/******************************* ** Global parameters ** *******************************/ title = "SA 1 - 500k SNP panel"; nrep = 5; //Number of replicates h2 = 0.99; //Heritability 0.99 qtlh2 = 0.99; //QTL heritability phvar = 1; //Phenotypic variance /******************************* ** Historical population ** *******************************/ begin_hp; hg_size = 1000 [0] 50000 [1000] 20000 [2000]; //Size of the historical generations -> size [number of generation] nmlhg = 3000; //Number of males in the last generation end_hp; /******************************* ** Populations ** *******************************/ begin_pop = "p1"; begin_founder; male [n = 50, pop = "hp"]; female [n = 15000, pop = "hp"]; end_founder; ls = 1; //Litter size md = rnd; //random pmp = 0.3; //Proportion of male progeny sr = 0.8; //Sire replacement algumas females are selected based on pheno dr = 0.3; //Dam replacement ng = 20; //Number of generations sd = rnd; //Selection design ebv_est = blup /true_av; //Estimation method for bv /true additive genetic variance for each generation will be considered begin_popoutput; ld /gen 15 16 17 18 19 20; crossover /gen 15 16 17 18 19 20; data; stat; genotype /snp_code /gen 16 17 18 19 20; allele_freq; end_popoutput; end_pop; /******************************* ** Genome ** *******************************/ begin_genome; begin_chr = 1; // CHR 1 //number of chromosomes with the same parameter chrlen = 146; //Chromosome length cM nmloci = 34310; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 312; //Number of QTL qpos = rnd; //QTL positions nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 2 //number of chromosomes with the same parameter chrlen = 125; //Chromosome length cM nmloci = 28290; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 268; //Number of QTL qpos = rnd; //QTL positions nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 3 //number of chromosomes with the same parameter chrlen = 116; //Chromosome length cM nmloci = 25500; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 248; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 4 //number of chromosomes with the same parameter chrlen = 110; //Chromosome length cM nmloci = 25700; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 240 ; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 5 //number of chromosomes with the same parameter chrlen = 118; //Chromosome length cM nmloci = 22710; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 252; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 6 //number of chromosomes with the same parameter chrlen = 111; //Chromosome length cM nmloci = 25750; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 240; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 7 //number of chromosomes with the same parameter chrlen = 100; //Chromosome length cM nmloci = 23520; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 220; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 8 //number of chromosomes with the same parameter chrlen = 103; //Chromosome length cM nmloci = 24300; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 220; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 9 //number of chromosomes with the same parameter chrlen = 95; //Chromosome length cM nmloci = 20950; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 204; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 10 //number of chromosomes with the same parameter chrlen = 95; //Chromosome length cM nmloci = 22060; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 204; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 11 //number of chromosomes with the same parameter chrlen = 101; //Chromosome length cM nmloci = 22950; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 216; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 12 //number of chromosomes with the same parameter chrlen = 77; //Chromosome length cM nmloci = 17730; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 164; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 13 //number of chromosomes with the same parameter chrlen = 83; //Chromosome length cM nmloci = 18500; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 176; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 14 //number of chromosomes with the same parameter chrlen = 82; //Chromosome length cM nmloci = 18310; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 176; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 15 //number of chromosomes with the same parameter chrlen = 75; //Chromosome length cM nmloci = 17620; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 160; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 16 //number of chromosomes with the same parameter chrlen = 72; //Chromosome length cM nmloci = 17260; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 156; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 17 //number of chromosomes with the same parameter chrlen = 70; //Chromosome length cM nmloci = 16000; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 148; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 18 //number of chromosomes with the same parameter chrlen = 62; //Chromosome length cM nmloci = 13760; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 132; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 19 //number of chromosomes with the same parameter chrlen = 63; //Chromosome length cM nmloci = 14200; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 136; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 20 //number of chromosomes with the same parameter chrlen = 68; //Chromosome length cM nmloci = 15680; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 144; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 21 //number of chromosomes with the same parameter chrlen = 63; //Chromosome length cM nmloci = 14830; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 136; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 22 //number of chromosomes with the same parameter chrlen = 59; //Chromosome length cM nmloci = 13240; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 128; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 23 //number of chromosomes with the same parameter chrlen = 48; //Chromosome length cM nmloci = 10920; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 104; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 24 //number of chromosomes with the same parameter chrlen = 60; //Chromosome length cM nmloci = 13120; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 128; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 25 //number of chromosomes with the same parameter chrlen = 42; //Chromosome length cM nmloci = 10040; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 88; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 26 //number of chromosomes with the same parameter chrlen = 47; //Chromosome length cM nmloci = 11160; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 100; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 27 //number of chromosomes with the same parameter chrlen = 43; //Chromosome length cM nmloci = 9810; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 92; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 28 //number of chromosomes with the same parameter chrlen = 40; //Chromosome length cM nmloci = 9810; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 84; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // begin_chr = 1; // CHR 29 //number of chromosomes with the same parameter chrlen = 45; //Chromosome length cM nmloci = 10870; //Number of markers mpos = even; //Marker positions nma = all 2; //Number of marker alleles maf = eql; //Marker allele frequencies nqloci = 96; //Number of QTL qpos = rnd; nqa = all 2; //Number of QTL alleles qaf = eql; //QTL allele frequencies cld = mq; //LD compelte on markers qae = rndg 0.4; //QTL allele effects ~ Gamma end_chr; // mmutr = 2.5e-5 /recurrent; // marker mutation rate qmutr = 2.5e-5 /recurrent; //QTL mutation rate select_seg_loci /maft 0.05 /nmrk 500000 /nqtl 2000; //maft[v] is minor allele frequency threshold. Loci with minor allele frequency larger than or equal to v will be selected end_genome; //nmrk[v] is the number of markers to be selected randomly /******************************* ** Output options ** *******************************/ begin_output; linkage_map; allele_effect; end_output;