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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

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 .
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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 .

Mentions: We show in Figure 3 results for the changes in each of the four measures used of coancestry with each selection scenario. We have used a logarithmic scale as overall, the differences between genealogical based selection and genomic based selection were very large. That is, line “A” shows the results for genealogical coancestry resulting from selecting based on this coancestry fA and so on for scenarios G, R, and V. The results for inbreeding are not shown as they display a very similar pattern. In order to better appreciate the differences between the four measures of coancestries, we show log[(1 − f)/(1 − f7)] in Figure 3. In this way, we compare the speed of increase in each average coancestry scaled with their values at generation 7 (f7), right before selection started. The increase in genealogical coancestry (the decay in this log scale) is the largest, followed by ROH-based coancestry. Changes in fV and fG are hardly distinguishable and very similar to fR for small heritability. The smaller the population, the larger the increase in any measure of coancestry. The differences in fG and fV are hardly different as heritability increases from h2 = 0.25 to h2 = 0.5.


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)

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

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

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 .
Mentions: We show in Figure 3 results for the changes in each of the four measures used of coancestry with each selection scenario. We have used a logarithmic scale as overall, the differences between genealogical based selection and genomic based selection were very large. That is, line “A” shows the results for genealogical coancestry resulting from selecting based on this coancestry fA and so on for scenarios G, R, and V. The results for inbreeding are not shown as they display a very similar pattern. In order to better appreciate the differences between the four measures of coancestries, we show log[(1 − f)/(1 − f7)] in Figure 3. In this way, we compare the speed of increase in each average coancestry scaled with their values at generation 7 (f7), right before selection started. The increase in genealogical coancestry (the decay in this log scale) is the largest, followed by ROH-based coancestry. Changes in fV and fG are hardly distinguishable and very similar to fR for small heritability. The smaller the population, the larger the increase in any measure of coancestry. The differences in fG and fV are hardly different as heritability increases from h2 = 0.25 to h2 = 0.5.

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