- Volume 26 Issue 6
DOI QR Code
Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data
- Tang, G.Q. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Xue, J. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Lian, M.J. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Yang, R.F. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Liu, T.F. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Zeng, Z.Y. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Jiang, A.A. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Jiang, Y.Z. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Zhu, L. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Bai, L. (College of Animal Science and Technology, Sichuan Agricultural University) ;
- Wang, Z. (Department of Agricultural, Food and Nutritional Science, University of Alberta) ;
- Li, X.W. (College of Animal Science and Technology, Sichuan Agricultural University)
- 투고 : 2012.11.15
- 심사 : 2013.01.28
- 발행 : 2013.06.01
The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD), Landrace (CL) and Yorkshire (CY) swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.
- Alves, E., C. Ovilo, M. C. Rodriguez and L. Silio. 2003. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim. Genet. 34:319-324. https://doi.org/10.1046/j.1365-2052.2003.01010.x
- Berg, P. 2003. EVA version 1.4. Evolutionary algorithm for mate selection. User's guide. Danish Institute of Agricultural Sciences, Foulum, Denmark.
- Boichard, D., L. Maignel and E. Verrier. 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Sel. Evol. 29:5-23. https://doi.org/10.1186/1297-9686-29-1-5
- Boichard, D. 2002. PEDIG: a fortran package for pedigree analysis suited for large populations. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, 19-23. INRA, Castanet-Tolosan, France.
- Barker, J. S. F. 2001. Conservation and management of genetic diversity: a domestic animal perspective. Can. J. For. Res. 31:588-595. https://doi.org/10.1139/x00-180
- Caballero, A. and M. A. Toro. 2000. Interrelations between effective population size and other tools for management of conserved populations. Genet. Res. 75:331-343. https://doi.org/10.1017/S0016672399004449
- FAO. 2000. Secondary guidelines for development of farm animal genetic resources management plans. Management of small populations at risk. FAO, Rome, Italy.
- FAO. 2007. The state of the world's animal genetic resources for food and agriculture. UN Food and Agric. Org. http://www.fao.org/docrep/010/a1250e/a1250e00.htm. Accessed Aug. 19, 2009.
- Falconer, D. S. and T. F. C. Mackay. 1996. Introduction to quantitative genetics. Longman, Harlow.
- Fernandez, J., B. Villanueva, R. Pong-Wong and M. A. Toro. 2005. Efficiency of the use of pedigree and molecular marker information in conservation programs. Genetics 170:1313-1321. https://doi.org/10.1534/genetics.104.037325
- Fernandes, S. D., S. Malovrh, M. Kovac and V. A. P. Cadavez. 2010. Study of genetic diversity of Bísaro pigs breed by pedigree analysis. Uasvm Iasi Faculty of Animal Sciences 53:178-182.
- Gutierrez, J. P. and F. Goyache. 2005. A note on ENDOG: a computer program for analysing pedigree information. J. Anim. Breed. Genet. 122:172-176. https://doi.org/10.1111/j.1439-0388.2005.00512.x
- Gutierrez, J. P., I. Cervantes, A. Molina, M. Valera and F. Goyache. 2008. Individual increase in inbreeding allows estimating realised effective sizes from pedigrees. Genet. Sel. Evol. 40:359-378. https://doi.org/10.1186/1297-9686-40-4-359
- Gutierrez, J. P., I. Cervantes and F. Goyache. 2009. Improving the estimation of realised effective population sizes in farm animals. J. Anim. Breed. Genet. 126:327-332. https://doi.org/10.1111/j.1439-0388.2009.00810.x
- Honda, T., T. Nomura, Y. Yamaguchi and F. Mukai. 2004. Monitoring of genetic diversity in the Japanese Black cattle population by the use of pedigree information. J. Anim. Breed. Genet. 121:242-252. https://doi.org/10.1111/j.1439-0388.2004.00452.x
- Lacy, R. C. 1987. Loss of genetic diversity from managed populations. Interacting effects of drift, mutation, immigration, selection and population subdivision. Conserv. Biol. 1:143-158. https://doi.org/10.1111/j.1523-1739.1987.tb00023.x
- Lacy, R. C. 1989. Analysis of founder representation in pedigrees: Founder equivalents and Founder genome equivalents. Zoo Biol. 8:111-123. https://doi.org/10.1002/zoo.1430080203
- Lacy, R. C. 1995. Classification of genetic terms and their use in the management of captive populations. Zoo Biol. 14:565-578. https://doi.org/10.1002/zoo.1430140609
- MacCluer, J. W., A. J. Boyce, B. Dyke, L. R. Weitkamp, D. W. Pfennig and C. J. Parsons. 1983. Inbreeding and pedigree structure in Standardbred horses. J. Hered. 74:394-399.
- Maignel, L., D. Boichard and E. Verrier. 1996. Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bull 14:49-54.
- Melka, M. G., K. Stachowicz, M. Sargolzaei, F. Miglior and F. S. Schenkel. 2008. Assessment of genetic diversity in Canadian colored dairy breeds using pedigree data. Proc. Canadian Soc. Anim. Sci. Annu. Mtg., Guelph, Ontario, Canada.
- Melka M. G. and F. Schenkel. 2010. Analysis of genetic diversity in four Canadian swine breeds using pedigree data. Can. J. Anim. Sci. 90:331-340. https://doi.org/10.4141/CJAS10002
- Meuwissen, T. H. E. 1997. Maximizing the response of selection with predefined rate of inbreeding. J. Anim. Sci. 75:934-940.
- Ruane, J. 2000. A framework for prioritizing domestic animal breeds for conservation purposes at the national level: A Norwegian case study. Conserv. Biol. 14:1385-1393. https://doi.org/10.1046/j.1523-1739.2000.99276.x
- Sargolzaei, M., H. Iwaisaki and J. J. Colleau. 2005. A fast algorithm for computing inbreeding coefficients in large populations. J. Anim. Breed. Genet. 122:325-331. https://doi.org/10.1111/j.1439-0388.2005.00538.x
- Sargolzaei, M., H. Iwaisaki and J. J. Colleau. 2006. CFC: A tool for monitoring genetic diversity. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production. 27-28, Belo Horizonte, Brazil.
- Simianer, H. 2005. Using expected allele number as objective function to design between and within breed conservation of farm animal biodiversity. J. Anim. Breed. Genet. 122:177-187. https://doi.org/10.1111/j.1439-0388.2005.00523.x
- Sorensen, A. C., M. K. Sorensen and P. Berg. 2005. Inbreeding in Danish dairy cattle. J. Dairy Sci. 88:1865-1872. https://doi.org/10.3168/jds.S0022-0302(05)72861-7
- Uimari, P. and M. Tapio. 2010. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J. Anim. Sci. 89:609-614.
- Vicente, A. A., M. I. Carolino, M. C. O. Sousa, C. Ginja, F. S. Silva, A. M. Martinez, J. L. Vega-Pla, N. Carolino and L. T. Gama. 2008. Genetic diversity in native and commercial breeds of pigs in Portugal assessed by microsatellites. J. Anim. Sci. 86:2496-2507. https://doi.org/10.2527/jas.2007-0691
- Welsh, C. S., T. S. Stewart, C. Schwa and H. D. Blackburn. 2010. Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation. J. Anim. Sci. 88:1610-1618. https://doi.org/10.2527/jas.2009-2537
- Woolliams, J. 2007. Genetic contributions and inbreeding. Pages in 147-165 in K. Oldenbroek, ed. Utilization and conservation of farm animal genetic resources Wageningen Academic Publishers, Wageningen, the Netherlands.
- Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny vol.48, pp.1, 2016, https://doi.org/10.1186/s12711-016-0269-y
- Tracing the breeding farm of domesticated pig using feature selection (Sus scrofa) vol.30, pp.11, 2017, https://doi.org/10.5713/ajas.17.0561