Estimation of genomic inbreeding coefficient and effective population size in Zandi sheep breed using density SNP markers (50K SNPChip)

Document Type : Research Paper

Authors

1 Department of animal science, University of Tabriz

2 animal science- university of Tabriz

3 Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran.

4 Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz

5 Department of Animal Sciences, Faculty of Agriculture and Natural Resources, University of Arak

Abstract

The aim of this study was to investigate genome-wide Inbreeding and effective population size using the information obtained from 96 Zandi sheep breed using a density SNP panel (50K SNPChip). For this purpose, after quality control of SNP markers data, 40,879 SNPs were remained for computing inbreeding and effective population size. Effective number of breeders was estimated per each chromosome using NEESTIMATOR software based on heterozygote-excess method., and inbreeding coefficient was derived using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using GCTA software and run of homozygosity (FROH) using PLINK software. Average expected and observed heterozygosity ranged 0.393 and 0.407 respectively. Average chromosome-wise effective number of breeders was equal to 69 and corresponding average confidence interval was between 40.0 and 93.26. The magnitude of inbreeding coefficient using FGRM, FHOM, and FUNI was similar (0.064) and it was estimated 0.053 using Run of homozygosity. Generally, the results indicated that although a considerable genetic variation exists in Zandi population in case study, however effective population has been decreased strongly in Zandi sheep breed during recent years and designing of appropriate programs is necessary to conserve remaining purebred animals of this indigenous sheep breed.

Keywords

References

مرادی، م.­­ ح.، فراهانی، ا. ح. و نجاتی جوارمی، ا. (1396). ارزیابی ژنگانی اندازه مؤثر جمعیت برخی از نژادهای گوسفند ایرانی با استفاده از اطلاعات عدم تعادل پیوستگی. مجله علوم دامی ایران. دوره 48، شماره 1، ص ص 49-39.
کریمی، ک.، اسماعیلی زاده کشکوئیه، ع. و اسدی فوزی، م. (1394). برآورد اندازه مؤثر جمعیت در گاو سرابی براساس نشانگرهای چند شکل تک نوکلئوتیدی. مجله علوم دامی ایران. دوره 46، شماره 3، ص ص 343-335.
Al‑Mamun, H.A., Clark, S.A., Kwan P. and Gondro, C. (2015). Genome‑wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetic Selection Evolution, 47:90.
Burren,  A.,  Signer-Hasler,  H.,  Neuditschko,  M.,  Tetens,  J.,  Kijas,  J. W.,  Drögemüller,  C. and et al. (2014).  Fine-scale  population  structure  analysis  of  seven  local  Swiss  sheep  breeds  using  genome wide SNP data. Animal Genetic Resources, 55, 67-76.
Corbin, LJ., Blott, S.C., Swinburne, J.E., Vaudin, M., Bishop, S.C. and Woolliams, J.A. (2010). Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics, 41, 8-15.
Chitneedi, P.K., Arranz, J.J., Suarez-Vega, A., Garcıa-Gamez E. and Gutierrez-Gil, B. (2017). Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes. Animal Genetics, 1:11.
Danchin-Burge, C., Palhière, I., François, D., Bibé, B., Leroy, G. and Verrier, E. (2010).  Pedigree analysis  of  seven  small  French  sheep  populations  and  implications  for  the management  of  rare breeds. Journal of Animal Science, 88, 505-516.
Do, C., Waples, R.S. Peel, D., Macbeth, G.M., Tillett, B.J. and Ovenden, J.R. (2014). Ne Estimator v2.0: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14, 209–214. 
Esmaeilkhanian, E. and Banabazi, M.H. (2006). Genetic variation within and between five Iranian sheep populations using microsatellite markers. Pakistan Journal of Biological Science, 9(3), 2488-2492.
Flury, C., Tapio, M., Sonstegard, T., Drogemuller, C., Leeb, T., Simianer, H. and et al., (2010). Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding Genetics, 127, 339-347.
Frankham R. (2005). Genetics and extinction. Biological Conservation, 126:131–140.
Frankham, R., Bradshaw, C. J.A. and Brook, B.W. (2014). Genetics  in conservation  and management:  Revised  recommendations  for  the  50/500  rules,  Red  List  criteria  and  population viability analyses. Biological Conservation, 170, 56-63.
Gomez‑Raya, L., Rodríguez, C., Barragan, C., and Silio, L. (2015). Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genetic Selection Evolution, 47:81.
Gautier, M., Flori, L., Riebler, A., Jaffrézic, F., Laloé, D., Gut, and et al. (2009). A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics, 10, 550-568.
Gautier, M., Laloe, D. and Moazami-Goudarzi, K. (2010). Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS One, 5(9), 13038-13049.
Ghafouri-Kesbi, F. (2010a). Analysis of genetic diversity in a close population of Zandi sheep using genealogical information. Journal of Genetics, 89, 479-483.
Ghafouri-Kesbi, F. (2010b). Change in genetic size of small-closed populations: Lessons from a domestic mammal population. Genetics and Molecular Biology, 33, 657-662.
Ghafouri-Kesbi, F. (2012). Using pedigree information to study genetic diversity and reevaluating a selection program in an experimental flock of Afshari sheep. Archiv fur Tierzucht, 55: 375-384.
Gibson, J., Morton, NE. and Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics, 15(5), 789–795.
Kijas, J. W., Lenstra, J. A., Hayes, B. J., Boitard, S., Porto Neto, L. R., San Cristobal, M. and  et al .(2012). Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10, e1001258.
Ibeagha-Awemu, E.M. and Erhardt, G. (2005). Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms. Journal of Animal Breeding and Genetics, 122(1), 12-20.
Kirin, M., McQuillan, R., Franklin, C.S., Campbell, H., McKeigue, P.M. and Wilson, J.F. (2010). Genomic runs of homozygosity record population history and consanguinity. PLoS One, 5(11), 13996-14003.
Mastrangelo, S., Tolone, M., Gerlando, R.D., Fontanesi, L., Sardina, M.T., Portolano, B. (2016). Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, 10:5, 746–754.
McQuillan, R., Leutenegger, A.L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L. et al. (2008). Runs of homozygosity in European populations. American Journal of Human Genetics, 83(3), 359–72.
Mokhtari, M. S., Miraei-Ashtiani, S. R., Jafaroghli, M. and Gutiérrez, J. P. (2015). Studying genetic diversity in Moghani sheep using pedigree analysis. Journal of Agricultural Science and Technology, 17, 1151-1160.
Leroy, G., Mary-Huard, T., Verrier, E., Danvy, S., Charvolin, E. and Danchin-Burge, C. (2013). Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetic Selection and Evolution, 45, 1-10
Prieur, V., Clarke, S.M., Brito, L.F., McEwan, J.C., Lee, M.A., Brauning, R. and et al. (2017). Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps. BMC Genetics,18: 68.
Pons, A. L., Landi, V., Martinez, A. and Delgado, J. V. (2015). The biodiversity and genetic structure of Balearic sheep breeds. Journal of Animal Breeding Genetics, 132(3), 268-76.
Purfield, D.C., Berry, D.P., McParland, S. and Bradley, D.G. (2012). Runs of homozygosity and population history in cattle. BMC Genetics, 13(70), 1471-1482.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D., and et al. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics 81: 559-575.
Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R. and Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics, 41, 346-356.
Tahmoorespur, M. and Sheikhloo, M. (2011). Pedigree analysis of the closed nucleus of Iranian Baluchi sheep. Small Ruminant Research, 99, 1-6.
Teo, Y.Y, Fry, A.E., Clark, T.G., Tai, E.S., Seielstad, M. (2007). On the usage of HWE for identifying genotyping errors. Annals of Human Genetics, 71: 701-703.
Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D.L., Clarke, G. M., Goddard, M. E. and Visscher P.M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17, 520-526.
Uimari, P.  and Tapio, M.  (2011).  Extent  of  linkage  disequilibrium  and  effective  population  size  in Finnish Landrace and Finnish Yorkshire pig breeds. Journal of Animal Science, 89, 609-614.
VanRaden, P.M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414–23.
Wright, L.I., Tregenza, T. and Hosken, D.J. (2008). Inbreeding, inbreeding depression and extinction. Conservation Genetics, 9:833–843.
Yang, J.A., Lee, S.H., Goddard, M.E. and Visscher, P.M. (2011). GCTA: a tool for genome-wide complex trait analysis. American Journal of Human Genetics, 88(1), 76–82.
Zhang, Q., PL-Calus, M., Guldbrandtsen, B., S Lund, M. and Sahana, G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genetics,16(88): 1186-1197.
Zhao, F., Wang, G., Zeng, T., Wei, C., Zhang, L. Wi, D., and et al.  (2014). Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livestock Science, 170, 22-2.
Zhdanova, O. and Pudovkin, A.I. (2008) Nb-HetEx: A Program to Estimate the Effective Number of Breeders. Journal of Heredity, 99, 694-695.
Animal Sciences Journal
Volume 31, Issue 119
September 2018
Pages 129-142

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