Artificial selection with traditional or genomic relationships: consequences in coancestry and genetic diversity

Estimated breeding values (EBVs) are traditionally obtained from pedigree information. However, EBVs from high-density genotypes can have higher accuracy than EBVs from pedigree information. At the same time, it has been shown that EBVs from genomic data lead to lower increases in inbreeding compared with traditional selection based on genealogies. Here we evaluate the performance with BLUP selection based on genealogical coancestry with three different genome-based coancestry estimates: (1) an estimate based on shared segments of homozygosity, (2) an approach based on SNP-by-SNP count corrected by allelic frequencies, and (3) the identity by state methodology. We evaluate the effect of different population sizes, different number of genomic markers, and several heritability values for a quantitative trait. The performance of the different measures of coancestry in BLUP is evaluated in the true breeding values after truncation selection and also in terms of coancestry and diversity maintained. Accordingly, cross-performances were also carried out, that is, how prediction based on genealogical records impacts the three other measures of coancestry and inbreeding, and viceversa. Our results show that the genetic gains are very similar for all four coancestries, but the genomic-based methods are superior to using genealogical coancestries in terms of maintaining diversity measured as observed heterozygosity. Furthermore, the measure of coancestry based on shared segments of the genome seems to provide slightly better results on some scenarios, and the increase in inbreeding and loss in diversity is only slightly larger than the other genomic selection methods in those scenarios. Our results shed light on genomic selection vs. traditional genealogical-based BLUP and make the case to manage the population variability using genomic information to preserve the future success of selection programmes.