Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms
2
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
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 r2 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.
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 r2 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.
참고문헌 (27)
- Abecasis, G. R., "Extent and distribution of linkage disequilibrium in three genomic regions", Am. J. Hum. Genet, 68, pp.191~197 (2001)
- Ai, H., "Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers", PLoS ONE, 8, pp.e56001~ (2013)
- Chen, Y., "Volume measures for linkage disequilibrium", BMC Genet, 7, pp.54~ (2006)
- Duran, C., "Molecular genetic markers: Discovery, applications, data storage and visualization", Curr. Bioinform, 4, pp.16~27 (2009)
- Excoffier, L., "Arlequin (version 3.0): an integrated software package for population genetics data analysis", Evol. Bioinform. Online, 1, pp.47~50 (2005)
- Ficetola, G. F., "Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latastei", Mol. Ecol, 16, pp.1787~1797 (2007)
- Food and Agriculture Organization of the United Nations, "The state of the world’s animal genetic resources for food and agriculture – in brief" (2007)
- Giuffra, E., "The origin of the domestic pig: Independent domestication and subsequent introgression", Genetics, 154, pp.1785~1791 (2000)
- Hill, W. G., "Estimation of effective population size from data on linkage disequilibrium", Genet. Res, 38, pp.209~216 (1981)
- Larson, G., "Worldwide phylogeography of wild boar reveals multiple centers of pig domestication", Science, 307, pp.1618~1621 (2005)
- LiLiu, K., "PowerMarker: Integrated analysis environment for genetic marker analysis", Bioinformatics, 21, pp.2128~2129 (2005)
- Kijas, J. M., "A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome", J. Mol. Evol, 52, pp.302~308 (2001)
- Kim, K. S., "Genetic structure of Korean native pig using microsatellite markers", Kor. J. Genet, 24, pp.1~7 (2002)
- Kim, K. I., "Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA Dloop sequence polymorphism", Anim. Genet, 33, pp.19~25 (2002)
- Kim, T. H., "Genetic structure of pig breeds from Korea and China using microsatellite loci analysis", J. Anim. Sci, 83, pp.2255~2263 (2005)
- S.W. Kim, "QTL Scan for Meat Quality Traits Using High-density SNP Chip Analysis in Cross between Korean Native Pig and Yorkshire", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 24(9), pp.1184~1191 (2011), 아세아·태평양축산학회
- Nidup, K., "Genetic diversity of domestic pigs as revealed by microsatellites: A mini review", Genomics Quant. Genet, 2, pp.5~18 (2001)
- Nsengimana, J., "Linkage disequilibrium in the domesticated pig", Genetics, 166, pp.1395~1404 (2004)
- Park, B. Y., "Effect of fiber type on postmortem proteolysis in longisimus muscle of Landrace and Korean native black pigs", Meat Sci, 77, pp.482~491 (2007)
- Pritchard, J. K., "Inference of population structure using multilocus genotype data", Genetics, 155, pp.945~959 (2000)
- Ramos, A. M., "Design of a high-density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology", PLoS One, 4, pp.e6524~ (2009)
- Reynolds, J., "Estimation of the coancestry coefficient: basis for a short-term genetic distance", Genetics, 105, pp.767~779 (1983)
- Suh, Y., "SNP discovery in associating genetic variation with human disease phenotypes", Mutat. Res. Fundam. Mol. Mech. Mutagen, 573, pp.41~53 (2005)
- Weir, B. S., "Estimating F-statistics for the analysis of population structure", Evolution, 38, pp.1358~1370 (1984)
- Yang, S. L., "Genetic variation and relationships of eighteen Chinese indigenous pig breeds", Genet. Sel. Evol, 35, pp.657~671 (2003)
- Yeo, J. S., "Utilization of DNA marker-assisted selection in Korean native animals", Biotechnol. Bioprocess Eng, 5, pp.71~78 (2000)