- Volume 33 Issue 1
DOI QR Code
A double-labeling marker-based method for estimating inbreeding and parental genomic components in a population under conservation
- Li, Wenting (College of Animal Science and Technology, China Agricultural University) ;
- Zhang, Mengmeng (College of Animal Science and Technology, China Agricultural University) ;
- Wang, Kejun (College of Animal Sciences and Veterinary Medicine, Henan Agricultural University) ;
- Lu, Yunfeng (School of Life Science and Technology, Nanyang Normal University) ;
- Tang, Hui (College of Animal Science and Veterinary Medicine, Shandong Agricultural University) ;
- Wu, Keliang (College of Animal Science and Technology, China Agricultural University)
- Received : 2019.01.12
- Accepted : 2019.06.11
- Published : 2020.01.01
Objective: The objective of a conservation program is to maintain maximum genetic diversity and preserve the viability of a breed. However, the efficiency of a program is influenced by the ability to accurately measure and predict genetic diversity. Methods: To examine this question, we conducted a simulation in which common measures (i.e. heterozygosity) and novel measures (identity-by-descent probabilities and parental genomic components) were used to estimate genetic diversity within a conserved population using double-labeled single nucleotide polymorphism markers. Results: The results showed that the accuracy and sensitivity of identity-by-state probabilities and heterozygosity were close to identity by descent (IBD) probabilities, which reflect the true genetic diversity. Expected heterozygosity most closely aligned with IBD. All common measures suggested that practices used in the current Chinese pig conservation program result in a ~5% loss in genetic diversity every 10 generations. Parental genomic components were also analyzed to monitor real-time changes in genomic components for each male and female ancestor. The analysis showed that ~7.5% of male families and ~30% of female families were lost every 5 generations. After 50 generations of simulated conservation, 4 male families lost ~50% of their initial genomic components, and the genomic components for 24.8% of the female families were lost entirely. Conclusion: In summary, compared with the true genetic diversity value obtained using double-labeled markers, expected heterozygosity appears to be the optimal indicator. Parental genomic components analysis provides a more detailed picture of genetic diversity and can be used to guide conservation management practices.
Supported by : Natural Science Foundation of Henan Province of China
- Frankham R, Ballou JD, Briscoe DA. Introduction to conservation genetics. Cambridge, UK: Cambridge University Press; 2002.
- Oldenbroek JK. Utilization and conservation of farm animal genetic resources. Wageningen, The Netherlands: Wageningen Academic Publishers; 2007.
- Lush JL. Chance as a cause of changes in gene frequency within pure breeds of livestock. Am Nat 1946;80:318-42. https://doi. org/10.1086/281448 https://doi.org/10.1086/281448
- Falconer DS, Mackay TFC. Introduction to quantitative genetics. Essex, UK: Longman Group; 1996.
- Engelsma KA, Calus MP, Bijma P, Windig JJ. Estimating genetic diversity across the neutral genome with the use of dense marker maps. Genet Sel Evol 2010;42:12. https://doi.org/10.1186/1297-9686-42-12 https://doi.org/10.1186/1297-9686-42-12
- Silio L, Fernandez A, Mercade A, et al. Measuring inbreeding in a closed pig strain from high-density SNPs genotypes. In: Proceedings of the 9th World Congress Genetics Applied Livestock Production Congress 2010; 2010 August 1-6: Leipzig, Germany.
- Fernandez J, Villanueva B, Pong-Wong R, Toro MA. Efficiency of the use of pedigree and molecular marker information in conservation programs. Genetics 2005;170:1313-21. https://doi.org/10.1534/genetics.104.037325 https://doi.org/10.1534/genetics.104.037325
- Carothers AD, Rudan I, Kolcic I, et al. Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Ann Hum Genet 2006;70:666-76. https://doi.org/10.1111/j.1469-1809.2006.00263.x https://doi.org/10.1111/j.1469-1809.2006.00263.x
- de Cara MA, Fernandez J, Toro MA, Villanueva B. Using genome-wide information to minimize the loss of diversity in conservation programmes. J Anim Breed Genet 2011;128:456-64. https://doi.org/10.1111/j.1439-0388.2011.00971.x https://doi.org/10.1111/j.1439-0388.2011.00971.x
- Daetwyler HD, Schenkel FS, Robinson JAB. Relationship of multilocus homozygosity and inbreeding in Canadian Holstein sires. Can J Anim Sci 2006;86:578-9.
- Gomez-Romano F, Villanueva B, de Cara MA, Fernandez J. Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size. Genet Sel Evol 2013;45:38. https://doi.org/10.1186/1297-9686-45-38 https://doi.org/10.1186/1297-9686-45-38
- Lu Y, Li H, Wu K, Wu C. Dynamic change of genetic diversity in conserved populations with different initial genetic architectures. J Integr Agric 2013;12:1225-33. https://doi.org/10.1016/S2095-3119(13)60439-6 https://doi.org/10.1016/S2095-3119(13)60439-6
- Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 1973;70:3321-3. https://doi.org/10.1073/pnas.70.12.3321 https://doi.org/10.1073/pnas.70.12.3321
- Toro MA, Caballero A. Characterization and conservation of genetic diversity in subdivided populations. Philos Trans R Soc Lond B Biol Sci 2005;360:1367-78. https://doi.org/10.1098/rstb.2005.1680 https://doi.org/10.1098/rstb.2005.1680
- Ai H, Huang L, Ren J. Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers. PLoS ONE 2013;8:e56001. https://doi.org/10.1371/journal.pone.0056001 https://doi.org/10.1371/journal.pone.0056001
- Windig JJ, Meuwissen THE. Rapid haplotype reconstruction in pedigrees with dense marker maps. J Anim Breed Genet 2004;121:26-39. https://doi.org/10.1046/j.1439-0388.2003.00439.x https://doi.org/10.1046/j.1439-0388.2003.00439.x
- Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76-82. https://doi.org/10.1016/j.ajhg.2010.11.011 https://doi.org/10.1016/j.ajhg.2010.11.011
- Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 2014;14:209-14. https://doi.org/10.1111/1755-0998.12157 https://doi.org/10.1111/1755-0998.12157
- Rodriguez De Cara MA, Villanueva B, Angel Toro M, Fernandez J. Using genomic tools to maintain diversity and fitness in conservation programmes. Mol Ecol 2013;22:6091-9. https://doi. org/10.1111/mec.12560 https://doi.org/10.1111/mec.12560
- Gomez-Romano F, Villanueva B, Solkner J, et al. The use of coancestry based on shared segments for maintaining genetic diversity. J Anim Breed Genet 2016;133:357-65. https://doi.org/10.1111/jbg.12213 https://doi.org/10.1111/jbg.12213
- Groeneveld LF, Lenstra JA, Eding H, et al. Genetic diversity in farm animals--a review. Anim Genet 2010;41(Suppl 1):6-31. https://doi.org/10.1111/j.1365-2052.2010.02038.x https://doi.org/10.1111/j.1365-2052.2010.02038.x
- Engelsma KA, Veerkamp RF, Calus MP, Bijma P, Windig JJ. Pedigree- and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle. J Anim Breed Genet 2012;129:195-205. https://doi.org/10.1111/j.1439-0388.2012.00987.x https://doi.org/10.1111/j.1439-0388.2012.00987.x
- FAO. Molecular genetic characterization of animal genetic resources. Rome, Italy: FAO Animal Production and Health Guidelines; 2011.
- FAO. Draft guidelines on in vivo conservation of animal genetic resources. Commission on Genetic Resources for Food and Agriculture. Rome, Italy: FAO; 2012.
- Bosse M, Megens HJ, Madsen O, et al. Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations. Genome Res 2015;25:970-81. https://doi.org/10.1101/gr.187039.114 https://doi.org/10.1101/gr.187039.114
- Hall SJ, Lenstra JA, Deeming DC, European Cattle Genetic Diversity Consortium. Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds. J Anim Breed Genet 2012;129:218-25. https://doi.org/10.1111/j.1439-0388.2011.00949.x https://doi.org/10.1111/j.1439-0388.2011.00949.x