Evaluation of genetic gain and inbreeding trend of simulated populations based on mating designs and different relationship matrices

Genomic information offers new possibilities to control the level of progeny inbreeding. Traditionally, mating plans constrain the inbreeding of predicted progeny by using a matrix of relationships among individuals. In this study aims to improve genetic gain and restrict the inbreeding level of progeny, a founder population, with effective population size 1000 and 1000 generations, was simulated using the QMSim program to generate linkage disequilibrium. Thereafter, 500 males and 500 females were used to generate a secondary 10-generation population, with 1000 individuals per generation and its corresponding phenotype and genotype in SNP terms. Five hundred sires and 500 dams from generation 1010 were randomly selected to create generation G0 and a trait with heritability of 0.3 was simulated. The eight strategies consisting of two mating designs: minimum_inbreeding (minf) and random (rnd) and four relationship matrices as matrices of A, GRM, IBS and Weighted were used to estimate breeding value for ten generations. Comparison of strategies showed that type of mating designs and different relationship matrices had significant effect on amount of genetic gain, homozygosity and inbreeding (p < 0.05). The type of relationship matrix affected the accuracy of predictions. In strategies with weighted matrix (Gweighted), average of genetic gain during 10 generations was less than strategies using A, GRM and IBS matrices. In strategies with random mating, inbreeding rate had increasing trend. Accuracy of selection (0.63) in strategies with A matrix was lower than other strategies. In general,