Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris)
4
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
Effective population size (N_e) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate N_e in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The N_e estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for N_e estimation, i.e. pair-wise r^2 values using a simple expectation of distance and r^2 values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise N_e estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average N_e estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past Ne at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant N_e reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase N_e, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.
Abstract
Effective population size (N_e) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate N_e in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The N_e estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for N_e estimation, i.e. pair-wise r^2 values using a simple expectation of distance and r^2 values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise N_e estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average N_e estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past Ne at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant N_e reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase N_e, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.
참고문헌 (46)
- AKC, "The complete dog book" (1998), Howell Book House
- Aspi, J., "Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population", Mol. Ecol, 15, pp.1561~1576 (2006)
- Bartley, D., "Use of linkage disequilibrium data to estimate effective size of hatchery and natural fish populations", Conserv. Biol, 6, pp.365~375 (1992)
- Beaumont, M. A., "Conservation genetics, In Handbook of Statistical Genetics", pp.779~812 (2003), Wiley
- Calboli, F. C. F., "Population structure and inbreeding from pedigree analysis of pure bred dogs", Genetics, 179, pp.593~601 (2008)
- Colleau, J. J., "Optimized management of genetic variability in selected pig populations", J. Anim. Breed. Genet, 125, pp.291~300 (2008)
- Crow, J. F., "An introduction to population genetics theory" (1970), Burgess Publishing
- Daetwyler, H. D., "Inbreeding in genome-wide selection", J. Anim. Breed. Genet, 124, pp.369~376 (2007)
- Duchev, Z., "Early warning system for loss of diversity in European livestock breeds", Archiv. Anim. Breed, 49, pp.521~531 (2006)
- Falconer, D. S., "Introduction to Quantitative Genetics, 4th ed" (1996), Longman Group Ltd
- "Secondary guidelines for development of national farm animal genetic resources management plans: Management of small populations at risk" (1998)[URL]
- "Secondary guidelines for development of national farm animal genetic resources management plans: Management of small populations at risk" (2000)[URL]
- Gutierrez, J. P., "Individual increase in inbreeding allows estimating effective sizes from pedigrees", Genet. Sel. Evol, 40, pp.359~378 (2008)
- Gutierrez, J. P., "Improving the estimation of realized effective population sizes in farm animals", J. Anim. Breed. Genet, 126, pp.327~332 (2009)
- 한국일, "A Study on Morphology and Behavior of the Sapsaree: A Korean native dog(Canis familiaris)", 한국동물자원과학회지, 52(6), pp.481~490 (2010), 한국동물자원과학회
- Hayes, B. J., "Novel multi locus measure of linkage disequilibrium to estimate past effective population size", Genome Res, 13, pp.635~643 (2003)
- Hill, W. G., "Estimation of effective population size from data on linkage disequilibrium", Genet. Res, 38, pp.209~216 (1981)
- Hill, W. G., "Linkage disequilibrium in finite populations", Theor. Appl. Genet, 38, pp.226~231 (1968)
- Lander, E. S., "Genetic dissection of complex traits", Science, 265, pp.2037~2048 (1994)
- Leberg, P., "Genetic approaches for estimating the effective size of populations", J. Wildl. Manage, 69, pp.1385~1399 (2005)
- Lewontin, R. C., "The interaction of selection and linkage. I. General considerations: heterotic models", Genetics, 49, pp.49~67 (1964)
- Lindblad-Toh, K., "Genome sequence, comparative analysis and haplotype structure of the domestic dog", Nature, 438, pp.803~819 (2005)
- Lou, X. Y., "The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree", Mamm. Genome, 14, pp.555~564 (2003)
- MacCluer, J. W., "Inbreeding and pedigree structure in Standardbred horses", J. Hered, 74, pp.394~399 (1983)
- Maignel, L., "Genetic variability of French dairy breeds estimated from pedigree information", Bulletin – International Bull Evaluation Service, 14, pp.49~54 (1996)
- Meuwissen, T. H. E., "Maximising the response of selection with a predefined rate of inbreeding", J. Anim. Sci, 75, pp.934~940 (1997)
- Meuwissen, T. H. E., "Genetic management of small populations: A review", Acta Agric. Scand. Section A. Anim. Sci, 59, pp.71~79 (2009)
- Meuwissen, T. H. E., "Prediction of total genetic value using genome-wide dense marker maps", Genetics, 157, pp.1819~1829 (2001)
- Nomura, T., "Interval estimation of the effective population size from heterozygote-excess in SNP markers", Biometrical Journal, 51, pp.996~1016 (2009)
- Nomura, T., "Inbreeding and effective population size of Japanese Black cattle", J. Anim. Sci, 79, pp.366~370 (2001)
- Ostrander, E. A., "Unleashing the canine genome", Genome Res, 10, pp.1271~1274 (2000)
- Randi, E., "Mitochondrial DNA variability in Italian and east European wolves: detecting the consequences of small population size and hybridization", Conserv. Biol, 14, pp.464~473 (2000)
- Rogers, C. A., "The international encyclopedia of dogs" (1995), Howell Book House
- Sanchez, L., "Minimizing inbreeding by managing genetic contributions across generations", Genetics, 164, pp.1589~1595 (2003)
- Sargolzaei, M., "CFC (Contribution, Inbreeding and Coancestry) Release 1.0. A software package for pedigree analysis and monitoring genetic diversity. Graduate School of Science and Technology", pp.950~2181 (2006), Niigata University
- Schwartz, M. K., "Review of DNA-based census and effective population size estimators", Anim. Conserv, 1, pp.293~299 (1998)
- Sutter, N. B., "Extensive and breed-specific linkage disequilibrium in Canis familiaris", Genome Res, 14, pp.2388~2396 (2004)
- Sved, J. A., "Linkage disequilibrium and homozygosity of chromosome segments in finite populations", Theor. Popul. Biol, 2, pp.125~141 (1971)
- Tenesa, A., "Recent human effective population size estimated from linkage disequilibrium", Genome Res, 17, pp.520~526 (2007)
- Uimari, P., "Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds", J. Anim. Sci, 89, pp.609~614 (2011)
- Wang, J., "Estimation of effective population sizes from data on genetic markers", Philos. Trans. R. Soc. B, 360, pp.1395~1409 (2005)
- Weir, B. S, "Effect of mating structure on variation in linkage disequilibrium", Genetics, 95, pp.477~488 (1980)
- Wilcox, B., "Atlas of Dog Breeds of the World" (1995), T. F. H. Publications
- Wright, S., "Evolution and the genetics of populations: The Theory of Gene Frequencies, Vol. II" (1969), University of Chicago Press
- Young, C. W., "Estimates of inbreeding and relationship among registered Holstein females in the Unites States", J. Dairy Sci, 79, pp.502~505 (1996)