Genomics applied to management strategies in conservation programmes

Livestock Science

Volumn 166, Issue 1, 2014, Pages 48-53

  Toro, Miguel A ^a   Villanueva, Beatriz ^b   Fernández, Jesús ^b  

^a UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^b INIA   (Spain)

Author keywords

De introgression; Genetic management; IBD and IBS; Molecular coancestry

Indexed keywords

EID: 84905595319     PISSN: 18711413     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.livsci.2014.04.020     Document Type: Article

References (39)

1. Amador C., Fernández J., Meuwissen T.H.E. Advantages of using molecular coancestry in the removal of introgressed genetic information. Genet. Sel. Evol. 2013, 45:13.
2. Amador, C., Hayes, B.J., Daetwyler, H.D., 2014. Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds. Evol. Appl. 10.1111/eva.12113.
3. Amador C., Toro M.A., Fernández J. Removing exogenous information using pedigree data. Conserv. Genet. 2011, 12:1565-1573.
4. Amador C., Toro M.A., Fernández J. Using marker information to remove introgressed genetic background. PLoS One 2012, 7(11):e49409.
5. Caballero A., Keightley P. A pleiotropic nonadditive model of variation in quantitative traits. Genetics 1994, 138:883-900.
6. Caballero A., Toro M.A. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet. Res. 2000, 75:331-343.
7. de Cara M.A.R., Fernández J., Toro M.A., Villanueva B. Using genome-wide information to minimize the loss of diversity in conservation programmes. J. Anim. Breed. Genet. 2011, 128:456-464.
8. de Cara M.A.R., Villanueva B., Toro M.A., Fernández J. Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings. Heredity 2013, 110:530-537.
9. de Cara M.A.R., Villanueva B., Toro M.A., Fernández J. Using genomic tools to maintain diversity and fitness in conservation programmes. Mol. Ecol. 2013, 22:6091-6099.
10. Engelsma K.A., Veerkamp R.F., Calus M.P.L., Windig J.J. Consequences for diversity when prioritizing animals for conservation with pedigree or genomic information. J. Anim. Breed. Genet. 2011, 128:473-481.
11. Fernández J., Clemente I., Amador C., Membrillo A., Azor P., Molina A. Use of different sources of information in the recovery and genetic management of endangered populations: example on the extreme case of Iberian pig Dorado strain. Livest. Sci. 2012, 149:282-288.
12. Fernández J., Villanueva B., Pong-Wong R., Toro M.A. Efficiency of the use of pedigree and molecular marker information in conservation programs. Genetics 2005, 170:1313-1321.
13. Garcia-Cortes L.A., Legarra A., Chevalet C., Toro M.A. Variance and covariance of actual relationships between relatives at one locus. PLoS One 2013, 8(2):e57003.
14. Garcia-Dorado A., Caballero A. On the average degree of dominance of deleterious spontaneous mutations. Genetics 2000, 155:1991-2001.
15. Gómez-Romano F., Villanueva B., de Cara M.A.R., Fernández J. Maintaining genetic diversity using molecular coancestry: the effect of marker density and effective population size. Genet. Sel. Evol. 2013, 45:38.
16. Grundy B., Villanueva B., Woolliams J.A. Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development. Genet. Res. Camb. 1998, 72:159-168.
17. Gusev A., Lowe J.K., Stoffel M., Daly M.J., Altshuler D., Breslow J.L., Friedman J.M., Pe'er I. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 2009, 19:318-326.
18. Keller M.C., Simonson M.A., Ripke S., Neale B.M., Gejman P.V., Howrigan D.P., et al. Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoS Genet. 2012, 8(4):e1002656.
19. Keller M.C., Visscher P.M., Goddard M.E. Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics 2011, 189:237-249.
20. Malécot G. Les mathématiques de l'hérédité 1948, Masson.
21. McQuillan R., Leutenegger A.L., Abdel-Rahman R., Franklin C.S., Pericic M., Barac-Lauc L., et al. Runs of homozygosity in European populations. Am. J. Hum. Genet. 2008, 83:359-372.
22. Meuwissen T.H.E. Maximizing the response of selection with a predefined rate of inbreeding. J. Anim. Sci. 1997, 75:934-940.
23. Meuwissen T.H.E., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829.
24. Meuwissen T.H.E., Hayes B.J., Goddard M.E. Accelerating improvement of livestock with genomic selection. Annu. Rev. Anim. Biosci. 2013, 1:221-237.
25. Mukai T., Chigusa S.I., Mettler L.E., Crow J.F. Mutation rate and dominance of genes affecting viability in Drosophila melanogaster. Genetics 1972, 72:333-355.
26. Nei M. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 1973, 70:3321-3323.
27. Pemberton T.J., Absher D., Feldman M.W., Myers R.M., Rosenberg N.A., Li J.Z. Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet. 2012, 91:275-292.
28. Powell J.E., Visscher P.M., Goddard M.E. Reconciling the analysis of IBD and IBS in complex trait studies. Nat. Rev. Genet. 2010, 11:800-805.
29. Roughsedge T., Pong-Wong R., Woolliams J.A., Villanueva B. Restricting coancestry and inbreeding at a specific position on the genome by using optimised selection. Genet. Res. 2008, 90:199-208.
30. Saura M., Fernández A., Rodríguez M.C., Toro M.A., Barragán C., Fernández A.I., Villanueva B. Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs. PLoS One 2013, 8(10):e78314.
31. Saura, M., Fernández, A., Varona, L., Fernández, A.I., Toro, M.A., Rodríguez, M.C., Barragán, C.,Villanueva, B., 2013b. Genome-wide estimates of coancestry and inbreeding depression in an endangered strain of Iberian pigs. In: Proceedings of the 64th Annual Meeting of the European Association for Animal Production (EAAP), August 26-30. Nantes, France.
32. Slate J., David P., Dodds K.G., Veenvliet B.A., Glass B.C., Broad T.E., McEwan J.C. Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity 2004, 93:255-265.
33. Toro M.A., Barragan C., Ovilo C., Rodriganez J., Rodriguez C., Silió L. Estimation of coancestry in Iberian pigs using molecular markers. Conserv. Genet. 2002, 3:309-320.
34. Toro M.A., Fernández J., Caballero A. Molecular characterization of breeds and its use in conservation. Livest. Sci. 2009, 120:174-195.
35. Toro M.A., Garcia-Cortes L.A., Legarra A. A note on the rationale for estimating genealogical coancestry from molecular markers. Genet. Sel. Evol. 2011, 43:27.
36. VanRaden P. Genomic measures of relationship and inbreeding. INTERBULL Bull. 2007, 37:33-36.
37. Villanueva B., Pong-Wong R., Woolliams J.A., Avendaño S. Managing genetic resources in commercial breeding populations. Farm Animal Genetic Resources. BSAS Occasional Publication no. 30 2004, 113-132. Nottingham University Press, Nottingham, UK. G. Simm, B. Villanueva, K.D. Sinclair, S. Townsend (Eds.).
38. Villanueva B., Sawalha R.M., Roughsedge T., Rius-Vilarrasa E., Woolliams J.A. Development of a genetic indicator of biodiversity for farm animals. Livest. Sci. 2010, 129:200-207.
39. Wellmann R., Hartwig S., Bennewitz J. Optimum contribution selection for conserved populations with historic migration. Genet. Sel. Evol. 2012, 44:34.