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Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms.

Edea Z, Kim SW, Lee KT, Kim TH, Kim KS - Asian-australas. J. Anim. Sci. (2014)

Bottom Line: Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds.The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity.Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Suwon 441-706, Korea .

ABSTRACT
Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at r (2) 0.3, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

No MeSH data available.


Related in: MedlinePlus

Summary of estimate plots of Q for K = 5 in the five pig breeds. Each individual is represented by a single column divided into K colored segments, where K is the number of clusters assumed, with lengths proportional to each of the K inferred clusters. Black lines separate the populations indicated below the figure.
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f2-ajas-27-9-1263: Summary of estimate plots of Q for K = 5 in the five pig breeds. Each individual is represented by a single column divided into K colored segments, where K is the number of clusters assumed, with lengths proportional to each of the K inferred clusters. Black lines separate the populations indicated below the figure.

Mentions: The patterns of population structure were investigated using Structure and PCA. As shown in Figure 1, principal components one (PC1) and principal components two (PC2) explained approximately 35.06% (Eigenvalue = 7.89) and 25.20% (Eigenvalue = 5.67) of the total variation, respectively. The results indicate clear separations of DU and YK from the remaining breeds by PC1 and PC2, respectively. Excepting 13% of the sampled individual animals, DU pigs were separately clustered from the remaining breeds. The Bayesian approach of Structure analysis for inferred populations with K values from 2 to 5 is shown in Figure 2. When K = 2, with the exception of the DU animals, all of the breeds shared a common cluster (91%). Only 13.20% of KNP and 18.6% of LR individuals shared common ancestry with DU. Surprisingly, when K = 3, over 86% of KNP individuals were in a common cluster with YK and LR, while LR was the most admixed breed, with 60%, 24%, and 16% of its individuals in clusters with YK, BK, and DU, respectively. When four clusters were inferred, the majority (91%) of the breeds were assigned into separate groups, with the exception of LR, which showed consistent admixture with YK (43%) and BK (25%). When K = 4 or 5, approximately 91% of the KNP individuals were clustered into a separate group (Table 3).


Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms.

Edea Z, Kim SW, Lee KT, Kim TH, Kim KS - Asian-australas. J. Anim. Sci. (2014)

Summary of estimate plots of Q for K = 5 in the five pig breeds. Each individual is represented by a single column divided into K colored segments, where K is the number of clusters assumed, with lengths proportional to each of the K inferred clusters. Black lines separate the populations indicated below the figure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150192&req=5

f2-ajas-27-9-1263: Summary of estimate plots of Q for K = 5 in the five pig breeds. Each individual is represented by a single column divided into K colored segments, where K is the number of clusters assumed, with lengths proportional to each of the K inferred clusters. Black lines separate the populations indicated below the figure.
Mentions: The patterns of population structure were investigated using Structure and PCA. As shown in Figure 1, principal components one (PC1) and principal components two (PC2) explained approximately 35.06% (Eigenvalue = 7.89) and 25.20% (Eigenvalue = 5.67) of the total variation, respectively. The results indicate clear separations of DU and YK from the remaining breeds by PC1 and PC2, respectively. Excepting 13% of the sampled individual animals, DU pigs were separately clustered from the remaining breeds. The Bayesian approach of Structure analysis for inferred populations with K values from 2 to 5 is shown in Figure 2. When K = 2, with the exception of the DU animals, all of the breeds shared a common cluster (91%). Only 13.20% of KNP and 18.6% of LR individuals shared common ancestry with DU. Surprisingly, when K = 3, over 86% of KNP individuals were in a common cluster with YK and LR, while LR was the most admixed breed, with 60%, 24%, and 16% of its individuals in clusters with YK, BK, and DU, respectively. When four clusters were inferred, the majority (91%) of the breeds were assigned into separate groups, with the exception of LR, which showed consistent admixture with YK (43%) and BK (25%). When K = 4 or 5, approximately 91% of the KNP individuals were clustered into a separate group (Table 3).

Bottom Line: Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds.The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity.Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Suwon 441-706, Korea .

ABSTRACT
Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at r (2) 0.3, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

No MeSH data available.


Related in: MedlinePlus