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

Abstract

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.

Keywords: breeding value; coancestry; genetic diversity; genomic selection; inbreeding.

Figure 1

Histograms of the coancestries at generation 6 right before selection. Top row shows the histogram for genealogical coancestry f_A for 10, 30, and 50 individuals from left to right. Similarly, the second row shows the histogram for molecular marker-by-marker coancestry f_G. The third row shows the histograms for segment-based coancestry f_R, for N = 10, N = 30, and N = 50 from left to right. The bottom row shows the histogram for molecular marker-by-marker coancestry corrected by allelic frequencies f_V, for N = 10, N = 30, and N = 50 from left to right. The variance of each histogram is given within each plot.

Figure 2

Mean true breeding values (TBV) for different marker densities (bottom row), heritability (middle row), and population size (top row) vs. generations of selection. TBV values are shown minus the value right before truncation selection started. The default values are 50 sires and 50 dams, a heritability of 0.25 and 10,100 markers, unless the value at the top of the figure indicates otherwise.

Figure 3

Change in each coancestry for different marker densities (bottom row), heritability (middle row), and population size (top row) vs. generations of selection. The change in each coancestry is shown as $log\left(\frac{1-f}{1-f_7}\right)$.

Figure 4

Changes in genealogical coancestry for different marker densities (bottom row), heritability (middle row), and population size (top row) vs. generations of selection. The change in each coancestry is shown as $log\left(\frac{1-f_A}{1-f_A(7)}\right)$, where f_A is the genealogical coancestry at each generation and f_A(7) is the value before selection starts.

Figure 5

Changes in molecular coancestry as a measure of change in diversity for different marker densities (bottom row), heritability (middle row), and population size (top row) vs. generations of selection. This change is shown as $log\left(\frac{1-f_G}{1-f_G(7)}\right)$, where f_G is the value of molecular coancestry at each generation and f_G(7) is the value before selection starts.