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

Rodríguez-Ramilo ST, García-Cortés LA, de Cara MÁ - Front Genet (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Mejora Genetica Animal, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria Madrid, Spain.

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.

No MeSH data available.


Related in: MedlinePlus

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4388001&req=5

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.

Mentions: Changes in TBVs obtained with the four relationship matrices for three population sizes N = 10, N = 30, and N = 50, three heritabilities h2 = 0.1, h2 = 0.25, and h2 = 0.50, as well as three marker densities of 2525, 5050, and all 10,100 per chromosome are shown in Figure 2 vs. generations. We only show results after generation 7, when selection starts. For a better comparison between the different coancestries here used, we show the value at each generation minus the initial value right before selection (i.e., at generation 7). Overall, all four methods performed similarly in terms of genetic gain for the sizes here studied. As expected, the final TBV increased with the number of individuals and with the heritability of the trait. The density of markers had no effect when selecting with the genealogical coancestry fA, as expected, and, within the range of densities here studied no differences were detected in the genetic gains achieved by the genomic based estimates fV and fG. The most surprising result is that for a low density of markers, the genetic gain is larger performing selection based on fR. It must be noticed that the size for a region of homozygosity to be considered as such was kept constant and thus, a ROH of 100 contiguous markers covers a much longer stretch than for 10,100 marker per chromosome. This is also surprising as it has been pointed out that the longer the ROH, the more correlated ROH-based inbreeding is with genealogical inbreeding.


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

Rodríguez-Ramilo ST, García-Cortés LA, de Cara MÁ - Front Genet (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4388001&req=5

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.
Mentions: Changes in TBVs obtained with the four relationship matrices for three population sizes N = 10, N = 30, and N = 50, three heritabilities h2 = 0.1, h2 = 0.25, and h2 = 0.50, as well as three marker densities of 2525, 5050, and all 10,100 per chromosome are shown in Figure 2 vs. generations. We only show results after generation 7, when selection starts. For a better comparison between the different coancestries here used, we show the value at each generation minus the initial value right before selection (i.e., at generation 7). Overall, all four methods performed similarly in terms of genetic gain for the sizes here studied. As expected, the final TBV increased with the number of individuals and with the heritability of the trait. The density of markers had no effect when selecting with the genealogical coancestry fA, as expected, and, within the range of densities here studied no differences were detected in the genetic gains achieved by the genomic based estimates fV and fG. The most surprising result is that for a low density of markers, the genetic gain is larger performing selection based on fR. It must be noticed that the size for a region of homozygosity to be considered as such was kept constant and thus, a ROH of 100 contiguous markers covers a much longer stretch than for 10,100 marker per chromosome. This is also surprising as it has been pointed out that the longer the ROH, the more correlated ROH-based inbreeding is with genealogical inbreeding.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Mejora Genetica Animal, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria Madrid, Spain.

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.

No MeSH data available.


Related in: MedlinePlus