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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

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 , where fA is the genealogical coancestry at each generation and fA(7) is the value before selection starts.
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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 , where fA is the genealogical coancestry at each generation and fA(7) is the value before selection starts.

Mentions: In Figure 4 we show a similar plot for the change in pedigree based coancestry obtained under each selection scenario. All cases studied showed that the three genomic based selection led to lower increases in pedigree-based coancestry and the differences between the selection based on genomic relationships are hardly noticeable. The results are very similar for fV and fG based BLUPs on genealogical coancestry and it seems that fR-based BLUP leads to slightly larger genealogical coancestries.


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)

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 , where fA is the genealogical coancestry at each generation and fA(7) is the value before selection starts.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

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 , where fA is the genealogical coancestry at each generation and fA(7) is the value before selection starts.
Mentions: In Figure 4 we show a similar plot for the change in pedigree based coancestry obtained under each selection scenario. All cases studied showed that the three genomic based selection led to lower increases in pedigree-based coancestry and the differences between the selection based on genomic relationships are hardly noticeable. The results are very similar for fV and fG based BLUPs on genealogical coancestry and it seems that fR-based BLUP leads to slightly larger genealogical coancestries.

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