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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

Histograms of the coancestries at generation 6 right before selection. Top row shows the histogram for genealogical coancestry fA for 10, 30, and 50 individuals from left to right. Similarly, the second row shows the histogram for molecular marker-by-marker coancestry fG. The third row shows the histograms for segment-based coancestry fR, 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 fV, for N = 10, N = 30, and N = 50 from left to right. The variance of each histogram is given within each plot.
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Figure 1: Histograms of the coancestries at generation 6 right before selection. Top row shows the histogram for genealogical coancestry fA for 10, 30, and 50 individuals from left to right. Similarly, the second row shows the histogram for molecular marker-by-marker coancestry fG. The third row shows the histograms for segment-based coancestry fR, 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 fV, for N = 10, N = 30, and N = 50 from left to right. The variance of each histogram is given within each plot.

Mentions: Most likely, the differences in our results are going to be due to the distribution of coancestries, as the different selection strategies here performed are based on the matrix of relationships between individuals. We show in Figure 1 the distributions for the four measures of relationships prior to selection and give the variance within each figure. There we can see how the shape of the distribution of the genealogical coancestry is multimodal, given the sparse nature of the genealogical coancestry matrix and its distribution has the largest variance of all coancestry matrices, as well as the lowest mean. The distribution of coancestries fV and fG are fairly similar, the first one having a lower mean and a slightly larger variance although both distributions have a very small variance. Lastly, the distribution of coancestries fR has a mean considerably lower than the other genomic coancestries fV and fG and a substantially larger variance.


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)

Histograms of the coancestries at generation 6 right before selection. Top row shows the histogram for genealogical coancestry fA for 10, 30, and 50 individuals from left to right. Similarly, the second row shows the histogram for molecular marker-by-marker coancestry fG. The third row shows the histograms for segment-based coancestry fR, 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 fV, for N = 10, N = 30, and N = 50 from left to right. The variance of each histogram is given within each plot.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Histograms of the coancestries at generation 6 right before selection. Top row shows the histogram for genealogical coancestry fA for 10, 30, and 50 individuals from left to right. Similarly, the second row shows the histogram for molecular marker-by-marker coancestry fG. The third row shows the histograms for segment-based coancestry fR, 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 fV, for N = 10, N = 30, and N = 50 from left to right. The variance of each histogram is given within each plot.
Mentions: Most likely, the differences in our results are going to be due to the distribution of coancestries, as the different selection strategies here performed are based on the matrix of relationships between individuals. We show in Figure 1 the distributions for the four measures of relationships prior to selection and give the variance within each figure. There we can see how the shape of the distribution of the genealogical coancestry is multimodal, given the sparse nature of the genealogical coancestry matrix and its distribution has the largest variance of all coancestry matrices, as well as the lowest mean. The distribution of coancestries fV and fG are fairly similar, the first one having a lower mean and a slightly larger variance although both distributions have a very small variance. Lastly, the distribution of coancestries fR has a mean considerably lower than the other genomic coancestries fV and fG and a substantially larger variance.

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