Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study

Pocrnic, Obsteter, Gaynor, Wolc & Grojanc (2023)

DOI: 10.3389/fgene.2023.1168212

Link to published paper

• functions.R Various support functions needed for the simulation
• 1_Burnin_and_PTS.R Generating base population genomes; 10 years of conventional truncation selection on BLUP and random mating with equal contributions (PTS); 20 years of PTS
• 2_GTS.R 20 years of genomic truncation selection based on ssGBLUP and random mating with equal contributions (GTS)
• 3_MFGTS 20 years of GTS with optimized mating minimizing future progeny inbreeding with equal contributions (MFGTS)
• 4_GOCS: 20 years of genomic optimal contribution selection based on ssGBLUP with a constrained number of sires and random pairing of the optimized contributions (GOCS)
• 5_UGOCS.R: 20 years of genomic optimal contribution selection based on ssGBLUP with an unconstrained number of sires and random pairing of the optimized contributions (UGOCS)
• 6_Random.R Random selection program (negative control)
• Each script reads 2 input parameters: replicate number and number of sires (in our case 40 or 120). For example, Rscript 2_GTS.R 3 40. In addition, GOCS and UGOCS scripts need the trigonometric penalty degrees as well. For example, Rscript 4_GOCS 3 40 65.
• Please note that AlphaMate (Gorjanc & Hickey (2018), The Roslin Institute , UK) and AlphaRelate programs have to be installed on your system. For download and installation details, please consult AlphaGenes Github.
• Please note that BLUPF90 and RENUMF90 programs (Ignacy Misztal et al., University of Georgia, USA) have to be installed on your system. For download and installation details, please consult BLUPF90 website.
• You might need to change some lines of code in functions.R based on your OS and location of the binaries of aforementioned programs. For example:

 system(command = "echo renf90.par | $HOME/bin/blupf90 | tee blup.log")

or

 system(command = "$HOME/bin/AlphaMate | tee AlphaMate.log")

• N.B. simulations take a long time to run and we advise use of server/HPC to run them.