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A genome-wide association study in large white and landrace pig populations for number piglets born alive.

Bergfelder-Drüing S, Grosse-Brinkhaus C, Lind B, Erbe M, Schellander K, Simianer H, Tholen E - PLoS ONE (2015)

Bottom Line: It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects.In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction.No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Science, Department of Animal Genetics, University of Bonn, Bonn, Germany.

ABSTRACT
The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

No MeSH data available.


Q-Q plots of all association studies for all breed clusters.
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pone.0117468.g005: Q-Q plots of all association studies for all breed clusters.

Mentions: In order to ensure the power and accuracy of GWAS, it is essential to take possible population stratifications [13,25,26] into consideration. Therefore, associations between SNP and NBA were estimated within the genetically more or less overlapping clusters. In addition, PC which condensed the genetic relationships between the animals was used in the statistical model as covariates to correct for existing population stratification. Depending on the cluster, different numbers of PC were required in order to avoid negative effects of population stratification on the validity of the GWAS analysis. The number of PC used in the analyses of various clusters ranged from 22 (LR_3b) to 372 (LW_1). Genomic inflation factors in all clusters were close to one (Table 2). Cluster specific Q-Q plots (Fig. 5) contain regression lines which were calculated by a linear regression of expected test statistics (independent variable) on observed test statistic (dependent variable). The slopes of these lines correspond to the calculated inflation factor, which is close to 1 in all clusters analysed. This shows that possibly existing stratifications of the populations do not adversely affect the validity of corresponding GWAS analysis.


A genome-wide association study in large white and landrace pig populations for number piglets born alive.

Bergfelder-Drüing S, Grosse-Brinkhaus C, Lind B, Erbe M, Schellander K, Simianer H, Tholen E - PLoS ONE (2015)

Q-Q plots of all association studies for all breed clusters.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4363374&req=5

pone.0117468.g005: Q-Q plots of all association studies for all breed clusters.
Mentions: In order to ensure the power and accuracy of GWAS, it is essential to take possible population stratifications [13,25,26] into consideration. Therefore, associations between SNP and NBA were estimated within the genetically more or less overlapping clusters. In addition, PC which condensed the genetic relationships between the animals was used in the statistical model as covariates to correct for existing population stratification. Depending on the cluster, different numbers of PC were required in order to avoid negative effects of population stratification on the validity of the GWAS analysis. The number of PC used in the analyses of various clusters ranged from 22 (LR_3b) to 372 (LW_1). Genomic inflation factors in all clusters were close to one (Table 2). Cluster specific Q-Q plots (Fig. 5) contain regression lines which were calculated by a linear regression of expected test statistics (independent variable) on observed test statistic (dependent variable). The slopes of these lines correspond to the calculated inflation factor, which is close to 1 in all clusters analysed. This shows that possibly existing stratifications of the populations do not adversely affect the validity of corresponding GWAS analysis.

Bottom Line: It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects.In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction.No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Science, Department of Animal Genetics, University of Bonn, Bonn, Germany.

ABSTRACT
The number of piglets born alive (NBA) per litter is one of the most important traits in pig breeding due to its influence on production efficiency. It is difficult to improve NBA because the heritability of the trait is low and it is governed by a high number of loci with low to moderate effects. To clarify the biological and genetic background of NBA, genome-wide association studies (GWAS) were performed using 4,012 Large White and Landrace pigs from herdbook and commercial breeding companies in Germany (3), Austria (1) and Switzerland (1). The animals were genotyped with the Illumina PorcineSNP60 BeadChip. Because of population stratifications within and between breeds, clusters were formed using the genetic distances between the populations. Five clusters for each breed were formed and analysed by GWAS approaches. In total, 17 different significant markers affecting NBA were found in regions with known effects on female reproduction. No overlapping significant chromosome areas or QTL between Large White and Landrace breed were detected.

No MeSH data available.