H J
authors.initials: JH
authors.lastname: van der Werf
mesh_terms: D000818:Animals; D002417:Cattle; D003612:Dairying; D005260:Female; D008297:Male; D008962:Models, Theoretical; D040641:Quantitative Trait Loci; D027724:Reproductive Techniques, Assisted / Q000662:veterinary*; D012641:Selection, Genetic; D000068618:Selective Breeding; D012737:Sex Factors; D012756:Sheep