Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Assessment of population structure and genetic diversity of German Angora rabbit through pedigree analysis

  • Abdul Rahim (North Temperate Regional Station, ICAR-Central Sheep and Wool Research Institute) ;
  • K. S. Rajaravindra (ICAR-Directorate of Poultry Research (DPR)) ;
  • Om Hari Chaturvedi (North Temperate Regional Station, ICAR-Central Sheep and Wool Research Institute) ;
  • S. R. Sharma (ICAR-Central Sheep and Wool Research Institute)
  • Received : 2022.06.07
  • Accepted : 2022.10.30
  • Published : 2023.05.01
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Abstract

Objective: The main goals of this investigation were to i) assess the population structure and genetic diversity and ii) determine the efficiency of the ongoing breeding program in a closed flock of Angora rabbits through pedigree analysis. Methods: The pedigree records of 6,145 animals, born between 1996 to 2020 at NTRS, ICAR-CSWRI, Garsa were analyzed using ENDOG version 4.8 software package. The genealogical information, genetic conservation index and parameters based on gene origin probabilities were estimated. Results: Analysis revealed that, 99.09% of the kits had both parents recorded in the whole dataset. The completeness levels for the whole pedigree were 99.12%, 97.12%, 90.66%, 82.49%, and 74.11% for the 1st, 2nd, 3rd, 4th, and 5th generations, respectively, reflecting well-maintained pedigree records. The maximum inbreeding, average inbreeding and relatedness were 36.96%, 8.07%, and 15.82%, respectively. The mean maximum, mean equivalent and mean completed generations were 10.28, 7.91, and 5.51 with 0.85%, 1.19%, and 1.85% increase in inbreeding, respectively. The effective population size estimated from maximum, equivalent and complete generations were 58.50, 27.05, and 42.08, respectively. Only 1.51% of total mating was highly inbred. The effective population size computed via the individual increase in inbreeding was 42.83. The effective numbers of founders (fe), ancestors (fa), founder genomes (fg) and non-founder genomes (fng) were 18, 16, 6.22, and 9.50, respectively. The fe/fa ratio was 1.12, indicating occasional bottlenecks had occurred in the population. The six most influential ancestors explained 50% of genes contributed to the gene pool. The average generation interval was 1.51 years and was longer for the sire-offspring pathway. The population lost 8% genetic diversity over time, however, considerable genetic variability still existed in the closed Angora population. Conclusion: This study provides important and practical insights to manage and maintain the genetic variability within the individual flock and the entire population.

Keywords

Acknowledgement

We also gratefully acknowledge the contribution of previous project investigators and technical staff at the Angora Rabbit Unit of ICAR-CSWRI, NTRS, Garsa for management and recording of animals.

References

  1. Risam KS, Das GK, Bhasin V. Rabbit for meat and wool production in India: a review. Indian J Anim Sci 2015;75:365-82.
  2. Ossard H, Thebault RG, Vrillon JL, Allain D, DeRochambeau H. Economic overview of the French and world markets for Angora rabbit wool. European Fine Fibre Network 1995;5:35-47.
  3. Singh U, Sharma SR, Bhatt RS, Kumar D, Risam KS. Effect of shearing intervals on the growth and wool parameters of German Angora rabbits. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France. 2006;32:525-8.
  4. Pokharna AK, Gupta NP, Patni, Arora RK, Shakyawar, DB. Processing of Angora rabbit wool and Cashmere production and utilization; 2004; Sept 25-26. pp. 166-73.
  5. Gowane GR, Chopra A, Misra SS, Prince LL. Genetic diversity of a nucleus flock of Malpura sheep through pedigree analyses. Small Rumin Res 2014;120:35-41. https://doi.org/10.1016/j.smallrumres.2014.04.016
  6. Das AK, Kumar S, Rahim A, Mishra AK. Genetic variability in immunocompetence and performance status of Rhode Island Red chicken strains and its crosses. Int J Bio-Resour Stress Manag 2014;5:246-54. https://doi.org/10.5958/0976-4038.2014.00563.6
  7. Oliveira RR, Brasil LHA, Delgado JV, et al. Genetic diversity and population structure of the Spanish Murciano-Granadina goat breed according to pedigree data. Small Rumin Res 2016;144:170-5. https://doi.org/10.1016/j.smallrumres.2016.09.014
  8. Malhado CHM, Carneiro PLS, Pereira DG, Martins Filho R. Genetic progress and population structure in Nellore cattle in Bahia State, Brazil. Pesqui Agropecu Bras 2008;43:1163-9. https://doi.org/10.1590/S0100-204X2008000900010
  9. Gutierrez JP, Goyache F, Cervantes I. ENDOG v4.8: A Computer Program for Monitoring Genetic Variability of Populations Using Pedigree Information. User's Guide. Madrid, Spain: Universidad Complutense de Madrid Publication; 2010.
  10. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfenning DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses. J Hered 1983;74:394-9. https://doi.org/10.1093/oxfordjournals.jhered.a109824
  11. Berg P, Sorensen MK, Nielsen J. EVA interface user manual; 2007. 40 p.
  12. Maignel L, Boichard D, Verrier E. Genetic variability of French dairy breeds estimated form pedigree information. Interbull Bull 1996;14:49-54.
  13. Falconer DS, Mackay TFC. Introduction to quantitative genetics. Harlow, Essex, UK: Longmans Green; 1996.
  14. Wright S. Coefficients of inbreeding and relationship. Am Nat 1922;56:330-8. https://doi.org/10.1086/279872
  15. Meuwissen TI, Luo Z. Computing inbreeding coefficients in large populations. Genet Sel Evol 1992;24:305. https://doi.org/10.1186/1297-9686-24-4-305
  16. Gonzalez-Recio O, De Maturana EL, Gutierrez JP. Inbreeding depression on female fertility and calving ease in Spanish dairy cattle. J Diry Sci 2007;90:5744-52. https://doi.org/10.3168/jds.2007-0203
  17. Gutierrez JP, Cervantes I, Molina A, Valera M, Goyache F. Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genet Sel Evol 2008;40:359. https://doi.org/10.1051/gse:2008008
  18. Gutierrez JP, Cervantes I, Goyache F. Improving the estimation of realized effective population sizes in farm animals. J Anim Breed Genet 2009;126:327-32. https://doi.org/10.1111/j.1439-0388.2009.00810.x
  19. Gutierrez JP, Goyache F. A note on ENDOG: a computer program for analysing pedigree information. J Anim Breed Genet 2005;122:172-6. https://doi.org/10.1111/j.1439-0388.2005.00512.x
  20. Dunner S, Checa ML, Gutierrez JP, Martin JP, Canon J. Genetic analysis and management in small populations: the Asturcon pony as an example. Genet Sel Evol 1998;30:397. https://doi.org/10.1186/1297-9686-30-4-397
  21. Boichard D. PEDIG: a FORTRAN package for pedigree analysis suited for large populations. In: 7th world congress on genetics applied to livestock production; 2002, Jul 3-8; Rotterdam, The Netherlands.
  22. Lacy RC. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol 1989;8:111-23. https://doi.org/10.1002/zoo.1430080203
  23. Boichard D, Maignel L, Verrier E. The value of using probabilities of gene origin to measure genetic variability in a population. Genet Sel Evol 1997;29:5. https://doi.org/10.1186/1297-9686-29-1-5
  24. Caballero A, Toro MA. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res 2000;75:331-43. https://doi.org/10.1017/S0016672399004449
  25. Lacy RC. Clarification of genetic terms and their use in the management of captive populations. Zoo Biol 1995;14:565-77. https://doi.org/10.1002/zoo.1430140609
  26. Alderson GLH. A system to maximize the maintenance of genetic variability in small populations. In: Alderson L, Bodo L, editors. Conservation of domestic livestock. Wallingford, UK: CAB International; 1992. pp. 18-29.
  27. Sakthivel M, Balasubramanyam D, Kumarasamy P, et al. Genetic structure of a small closed population of the New Zealand White rabbit through pedigree analysis. World Rabbit Sci 2018;26:101-12. https://doi.org/10.4995/wrs.2018.7426
  28. Nagy I, Curik I, Radnai I, et al. Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses. J Anim Sci 2010;88:1267-75. https://doi.org/10.2527/jas.2009-2273
  29. Vyas J, Chopra A, Pannua U, Saran RK, Narula HK. Population structure of Marwari sheep through pedigree analysis. Small Rumin Res 2022;206:106590. https://doi.org/10.1016/j.smallrumres.2021.106590
  30. Moura ASAMT, Polastre R, Wechsler FS. Dam and litter inbreeding and environmental effects on litter performances in Botucatu rabbits. World Rabbit Sci 2000;8:151-7. https://doi.org/10.4995/wrs.2000.433
  31. Planinc M, Kermauner A, Kovac M, Malovrh S. Pedigree analysis in the Sika rabbits in Slovenia. Acta Agr Slov 2012;Suppl 3:171-3.
  32. Martin de la Rosa AJ, Cervantes I, Gutierrez JP. 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 2016;61:108-16. https://doi.org/10.17221/8783-CJAS
  33. Bijma P. Long-germ genetic contributions: Prediction of rates of inbreeding and genetic gain in selected populations [Ph. D. Thesis]. Wageningen, The Netherlands: Wageningen University; 2000.
  34. Bijma P, Wooliams JA. Prediction of rates of inbreeding in populations selected on best linear unbiased prediction of breeding value. Genet 2000;156;361-3. https://doi.org/10.1093/genetics/156.1.361
  35. Rafat SA, Allain D, de Rochambeau H. Genetic description of a divergent selection experiment in Angora rabbits with overlapping generations. J Anim Breed Genet 2009;126:189-97. https://doi.org/10.1111/j.1439-0388.2008.00769.x
  36. FAO 1998. Initiative for domestic animal diversity. Secondary guidelines for development of national farm animal genetic resources management plans: Management of small populations at risk. Rome, Italy: FAO; 1998.
  37. Santana ML, Bignardi AB. Status of the genetic diversity and population structure of the Pega donkey. Trop Anim Health Prod 2015;47:1573-80. https://doi.org/10.1007/s11250-015-0900-x
  38. Goyache F, Gutierrez JP, Fernandez I, et al. Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example. J Anim Breed Genet 2003;20:95-103. https://doi.org/10.1046/j.1439-0388.2003.00378.x
  39. Sorensen AC, Sorensen MK, Berg P. Inbreeding in Danish dairy cattle breeds. J Dairy Sci 2005;88:1865-72. https://doi.org/10.3168/jds.S0022-0302(05)72861-7
  40. Baneh H, Javanrouh A, Sadeghi SAT, et al. Characterization of population structure and genetic diversity of Adani goats. J Anim Sci Technol 2020;8:79-89. https://doi.org/10.22103/JLST.2020.15775.1315
  41. Mandal A, Baneh H, Subramanyam BV, Notter DR. Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India. Small Rumin Res 2020;191:106182. https://doi.org/10.1016/j.smallrumres.2020.106182