Pedigree relationships to control inbreeding in optimum-contribution selection realise more genetic gain than genomic relationships.

BACKGROUND: We tested the premise that optimum-contribution selection with pedigree relationships to control inbreeding (POCS) realises at least as much true genetic gain as optimum-contribution selection with genomic relationships (GOCS) at the same rate of true inbreeding. METHODS: We used stochastic simulation to estimate rates of true genetic gain realised by POCS and GOCS at a 0.01 rate of true inbreeding in three breeding schemes with best linear unbiased predictions of breeding values based on pedigree (PBLUP) and genomic (GBLUP) information. The three breeding schemes differed in number of matings and litter size. Selection was for a single trait with a heritability of 0.2. The trait was controlled by 7702 biallelic quantitative-trait loci (QTL) that were distributed across a 30-M genome. The genome contained 54,218 biallelic markers that were used in GOCS and GBLUP. A total of 6012 identity-by-descent loci were placed across the genome in base populations. Unique alleles at these loci were used to calculate rates of true inbreeding. Breeding schemes were run for 10 discrete generations. Selection candidates were genotyped and phenotyped before selection. RESULTS: POCS realised more true genetic gain than GOCS at a 0.01 rate of true inbreeding in all combinations of breeding scheme and prediction method. POCS realised 14 to 33% more true genetic gain than GOCS with PBLUP in the three breeding schemes. It realised 1.5 to 5.7% more true genetic gain than GOCS with GBLUP. CONCLUSIONS: POCS realised more true genetic gain than GOCS because it managed expected genetic drift without restricting selection at QTL. By contrast, GOCS penalised changes in allele frequencies at markers that were generated by genetic drift and selection. Because these marker alleles were in linkage disequilibrium with QTL alleles, GOCS restricted changes in allele frequencies at QTL. This provides little incentive to use GOCS and highlights that we have more to learn before we can control inbreeding using genomic relationships in selective-breeding schemes. Until we can do so, POCS remains a worthy method of optimum-contribution selection because it realises more true genetic gain than GOCS at the same rate of true inbreeding.

Management of Genetic Diversity in the Era of Genomics.

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.