Combining microsatellite and pedigree data to estimate relationships among Skyros ponies

• Autorzy: Bomcke E , Gengler N
• Języki publikacji: EN

Abstrakty

EN

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyros pony breed, which consists of less than 200 individuals, divided into 3 main herds or subpopulations. In this study, relationships between individuals were estimated using traditional estimators as well as the newly developed method. For this purpose, 99 Skyros ponies were genotyped at 16 microsatellite loci. It appeared that the limitation of the most common molecular-based estimators is the use of weights that assume relationships equal to 0. The results showed that, as a consequence of this limitation, negative relationship values can be obtained in small inbred populations, for example. By contrast, the combined estimator gave no negative values. Using principal component analysis, the combined estimator also enabled a better graphic differentiation between the 3 subpopulations defined previously. In conclusion, this new estimator can be a promising alternative to traditionally used estimators, especially in inbred populations, with both incomplete pedigree and molecular information.

• Wydawca: -
• Czasopismo: Journal of Applied Genetics
• Rocznik: 2009
• Tom: 50
• Numer: 2
• Opis fizyczny: p.133-143,fig.,ref.

Twórcy

autor

Bomcke E

• Animal Science Unit, Gembloux Agricultural University, Passage des Deportes 2, B-5030 Gembloux, Belgium
• F.R.I.A., Rue d'Egmont, Brussels, Belgium

autor

Gengler N

• Animal Science Unit, Gembloux Agricultural University, Passage des Deportes 2, B-5030 Gembloux, Belgium
• National Fund for Scientific Research, Rue d'Egmont, Brussels, Belgium

Bibliografia

• Baumung R, Sölkner J, 2003. Pedigree and marker information requirements to monitor genetic variability. Genet Sel Evol 35: 369-383.
• Boichard D, Maignel L, Verrier E, 1996. Analyse généalogique des races bovines françaises. INRA Prod Anim 9: 323-335.
• Bömcke E, 2007. Conservation of animal genetic resources: Improvement of the relationship matrix. Master, Gembloux Agricultural University, Belgium.
• Botstein D, White RL, Skolnick M, Davis RW, 1980. Construction of a genetic linkage map in man using restriction fragment polymorphisms. Am J Hum Genet 32: 314-331.
• Caballero A, Toro MA, 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res 75: 331-343.
• Caballero A, Toro MA, 2002. Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 3: 289-299.
• Csilléry K, Johnson T, Beraldi D, Cletton-Brock T, Coltman D, Hansson B, et al. 2006. Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173: 2091-2101.
• DAD-IS, 2007. Domestic Animal Diversity Information System (DAD-IS), Food and Agriculture Organization of the United Nations. Retrieved October 07, 2007, from http://dad.fao.org
• Dimsoski P, 2003. Development of a 17-plex microsatellite polymerase chain reaction kit for genotyping horses. Croat Med J 44: 332-335.
• Eding H, Meuwissen THE, 2001. Marker-based estimates of between and within population kinships for the conservation of genetic diversity. J Anim Breed Genet 118: 141-159.
• Engh AL, Funk SM, van Horn RC, Scribner KT, Bruford MW, Libants S, et al. 2002. Reproductive skew among males in a female-dominated society. Behav Ecol 13: 193-200.
• FAO, 1998. Secondary Guidelines for Development of National Farm Animal Genetic Resources Management Plans. Management of Small Populations at Risk. Initiative for Domestic Animal Diversity. Food and Agriculture Organization of the United Nations, Rome.
• Glaubitz JC, Rhodes Jr OE, Dewoody JA, 2003. Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol Ecol 12: 1039-1047.
• Goodisman MAD, Crozier RH, 2002. Population and colony genetic structure of the primitive termite Mastotermes darwiniensis. Evolution 56: 70-83.
• Goodnight KF, Queller DC, 1999. Computer software for performing likelihood test of pedigree relationship using genetic markers. Mol Ecol 8: 1231-1234.
• Hedrick PW, Miller PS, 1992. Conservation genetics: techniques and fundamentals. Ecol Appl 2: 30-46.
• Heg D, van Treuren R, 1998. Female-female cooperation in polygynous oystercatchers. Nature 391: 687-691.
• Henderson CR, 1976. A simple method for computing the inverse of a numerator relationship matrix use in prediction of breeding values. Biometrics 32:69-83.
• Huby M, Griffon L, Moureaux S, De Rochambeau H, Danchin-Burge C, Verrier E, 2003. Genetic variability of six French meat sheep breeds in relation to their genetic management. Genet Sci Evol 35: 637-655.
• Jones KL, Glenn TC, Lacy RC, Pierce JR, Unruh N, Mirande CM, et al. 2002. Refining the whooping crane studbook by incorporating microsatellite DNA and leg-banding analyses. Conserv Biol 16: 789-799.
• Li CC, Weeks DE, Chakravarti A, 1993. Similarity of DNA fingerprints due to chance and relatedness. Hum Hered 43: 45-52.
• Lynch M, Ritland K, 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-1766.
• Maignel L, Boichard D, Verrier E, 1996. Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bull 14: 49-54.
• Malécot G, 1948. Les mathématiques de l’hérédité. Paris: Masson et Cie. Cited by Van Vleck (1987) and Minvielle (1990).
• Meuwissen THE, Luo Z, 1992. Computing inbreeding coefficients in large populations. Genet Sci Evol 24: 305-313.
• Minvielle F, 1990. Principes d’amélioration génétique des animaux domestiques. Paris: INRA & Québec: PUL (Les presses Universitaires de Laval).
• Morin PA, Moore JJ, Chakraborty R, Jin L, Goodall J, Woodruff DS, 1994. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science 265: 1193-1201.
• Mousseau TA, Ritland K, Heath DD, 1998. A novel method for estimating heritability using molecular markers. Heredity 80: 218-224.
• Nejati-Javaremi A, Smith C, Gibson JP, 1997. Effect of total allelic relationship on accuracy of evaluation and response to selection. J Anim Sci 75: 1738-1745.
• Oliehoek PA, Windig JJ, van Arendonk JAM, Bijma P, 2006. Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics 173: 483-496.
• Pamilo P, Crozier RH, 1982. Measuring genetic relatedness in natural populations - methodology. Theor Popul Biol 21: 171-193.
• Queller DC, Goodnight KF, 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.
• Ritland K, 2000. Marker-inferred relatedness as a tool for detecting heritability in nature. Mol Ecol 9: 1195-1204.
• Rochambeau H (de), Fournet-Hanocq F, Vu Tien Khang J, 2000. Measuring and managing genetic variability in small populations. Ann Zootech 49: 77-93.
• SAS Institute, 1999. SAS/STAT User’s Guide: Version 8. SAS Inst. Inc., Cary, NC.
• Thomas SC, Hill WG, 2002. Sibship reconstruction in hierarchical population structure using Markov chain Monte Carlo techniques. Genet Res 79: 227-234.
• Toro M, Barragán C, Óvilo C, Rodrigańez J, Rodriguez C, Silió L, 2002. Estimation of coancestry in Iberian pigs using molecular markers. Conserv Genet 3: 309-320.
• Van de Casteele T, Galbusera P, Matthysen E, 2001. A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol 10: 1539-1549.
• VanRaden PM, 1992. Accounting for inbreeding and crossbreeding in genetic evaluation of large populations. J Dairy Sci 75: 3136-3144.
• VanRaden PM, 2007. Genomic measures of relationship and inbreeding. Interbull Annual Meeting Proceedings. Interbull Bull 37: 33-36
• Van Vleck LD, Poliak EJ, Oltenacu EAB, 1987. Genetics for the animal sciences. New York: Freeman.
• Verrier E, Rognon X, de Rochambeau H, Laloe D, 2005. Les outils et méthodes de la génétique pour la caractérisation, le suivi et la gestion de la variabilité génétique des populations animales. Ethnozootechnie 76: 67-82.
• Wright S, 1922. Coefficients of inbreeding and relationship. Am Nat 56: 330. Cited by Van Vleck et al. (1987) and Henderson (1976).
• Wright S, McPhee HC, 1925. An approximate method of calculating coefficients of inbreeding and relationship from livestock pedigrees. J Agr Res 31: 377-383.