Pedigree Analysis and Inbreeding Investigation in Lori-Bakhtiari Sheep

پژوهشهای علوم دامی ایران

Article 10, Volume 9, Issue 3 - Serial Number 31, September 2018, Pages 376-386   

Document Type: Genetics & breeding

DOI: 10.22067/ijasr.v9i3.58603

Authors

Mohammad Keshavarzpour; Mohammad Reza Bahreini Behzadi^* ; Mostafa Muhaghegh dolatabadi

Yasouj university

Abstract

Introduction Control and management of genetic diversity of breeds is necessary for their sustainable use in the future because a limited number of breeding animals will unavoidably lead to increased inbreeding and thus to a reduction in additive genetic variance, and maybe to inbreeding depression. Managing inbreeding is usually one of the major goals in conservation and selection programs of breeds. Some of descriptive parameters of population structure are the inbreeding coefficient, effective population size, effective number of founders, effective number of ancestors, effective number of founder genomes, effective number of non-founder genomes and average generation interval, which are indicative of genetic diversity levels in a population. In a breeding program, the inbreeding coefficient and the rate of annual inbreeding should be monitored because of their influence on production and on the estimation of genetic parameters. The Lori-Bakhtiari sheep is one of the most important native breeds of Iran. With more than 1.7 million head population are mostly kept on village or semi-migratory system in Chaharmahal and Bakhtiari province. This breed has the largest fat-tail size among all of sheep breeds in Iran. The objective of this study was to investigate genetic structure and genetic diversity of Lori–Bakhtiari sheep using pedigree analysis and the inbreeding depression of body weight traits was estimated.
Materials and methods The pedigree information of 7693 Lori–Bakhtiari lambs (2478 male and 5215 female) from 274 rams and 2006 ewes collected from 1990 to 2011, were used. The data were collected at Shooli sheep breeding station in Shahrekord, Chaharmahal and Bakhtiari province. Estimation of inbreeding coefficients was done by CFC software and Endog (v4.8) software was used to compute other pedigree analyses including mean coancestry, effective population size, probability of gene origin parameters and average generation interval. Parameters based on the probability of gene origin were used to describe genetic variability. To investigate the effect of inbreeding on body weight traits, the data of birth weights, weaning weights, weights at six months of age, weights at nine months of age and weights at 12 months of age were used. Inbreeding depression was estimated as the regression of these performance records on the individual inbreeding coefficients by fitting an animal model. WOMBAT software was used for estimating the inbreeding depression of body weight traits.
Results and Discussion Total number of founders, effective number of founders, effective number of ancestors, effective number of founder genomes and effective number of non-founder genomes were 506, 105, 90, 65, 181 heads, respectively. Average generation interval and effective population size were 4.23 years and 249 heads, respectively. The generation interval in the dam-progeny pathway was shorter than in sire-progeny pathway. Estimated average coancestry and inbreeding coefficient were 0.76 and 0.56, respectively. Animals with progeny were 29.7 % and those of without progeny 70.3 % of the total animals. Animals with both known parents and one unknown parent constituted 92 % of the population. Between all the registered animals, 28 % were inbred. The average inbreeding coefficient during the study period for inbred and all animals were 2 and 0.56 %, respectively. The most inbred animals, equivalent to 25% of the inbreeds, had inbreeding coefficients equal to or lower than 5 %. The regression coefficients for birth weight, weaning weight, weight at 6, 9 and 12 months of age on inbreeding were -11, -106.6, -259.7, -161.2 and -239.9 g, respectively.
Conclusion Considering the parameters obtained from the probability of gene origin analysis, the contribution rate of founders and major ancestors have been unbalanced due to the selection of animals that led to decrease of genetic diversity. Estimated inbreeding depression of body weight traits for this breed was higher than other sheep breeds of Iran and showed high degree of close mating in this herd. Due to the deleterious effect of inbreeding on body weight traits it is suggested that this breeding station should use a better breeding plan to avoid mating of close relative animals. At this study, the presence of inbreeding depression for body weight traits also confirmed reduction of genetic diversity in this population. The results of this study also indicate that genetic variability within this population has to be monitored constantly in order to prevent or minimize loss of founder alleles due to genetic drift or selection. The authors suggested that pedigree analysis should be done periodically in this breeding station. Doing this analysis would also prevent or control kinship in this breeding population.

Keywords

Inbreeding; Growth traits; Lori-Bakhtiari sheep; Pedigree structure

References

1- Adeli Khah, M. H., R. Vaez Torshizi., M. Rokouei, and D. Tohidi. 2008. Inbreeding and its effects on production traits Iranian Zandi sheep. Pages 1-4 in Proc. 3rd Congress on Animal Science, Mashhad, Iran. (In Persian).

2- Bahri Binabaj, F., H. Faraji Arogh., M. Rokouei., M. Jafari, and A. Mohammad Hashemi. 2012. Estimation of inbreeding trend and its effect on growth traits, longevity and skin score of Karakul sheep breed. Pages 760-764 in Proc. 5th Congress on Animal Science, Isfahan, Iran. (In Persian).

3- Barker, J. S. F. 2001. Conservation and management of genetic diversity: a domestic animal perspective. Canadian Journal of Forest Research, 31(4): 588-595.

4- Boichard, D., L. Maignel, and E. Verrier. 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 29: 5–23.

5- Caballero, A., and M. A. Toro. 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research, 75: 331–343.

6- Cassell, B. G., V. Adamec, and R. E. Pearson. 2003. Effects Effects of incomplete pedigree on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys. Journal of Dairy Science, 86: 2967–2976.

7- Dorostkar, M., H. Faraji Arough., J. Shodja., S. A. Rafat., M. Rokouei, and H. Esfandyari. 2012. Inbreeding and inbreeding depression in Iranian Moghani sheep breed. Journal of Agriculture Science and Technology, 14: 549-556.

8- Duchev, Z., O. Distl, and E. Groeneveld. 2006. Early warning system for loss of diversity in European livestock breeds. Archiv Tierzucht, 49: 521-531.

9- Falconer, D. S., and F. C. Mackay. 1996. Introduction to Quantitative Genetics. Longman, Harlow, UK.

10- FAO, 1998. Secondary guidelines for development of national farm animal genetic resources management plans: management of small populations at risk. Food and Agriculture Organization, Rome, Italy.

11- Ghafouri-Kesbi, F. 2010. Analysis of genetic diversity in a close population of Zandi sheep using genealogical information. Journal of Genetics, 89: 479–483.

12- Ghafouri-Kesbi, F. 2012. Using pedigree information to study genetic diversity and reevaluating a selection program in an experimental flock of Afshari sheep. Archiv Tierzucht, 55(4): 375–384.

13- Gholambabaeian, M. M., A. Rashidi., M. Razmkabir, and E. Mirzamohammadi. 2012. Inbreeding coefficient estimate and its effects on pre-weaning traits in Moghani sheep. Pages 71-75 in Proc. 5th Congress on Animal Science, Isfahan, Iran. (In Persian).

14- Goyache, F., J. P. Gutierrez., I. Fernandez., E. Gomez., I. Alvarez., J. Dıez, and L. J. Royo. 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: 95–103.

15- Gutierrez, J. P., and F. Goyache. 2005. A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122(3): 172-176.

16- Gutierrez, J. P., I. Cervantes, and F. Goyache. 2009. Improving the estimation of realized effective population sizes in farm animals. Journal of Animal Breeding and Genetics, 126(4): 327–332.

17- Huby, M., L. Griffon., S. Moureaux., H. De Rochambeau., C. Danchin-Burge, and E. Verrier. 2003. Genetic variability of six French meat sheep breeds in relation to their genetic management. Genetics Selection Evolution, 35(6):637–655.

18- Lacy, R. C. 1989. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivlents. Zoo Biology, 8(2): 111-123.

19- Li, M. H., I. Stranden, and J. Kantanen. 2009. Genetic diversity and pedigree analysis of the Finnsheep breed. Journal of Animal Science, 87(5): 1598–1605.

20- Mehmannavaz, Y., R. Vaez Torshizi., A. Salehi, and A. Shourideh. 2002. Inbreeding and its effects on production traits in Iranian Baluchi sheep. Pages 264-269 in Proc. the first seminar on genetics and breeding applied to livestock, poultry and aquatics, Karaj, Iran. (In Persian).

21- Melka, M. G, and F. S. Schenkel. 2010. Analysis of genetic diversity in four Canadian Swine breeds using pedigree data. Canadian Journal of Animal Science, 90(3): 331-340.

22- Meuwissen, T. I, and Z. Luo. 1992. Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24(4): 305–313.

23- Meyer, K. 2007. WOMBAT – A tool for mixed model analyses in quantitative genetics by REML. Journal of Zhejiang University-Science B, 8:815–821.

24- Mucha, S, and J. J. Windig. 2009. Effects of incomplete pedigree on genetic management of Dutch Landrace goat. Journal of Animal Breeding and Genetics, 126(3): 250-256.

25- Nadery Choploo, A., Sh. Ghoraishy., M. Rokouei, and M. Mansoori. 2012. Pedigree analysis of the closed nucleus of Iranian Markhoz goats. Pages 614-619 in Proc. 5th Congress on Animal Science, Isfahan, Iran. (In Persian).

26- Norberg, E, and A. C. Sorensen. 2007. Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire and Oxford Down. Journal of Animal Science, 85(2): 299–304.

27- Paiva, S. R., O. Faco., D. A. Faria., T. Lacerda., G. B. Barretto., P. L. S. Carneiro., R. N. B. Lobo, and C. McManus. 2011. Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep. Tropical Animal Health and Production, 43(7): 1449-1457.

28- Pedrosa, V. B., J. M. L. Santana., P. S. Oliveira., J. P. Eler, and J. B. S. Ferraz. 2010. Population structure and inbreeding effects on growth traits of Santa Inês sheep in Brazil. Small Ruminant Research, 93(2-3): 135–139.

29- Rashedi Dehsahraei, A., J. Fayazi, and M. Vatankhah. 2013. Investigating inbreeding trend and its impact on growth traits of Lori-Bakhtiari Sheep. Journal of Ruminant Research, 1: 65-78. (In Persian).

30- Rochambeau, H. C., F. Fournet-Hanocq, and J. V. T. Khang. 2000. Measuring and managing genetic variability in small populations. Annales de Zootechnie, 49(2): 77-93.

31- Sargolzaei, M., H. Iwaisaki, and J. J. Colleau. 2006. CFC: a tool for monitoring genetic diversity. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil.

32- Sheikhloo, M., M. Tahmoorespur, and A. A. Aslaminejad. 2012. A study of inbreeding of Baluchi Sheep in Abbas Abad breeding center of Mashhad. Iranian Journal of Animal Science Research, 3: 453-458. (In Persian).

33- Sheikhloo, M., M. Tahmoorespur, and A. A. Aslaminejad. 2013. Study of genetic variability of breeding flock of Makooyi sheep using pedigree analysis. Pages 1116-1120 in Proc. 1st National Conference on Livestock and Poultry Production in Northern Iran, Sari, Iran. (In Persian).

34- Tahmoorespour, M, and M. Sheikhloo. 2011. Pedigree analysis of the closed nucleus of Iranian Baluchi sheep. Small Ruminant Research, 99(1): 1–6.

35- Vatankhah, M., M. Moradi Shahrbabak., A. Nejati javarami., R. Miraei Ashtiani, and R. Vaez Torshizi. 2009. Determination of breeding objective and economic values for Lori-Bakhtiari breed of sheep in the village system. Animal Science Research, 82: 17-25. (In Persian).