Hostname: page-component-cd9895bd7-mkpzs Total loading time: 0 Render date: 2024-12-26T20:03:15.013Z Has data issue: false hasContentIssue false
  • English
  • Français

Assessing the genetic diversity in small farm animal populations*

Published online by Cambridge University Press:  05 April 2011

M. A. Toro ,
T. H. E. Meuwissen ,
J. Fernández ,
I. Shaat  and
A. Mäki-Tanila
M. A. Toro*
Affiliation:
Departamento de Producción Animal, ETS Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28040 Madrid, Spain
T. H. E. Meuwissen
Affiliation:
Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, PO Box 1432, Ås, Norway
J. Fernández
Affiliation:
Departamento de Mejora Genética Animal, Instituto Nacional de Investigaciones Agrarias, Ctra. Coruña Km 7.5, 28040 Madrid, Spain
I. Shaat
Affiliation:
MTT Agrifood Research Finland, Animal Breeding Section, 31600 Jokioinen, Finland
A. Mäki-Tanila
Affiliation:
MTT Agrifood Research Finland, Animal Breeding Section, 31600 Jokioinen, Finland
*
†E-mail: miguel.toro@upm.es
Get access

Abstract

Genetic variation is vital for the populations to adapt to varying environments and to respond to artificial selection; therefore, any conservation and development scheme should start from assessing the state of variation in the population. There are several marker-based and pedigree-based parameters to describe genetic variation. The most suitable ones are rate of inbreeding and effective population size, because they are not dependent on the amount of pedigree records. The acceptable level for effective population size can be considered from different angles leading to a conclusion that it should be at least 50 to 100. The estimates for the effective population size can be computed from the genealogical records or from demographic and marker information when pedigree data are not available. Marker information could also be used for paternity analysis and for estimation of coancestries. The sufficient accuracy in marker-based parameters would require typing thousands of markers. Across breeds, diversity is an important source of variation to rescue problematic populations and to introgress new variants. Consideration of adaptive variation brings new aspects to the estimation of the variation between populations.

Keywords

local breedsinbreedingeffective population size
Type
Full Paper
Information
animal , Volume 5 , Issue 11 , 26 September 2011 , pp. 1669 - 1683
Copyright
Copyright © The Animal Consortium 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

*

This review is based on an invited presentation at the 60th Annual Meeting of the European Association for Animal Production held in Barcelona, Spain, during August 2009.

References

Bennewitz, J, Meuwissen, THE 2005. A novel method for the estimation of the relative importance of breeds in order to conserve the total genetic variance. Genetics Selection Evolution 37, 315–337.CrossRefGoogle ScholarPubMed
Bennewitz, J, Simianer, H, Meuwissen, THE 2008. Investigations on merging breeds in genetic conservation schemes. Journal of Dairy Science 91, 2512–2519.CrossRefGoogle ScholarPubMed
Blouin, MS 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology & Evolution 18, 503–511.CrossRefGoogle Scholar
Boettcher, PJ, Tixier-Boichard, M, Toro, M, Simianer, H, Eding, H, Gandini, G, Joost, S, Garcia, D, Colli, L, Ajmone-Marsan, P, the GLOBALDIV Consortium 2010. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources. Animal Genetics 41 (suppl. 1), 1–14.CrossRefGoogle ScholarPubMed
Boichard, D, Maignel, L, Verrier, E 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution 29, 5–23.CrossRefGoogle Scholar
Bonin, A, Nicole, F, Pampanon, O, Miaud, C, Taberlet, P 2007. Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation. Conservation Biology 21, 697–708.CrossRefGoogle ScholarPubMed
Butler, K, Field, C, Herbinger, CM, Smith, BR 2004. Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data. Molecular Ecology 13, 1589–1600.CrossRefGoogle ScholarPubMed
Caballero, A 1994. Developments in the prediction of effective population size. Heredity 73, 657–679.CrossRefGoogle ScholarPubMed
Caballero, A, Toro, MA 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research 75, 331–343.CrossRefGoogle ScholarPubMed
Cockerham, CC 1969. Variance of gene frequencies. Evolution 23, 72–84.CrossRefGoogle ScholarPubMed
Colleau, JJ, Sargolzaei, M 2008. A proximal decomposition of inbreeding, coancestry and contributions. Genetics Research 90, 191–198.CrossRefGoogle ScholarPubMed
Crow, JF, Kimura, M 1970. An introduction to population genetics theory. Harper and Row, New York, NY, USA.Google Scholar
Cruden, D 1949. The computation of inbreeding coefficients for closed populations. Journal of Heredity 40, 248–251.CrossRefGoogle ScholarPubMed
De Roos, APW, Hayes, BJ, Spelman, R, Goddard, ME 2008. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 179, 1503–1512.CrossRefGoogle ScholarPubMed
Emik, LO, Terrill, CE 1949. Systematic procedures for calculating inbreeding coefficients. Journal of Heredity 40, 51–55.CrossRefGoogle ScholarPubMed
Falconer, DS, Mackay, TFC 1996. Introduction to quantitative genetics. Longman House, Harlow, UK.Google Scholar
Fernando, RL, Grossman, M 1989. Marker assisted selection using best linear unbiased prediction. Genetics Selection Evolution 21, 467–477.CrossRefGoogle Scholar
Fernández, J, Toro, MA 2006. A new method to estimate relatedness from molecular markers. Molecular Ecology 15, 1657–1667.CrossRefGoogle ScholarPubMed
Fernández, J, Toro, MA, Caballero, A 2004. Managing individuals’ contributions to maximize the allelic diversity maintained in small, conserved populations. Conservation Biology 18, 1358–1367.CrossRefGoogle Scholar
Fernández, J, Meuwissen, THE, Toro, MA, Mäki-Tanila, A 2011. Management of genetic diversity in small farm animal populations. Animal (accepted).CrossRefGoogle Scholar
Frankham, R, Ballou, JD, Briscoe, DA 2002. Introduction to conservation genetics. Cambridge University Press, Cambridge, UK.CrossRefGoogle Scholar
García-Cortés, A, Martínez-Ávila, JC, Toro, MA 2010. Fine decomposition of the inbreeding and the coancestry coefficients by using the tabular method. Conservation Genetics 11, 1945–1952.CrossRefGoogle Scholar
García-Dorado, A, Monedero, JL, López-Fanjul, C 1998. The mutation rate and the distribution of mutational effects of viability and fitness in Drosophila melanogaster. Genetica 102–103, 255–265.CrossRefGoogle ScholarPubMed
Groeneveld, LF, Lenstra, JA, Eding, H, Toro, MA, Scherf, B, Pilling, D, Negrini, R, Finlay, E, Jianlin, H, Groeneveld, E, Weigend, S, the GLOBALDIV Consortium 2010. Genetic diversity in farm animals – a review. Animal Genetics 41 (suppl. 1), 6–31.CrossRefGoogle ScholarPubMed
Grossman, M, Eisen, EJ 1989. Inbreeding, coancestry, and covariance between relatives for X-chromosomal loci. Journal of Heredity 80, 137–142.CrossRefGoogle ScholarPubMed
Gutiérrez, JP, Goyache, F 2005. A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics 122, 357–360.CrossRefGoogle ScholarPubMed
Gutiérrez, JP, Cervantes, I, Molina, A, Valera, M, Goyache, F 2008. Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genetics Selection Evolution 40, 359–378.CrossRefGoogle ScholarPubMed
Gutiérrez, JP, Altarriba, J, Diaz, C, Quintanilla, R, Cañon, J, Piedrafita, J 2003. Pedigree analysis of eight Spanish beef cattle breeds. Genetics Selection Evolution 35, 43–63.CrossRefGoogle ScholarPubMed
Hayes, BJ, Visscher, PM, McPartlan, HC, Goddard, ME 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research 13, 635–643.CrossRefGoogle ScholarPubMed
Hedrick, PW 2001. Conservation genetics: where are we now? Trends in Ecology & Evolution 16, 629–636.CrossRefGoogle Scholar
Hein, J, Schierup, MK, Wiuf, C 2005. Gene genealogies, variation and evolution. Oxford University Press, Oxford, UK.Google Scholar
Hiemstra, SJ, Haas, Y, Maki-Tanila, A, Gandini, G 2010. Local breeds in Europe: development of policies and strategies for self-sustaining breeds. Wageningen Academic Publishers, Wageningen, The Netherlands.CrossRefGoogle Scholar
Hill, WG 1979. A note on effective population size with overlapping generations. Genetics 92, 317–322.CrossRefGoogle ScholarPubMed
Hill, WG 1981. Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38, 209–216.CrossRefGoogle Scholar
Hill, WG 2000. Maintenance of quantitative genetic variation in animal breeding programmes. Livestock Production Science 63, 99–109.CrossRefGoogle Scholar
Hill, WG, Keightley, PD 1988. Interrelations of mutation, population size, artificial and natural selection. In Proceedings of the Second International Conference on Quantitative Genetics (ed. BS Weir, EJ Eisen, MM Goodman and G Namkoong), pp. 57–70. Sinauer, Sunderland, MA, USA.Google Scholar
Hill, WG, Mbaga, SH 1998. Mutation and conflicts between artificial and natural selection for quantitative traits. Genetica 102/103, 171–181.CrossRefGoogle ScholarPubMed
Hinrichs, D, Meuwissen, TH, Odegard, J, Holt, M, Vangen, O, Woolliams, JA 2007. Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding. Heredity 99, 81–88.CrossRefGoogle Scholar
International Chicken Map Consortium 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432, 717–722.CrossRefGoogle Scholar
James, JW, McBride, G 1958. The spread of genes by natural and artificial selection in a closed poultry flock. Journal of Genetics 56, 55–62.CrossRefGoogle Scholar
Jones, AG, Ardren, WR 2003. Methods of parentage analysis in natural populations. Molecular Ecology 12, 2511–2523.CrossRefGoogle ScholarPubMed
Keightley, PD 1998. Genetic basis of response to 50 generations of selection on body weight in inbred mice. Genetics 148, 1931–1939.CrossRefGoogle ScholarPubMed
Kimura, M 1957. Some problems of stochastic processes in genetics. Annals of Mathematical Statistics 28, 882–901.CrossRefGoogle Scholar
Kimura, M, Crow, JF 1963. The measurement of effective population number. Evolution 17, 279–288.CrossRefGoogle Scholar
Lacy, RC 1989. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalence. Zoo Biology 8, 111–124.CrossRefGoogle Scholar
Laval, G, San Cristobal, M, Chevalet, C 2002. Measuring genetic distances between breeds: use of some distances in various short term evolution models. Genetics Selection Evolution 34, 481–507.CrossRefGoogle ScholarPubMed
Lewontin, RC, Krakauer, J 1973. Distribution of gene frequency as a test of the theory of the selected neutrality of polymorphism. Genetics 74, 175–195.CrossRefGoogle Scholar
Luikart, G, Ryman, N, Tallmon, DA, Schwartz, MK, Allendorf, FW 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 11, 355–373.CrossRefGoogle Scholar
López-Fanjul, C, Fernández, A, Toro, MA 2003. The effect of nonadditive gene action on the neutral quantitative index of population divergence. Genetics 164, 1627–1633.CrossRefGoogle ScholarPubMed
Lynch, M 1996. A quantitative-genetic perspective on conservation issues. In Conservation genetics: case histories from nature (ed. J Avise and J Hamrick), pp. 471–501. Chapman & Hall, New York, NJ, USA.CrossRefGoogle Scholar
MacCluer, JW, VandeBerg, JL, Read, B, Ryder, OA 1986. Pedigree analysis by computer simulation. Zoo Biology 5, 147–160.CrossRefGoogle Scholar
Macleod, I, Meuwissen, THE, Hayes, BJ, Goddard, M 2009. A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genetics Research 91, 413–426.CrossRefGoogle ScholarPubMed
Maignel, L, Boichard, D, Verrier, E 1996. Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bulletin 14, 49–54.Google Scholar
Marshall, TC, Slate, J, Kruuk, LEB, Pemberton, JM 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7, 639–655.CrossRefGoogle ScholarPubMed
Meuwissen, THE 2009. Towards consensus on how to measure neutral genetic diversity? Journal of Animal Breeding and Genetics 126, 333–412.CrossRefGoogle ScholarPubMed
Meuwissen, THE, Luo, Z 1992. Computing inbreeding coefficients in large populations. Genetics Selection Evolution 24, 305–313.CrossRefGoogle Scholar
Meuwissen, THE, Woolliams, JA 1994. Effective sizes of livestock populations to prevent a decline in fitness. Theoretical and Applied Genetics 89, 1019–1026.CrossRefGoogle ScholarPubMed
Nicholas, FW 1980. Size of population required for artificial selection. Genetical Research 35, 85–105.CrossRefGoogle ScholarPubMed
Nomura, T 2005. Developments in prediction theories of the effective size. Animal Science Journal 76, 87–96.CrossRefGoogle Scholar
Pérez-Enciso, M, Fernando, RL 1992. Genetic evaluation with uncertain parentage: a comparison of methods. Theoretical and Applied Genetics 84, 173–179.CrossRefGoogle ScholarPubMed
Pollak, E 1983. A new method for estimating the effective population size from allele frequency changes. Genetics 104, 531–548.CrossRefGoogle ScholarPubMed
Robertson, A 1960. A theory of limits in artificial selection. Proceedings of the Royal Society of London B 153, 234–249.Google Scholar
Robertson, A 1961. Inbreeding in artificial selection programmes. Genetical Research 2, 189–194.CrossRefGoogle Scholar
Rochambeau, H, de La Fuente, LF, Rouvier, R, Ouhayoun, J 1989. Sélection sur la vitesse de croissance post-sevrage chez le lapin. Genetics Selection Evolution 21, 527–546.CrossRefGoogle Scholar
Rodríguez-Ramilo, ST, Toro, MA, Martínez, P, Castro, J, Bouza, C, Fernández, J 2007. Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus). Aquaculture 273, 434–442.CrossRefGoogle Scholar
Ruane, J 1999. Selecting breeds for conservation. In Gene banks and the conservation of farm animals genetic resources (ed. JK Oldenbroek), pp. 59–74. DLO Institute for Animal Science and Health, Lelystad, The Netherlands.Google Scholar
Santure, A, Wang, J 2009. The joint effects of selection and dominance on the QST _ FST contrast. Genetics 181, 259–276.CrossRefGoogle ScholarPubMed
Sargolzaei, M, Iwaisaki, H, Colleau, JJ 2005. A fast algorithm for computing inbreeding coefficients in large populations. Journal of Animal Breeding and Genetics 122, 325–331.CrossRefGoogle ScholarPubMed
Sbordoni, V, De Matheis, E, Cobolli-Sbordoni, M, La Rosa, G, Mottlcaccia, M 1986. Bottleneck effects and the depression of genetic variability in hatchery stocks of Penaeus japonicus (Crustacea, Decapoda). Aquaculture 57, 239–251.CrossRefGoogle Scholar
Slate, J, David, P, Dodds, KG, Veenvliet, BA, Glass, BC, Broad, TE, McEwan, JC 2004. Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity 93, 255–265.CrossRefGoogle ScholarPubMed
Spitze, K 1993. Population structure in daphnia obtusa: quantitative genetic and allozymic variation. Genetics 135, 367–374.CrossRefGoogle ScholarPubMed
Thomas, SC, Hill, WG 2000. Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics 155, 1961–1972.CrossRefGoogle ScholarPubMed
Thomas, SC, Hill, WG 2002. Sibship reconstruction in hierarchical population structures using Markov chain Monte Carlo techniques. Genetical Research 79, 227–234.CrossRefGoogle ScholarPubMed
Thompson, R 1977. The estimation of heritability with unbalanced data. II. Data available on more than two generations. Biometrics 33, 497–504.CrossRefGoogle Scholar
Toro, MA, Caballero, A 2005. Characterisation and conservation of genetic diversity in subdivided populations. Philosophical Transactions of the Royal Society B 360, 1367–1378.CrossRefGoogle ScholarPubMed
Toro, MA, Fernández, J, Caballero, A 2009. Molecular characterization of breeds and its use in conservation. Livestock Science 120, 174–195.CrossRefGoogle Scholar
Toro, MA, Barragán, C, Óvilo, C, Rodrigáñez, J, Rodriguez, C, Silió, L 2002. Estimation of coancestry in Iberian pigs using molecular markers. Conservation Genetics 3, 309–320.CrossRefGoogle Scholar
Van Eenennaam, AL, Weaber, RL, Drake, DJ, Penedo, MCT, Quaas, RL, Garrick, J, Pollak, EJ 2007. DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting. Journal of Animal Science 85, 3159–3169.CrossRefGoogle Scholar
Villa-Angulo, R, Matukumalli, LK, Gill, CA, Choi, J, Van Tassell, CP, Grefenstette, JJ 2009. High-resolution haplotype block structure in the cattle genome. BMC Genetics 10, 19.CrossRefGoogle ScholarPubMed
Villanueva, B, Sawalha, RM, Roughsedge, T, Rius-Vilarrasa, E, Woolliams, JA 2010. Development of a genetic indicator of biodiversity for farm animals. Livestock Science 129, 200–207.CrossRefGoogle Scholar
Wang, JL 2001. A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research 78, 243–257.CrossRefGoogle ScholarPubMed
Wang, JL 2005. Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B 360, 1395–1409.CrossRefGoogle ScholarPubMed
Waples, RS 1989. A generalised approach for estimating effective population size from temporal changes in allele frequency. Genetics 121, 379–391.CrossRefGoogle ScholarPubMed
Waples, RS, Do, C 2008. LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources 8, 753–756.CrossRefGoogle ScholarPubMed
Weir, BS, Anderson, AD, Hepler, AB 2006. Genetic relatedness analysis: modern data and new challenges. Nature Reviews Genetics 7, 771–780.CrossRefGoogle ScholarPubMed
Williamson, EG, Slatkin, M 1999. Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152, 755–761.CrossRefGoogle ScholarPubMed
Woolliams, JA, Bijma, P 2000. Predicting rates of inbreeding: in populations undergoing selection. Genetics 154, 1851–1864.CrossRefGoogle ScholarPubMed
Woolliams, JA, Mäntysaari, EA 1995. Genetic contributions of Finnish Ayrshire bulls over four generations. Animal Science 61, 177–187.CrossRefGoogle Scholar
Woolliams, JA, Toro, MA 2007. What is genetic diversity? In Utilisation and conservation of farm animal genetic resources (ed. K Oldenbroek), pp. 55–74. DLO Institute for Animal Science and Health, Lelystad, The Netherlands.CrossRefGoogle Scholar
Wray, NR, Thompson, R 1990. Predictions of rates of inbreeding in selected populations. Genetical Research 55, 41–54.CrossRefGoogle ScholarPubMed
Wright, S 1922. Coefficients of inbreeding and relationship. American Naturalist 15, 330–338.CrossRefGoogle Scholar
Wright, S 1931. Evolution in Mendelian populations. Genetics 16, 97–159.CrossRefGoogle ScholarPubMed
Wright, S 1938. Size of population and breeding structure in relation to evolution. Science 87, 430–431.Google Scholar
Wright, S 1969. Evolution and the genetics of populations, vol. 2: the theory of gene frequencies. University of Chicago, Chicago, IL, USA.Google Scholar