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Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

Saura M, Fernández A, Rodríguez MC, Toro MA, Barragán C, Fernández AI, Villanueva B - PLoS ONE (2013)

Bottom Line: Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data.However, estimates of effective population size obtained from changes in coancestry or inbreeding differed.Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.

ABSTRACT
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

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Related in: MedlinePlus

Predictions of SNP-based molecular coancestry (fM) and genealogical coancestry (fG). (A) Predictions of SNP-based molecular coancestry from genealogical coancestry. (B) Predictions of genealogical coancestry from molecular coancestry. The dataset included the 219 Guadyerbas animals with SNP genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations (including and excluding self-coancestries) are indicated.
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pone-0078314-g002: Predictions of SNP-based molecular coancestry (fM) and genealogical coancestry (fG). (A) Predictions of SNP-based molecular coancestry from genealogical coancestry. (B) Predictions of genealogical coancestry from molecular coancestry. The dataset included the 219 Guadyerbas animals with SNP genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations (including and excluding self-coancestries) are indicated.

Mentions: In order to investigate the accuracy of predicting genealogical coancestry from genome-wide data we performed regressions of Ln(1−fG) on Ln(1−fM). Similarly, the accuracy of predicting molecular coancestry from genealogical data was investigated by performing regressions of Ln(1−fM) on Ln(1−fG). Transforming f to Ln(1−f) permits a meaningful comparison between molecular and genealogical coefficients, given that correcting for base population allele frequencies is not possible. The results show that genealogical coancestry was a very good predictor of molecular coancestry (slope = 0.99 and 0.98 including or not self-coancestries, respectively) as expected, but also, and contrary to what it has been observed in previous studies using microsatellites, molecular coancestry was very accurate in predicting genealogical coancestry (slope = 0.86 and 0.77, including or not self-coancestries, respectively; Figure 2).


Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

Saura M, Fernández A, Rodríguez MC, Toro MA, Barragán C, Fernández AI, Villanueva B - PLoS ONE (2013)

Predictions of SNP-based molecular coancestry (fM) and genealogical coancestry (fG). (A) Predictions of SNP-based molecular coancestry from genealogical coancestry. (B) Predictions of genealogical coancestry from molecular coancestry. The dataset included the 219 Guadyerbas animals with SNP genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations (including and excluding self-coancestries) are indicated.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3814548&req=5

pone-0078314-g002: Predictions of SNP-based molecular coancestry (fM) and genealogical coancestry (fG). (A) Predictions of SNP-based molecular coancestry from genealogical coancestry. (B) Predictions of genealogical coancestry from molecular coancestry. The dataset included the 219 Guadyerbas animals with SNP genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations (including and excluding self-coancestries) are indicated.
Mentions: In order to investigate the accuracy of predicting genealogical coancestry from genome-wide data we performed regressions of Ln(1−fG) on Ln(1−fM). Similarly, the accuracy of predicting molecular coancestry from genealogical data was investigated by performing regressions of Ln(1−fM) on Ln(1−fG). Transforming f to Ln(1−f) permits a meaningful comparison between molecular and genealogical coefficients, given that correcting for base population allele frequencies is not possible. The results show that genealogical coancestry was a very good predictor of molecular coancestry (slope = 0.99 and 0.98 including or not self-coancestries, respectively) as expected, but also, and contrary to what it has been observed in previous studies using microsatellites, molecular coancestry was very accurate in predicting genealogical coancestry (slope = 0.86 and 0.77, including or not self-coancestries, respectively; Figure 2).

Bottom Line: Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data.However, estimates of effective population size obtained from changes in coancestry or inbreeding differed.Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.

ABSTRACT
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

Show MeSH
Related in: MedlinePlus