Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d’Eivissa)

https://doi.org/10.17221/8783-CJASCitation:Martín de la Rosa A.J., Cervantes I., Gutiérrez J.P. (2016): Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d’Eivissa). Czech J. Anim. Sci., 61: 108-116.
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The Ibicenco rabbit (Conill Pages D’Eivissa) is a rare breed mainly located on Ibiza Island, in rural areas. Today breeders are looking for a sustainable use and alternative routes for profitability of the population to avoid its extinction. The breed presents some variety in coat colour (brown, black, orange, and grey), and breeders would like to maintain these characteristics. The objectives of this study were to develop a method to design matings in a population with unbalanced pedigree depth in a scenario of maintaining the variety of coat colours, and to analyze the genealogical information of the Ibicenco rabbit to ascertain the genetic structure of the population. Equivalent effective population size mating was developed as a useful parameter to design the mating in this particular scenario. Results obtained by the initial application showed that this population was properly managed for maintaining the maximum genetic variability. This mating method is recommended to manage the genetic variability of this small rabbit population in a scenario of partial permanent colour structure. For the pedigree analysis, a reference population formed by 143 animals available for reproduction was used. A demographic study, a probability gene origin analysis, computation of inbreeding and effective size, and an analysis of genetic structure were done. The generation interval was approximately one year (11.8 months). The average number of equivalent generations was 3.4. The effective numbers of founders and ancestors were 10 and 11, respectively, and the founder genome equivalent was 6. The average inbreeding was 10.8%, but the mean inbreeding seems to have stopped increasing as a consequence of deeper monitoring in the mating design. The realized effective size was 9.6 (via inbreeding) and 17.5 (via coancestry). Regarding the genetic structure, the orange and black groups are the most distant genetically while grey and blacks are closer. 
References:
Anguera B. (2005): Conill Pagès d’Eivissa, Native Breeds of the Balearic Islands. Govern de les Illes Balears, Conselleria d’Agricultura i Pesca, Palma de Mallorca, Spain. (in Spanish)
 
Ballou J.D., Lacy R.C. (1995): Identifying genetically important individuals for management of genetic variation in pedigreed populations. In: Ballou J.D., Gilpin M., Foose T.J. (eds): Population Management for Survival and Recovery: Analytical Methods and Strategies in Small Population Management. Columbia University Press, New York, USA, 76–111.
 
Boichard D, Maignel L, Verrier É (1997): The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 29, 5-  https://doi.org/10.1186/1297-9686-29-1-5
 
CABALLERO ARMANDO, TORO MIGUEL A. (): Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research, 75, 331-343  https://doi.org/10.1017/S0016672399004449
 
Caballero A., Toro M.A. (2002): Analysis of genetic diversity for the management of conserved subdivided populations. Conservation Genetics, 3, 289–299. https://doi.org/10.1023/A:1019956205473
 
Cervantes I., Goyache F., Molina A., Valera M., Gutiérrez J. P. (2008): Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees. Journal of Animal Breeding and Genetics, 125, 301-310  https://doi.org/10.1111/j.1439-0388.2008.00755.x
 
Cervantes I., Goyache F., Molina A., Valera M., Gutiérrez J.P. (2011): Estimation of effective population size from the rate of coancestry in pedigreed populations. Journal of Animal Breeding and Genetics, 128, 56-63  https://doi.org/10.1111/j.1439-0388.2010.00881.x
 
Duchev Z., Distl O., Groeneveld E. (2006): Early warning system for loss of diversity in European livestock breeds. Archives of Animal Breeding, 49, 521–531.
 
Falconer D.S., Mackay F.C. (1996): Introduction to Quantitative Genetics. Longman Group Ltd., Harlow, UK.
 
FAO (1998): Secondary Guidelines for the National Farm Animal Genetic Resources Management Plans – Management of small populations at risk. FAO, Rome, Italy.
 
Fernandez J., Toro M.A., Caballero A. (2003): Fixed contributions designs vs. minimization of global coancestry to control inbreeding in small populations. Genetics, 165, 885–894.
 
Fontanesi L., Tazzoli M., Beretti F., Russo V. (2006): Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domestic rabbit (Oryctolagus cuniculus). Animal Genetics, 37, 489-493  https://doi.org/10.1111/j.1365-2052.2006.01494.x
 
Goyache F., Gutierrez J. P., Fernandez I., Gomez E., Alvarez I., Diez J., Royo L. J. (2003): Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example. Journal of Animal Breeding and Genetics, 120, 95-105  https://doi.org/10.1046/j.1439-0388.2003.00378.x
 
Gutierrez J.P., Goyache F. (2005): A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122, 172-176  https://doi.org/10.1111/j.1439-0388.2005.00512.x
 
Gutiérrez Juan, Altarriba Juan, Díaz Clara, Quintanilla Raquel, Cañón Javier, Piedrafita Jesús (2003): Pedigree analysis of eight Spanish beef cattle breeds. Genetics Selection Evolution, 35, 43-  https://doi.org/10.1186/1297-9686-35-1-43
 
Gutiérrez Juan, Cervantes Isabel, Molina Antonio, Valera Mercedes, Goyache Félix (2008): Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genetics Selection Evolution, 40, 359-  https://doi.org/10.1186/1297-9686-40-4-359
 
Gutiérrez J.P., Cervantes I., Goyache F. (2009): Improving the estimation of realized effective population sizes in farm animals. Journal of Animal Breeding and Genetics, 126, 327-332  https://doi.org/10.1111/j.1439-0388.2009.00810.x
 
Ivy J. A., Lacy R. C. (): A Comparison of Strategies for Selecting Breeding Pairs to Maximize Genetic Diversity Retention in Managed Populations. Journal of Heredity, 103, 186-196  https://doi.org/10.1093/jhered/esr129
 
James J.W. (1972): Computation of genetic contributions from pedigrees. Theoretical and Applied Genetics, 42, 272–273.
 
James J. W. (1977): A note on selection differential and generation length when generations overlap. Animal Production, 24, 109-112  https://doi.org/10.1017/S0003356100039271
 
Kerns Julie A., Newton J., Berryere Tom G., Rubin Edward M., Cheng Jan-Fang, Schmutz Sheila M., Barsh Gregory S. (2004): Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs. Mammalian Genome, 15, 798-808  https://doi.org/10.1007/s00335-004-2377-1
 
Lacy Robert C. (1989): Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biology, 8, 111-123  https://doi.org/10.1002/zoo.1430080203
 
Leroy Grégoire, Mary-Huard Tristan, Verrier Etienne, Danvy Sophie, Charvolin Eleonore, Danchin-Burge Coralie (2013): Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45, 1-  https://doi.org/10.1186/1297-9686-45-1
 
Malecot G. (1948): The Mathematics of Heredity. Masson et Cie, Paris, France. (in French)
 
Martin de la Rosa A., Cervantes I., Garcia-Garcia R.M., Rebollar P.G., Arias-Alvarez M., Lorenzo P.L., Gutierrez J.P. (2013): Initial study of genetic structure of Ibicenco rabbit from genealogical information. XV Conference on Animal Production, 14–15 May 2013, Zaragoza, Spain, 514–515.
 
Meuwissen T.H.E. (2009): Towards consensus on how to measure neutral genetic diversity? Journal of Animal Breeding and Genetics, 126, 333–334.
 
Nagy I., Curik I., Radnai I., Cervantes I., Gyovai P., Baumung R., Farkas J., Szendro Z. (): Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses. Journal of Animal Science, 88, 1267-1275  https://doi.org/10.2527/jas.2009-2273
 
Ryder M.L. (1976): Why should rare breeds of livestock be saved? International Zoo Yearbook, Wiley Online Library, 16, 244–249.
 
Toro M.A., Nieto B., Salgado C. (1988): A note on minimization of inbreeding in small-scale selection programmes. Livestock Production Science, 20, 317-323  https://doi.org/10.1016/0301-6226(88)90026-7
 
Wright S. (1978): Evolution and the Genetics of Populations. Volume 4: Variability within and among Natural Populations. University of Chicago Press, Chicago, USA.
 
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