Estimation of Effective Population Size and Genomic Inbreeding Coefficients in Baluchi Sheep Using Genome-Wide Single Nucleotide Polymorphisms (SNPs)
الموضوعات :م. پسندیده 1 , م. قلی زاده 2 , ق. رحیمی میانجی 3
1 - Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran
2 - Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran
3 - Department of Animal Science, Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Science and Natural Resources University, Sari, Iran
الکلمات المفتاحية: Baluchi sheep, effective population size, genome wide evaluation, inbreeding coeffi-cients,
ملخص المقالة :
The aim of this study was to estimate the effective population size (Ne) and genomic inbreeding coefficients in 96 Baluchi sheep genotyped using Illumina OvineSNP50 BeadChip. Using NEESTIMATOR software, the estimation of contemporary Ne based on heterozygote-excess and linkage disequilibrium (LD) methods was obtained 15 and 25, respectively. The historical Ne estimated with SNeP software showed a fast decreasing trend over the last 1000 generations. The Ne estimate for the previous 4 generations was ranged from 48 to 75. Three estimates of inbreeding coefficients including genomic relationship matrix (FGRM), excess of homozygosity (FHOM) and correlation between uniting gametes (FUNI) were calculated using GCTA software. The values of FGRM, FHOM and FUNI were calculated the same at -0.017. The average expected and observed heterozygosity using PLINK software were calculated as 0.374 and 0.383, respectively. Our results showed a considerable genetic variation in Baluchi sheep, however the low values of Ne emphasize that measures should be taken to avoid a further reduction in the effective population size. The results of this study provide guidance for future sheep breeding to increase the conservation activities of the native sheep breeds.
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. Genet. Sel. Evol. 47, 90-98.
Barbato M., Orozco-Terwengel P., Tapio M. and Bruford M.W. (2015). SNeP: A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front. Genet. 6, 109-119.
Burren A., Signer-Hasler H., Neuditschko M., Tetens J., Kijas J., Drögemüller C. and Flury C. (2014). Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data. Anim. Genet. Resour. 55, 67-76.
Corbin L.J., Liu A., Bishop S. and Woolliams J. (2012). Estimation of historical effective population size using linkage disequilibria with marker data. J. Anim. Breed. Genet. 129, 257-270.
Crow J.F. and Kimura M. (1970). An Introduction to Population Genetics Theory. Harper and Row, New York, USA.
Do C., Waples R.S., Peel D., Macbeth G., Tillett B.J. and Ovenden J.R. (2014). NeEstimator v2: Re implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14, 209-214.
Esmaeilkhanian S. and Banabazi M.H. (2006). Genetic variation within and between five Iranian sheep populations using microsatellites markers. Pakistan J. Biol. Sci. 9, 2488-2492.
Falconer D. and Mackay T. (1996). Introduction to Quantitative Genetics. Longman Group Ltd., Essex, United Kingdom.
Frankham R., Bradshaw C.J. and Brook B.W. (2014). Genetics in conservation management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biol. Conserv. 170, 56-63.
Ghafouri-Kesbi F. (2012). Using pedigree information to study genetic diversity and re-evaluating a selection program in an experimental flock of Afshari sheep. Arch. Anim. Breed. 55, 375-384.
Gholizadeh M. and Ghafouri-Kesbi F. (2016). Inbreeding depression in growth traits of Baluchi sheep. Small Rumin. Res. 144, 184-190.
Hayes B.J., Visscher P.M., McPartlan H.C. and Goddard M.E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 13, 635-643.
Hedgecock D., Launey S., Pudovkin A., Naciri Y., Lapegue S. and Bonhomme F. (2007). Small effective number of parents (N b) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Mar. Biol. 150, 1173-1182.
Hill W. and Robertson A. (1968). Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226-231.
Keller M.C., Visscher P.M. and Goddard M.E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics. 189, 237-249.
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. Genet. Sel. Evol. 45, 1-9.
Liu S., He S., Chen L., Li W., Di J. and Liu M. (2017). Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genom. 39, 733-745.
Mastrangelo S., Sardina M., Tolone M., Di Gerlando R., Sutera A., Fontanesi L. and Portolano B. (2018). Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal. 12, 2480-2488.
Mohammadi H., Rafat S.A., Moradi Shahrebabak H., Shodja J. and Moradi M.H. (2017). Estimation of genomic inbreeding coefficient and effective population size in Zandi sheep breed using density SNP markers. Anim. Sci. J. 119, 129-142.
Mokhtari M., Miraei-Ashtiani S., Jafaroghli M. and Gutiérrez J. (2015). Studying genetic diversity in Moghani sheep using pedigree analysis. J. Agr. Sci. Technol. 17, 1151-1160.
Mokhtari M., Shahrbabak M.M., Esmailizadeh A., Shahrbabak H.M. and Gutierrez J. (2014). Pedigree analysis of Iran-Black sheep and inbreeding effects on growth and reproduction traits. Small Rumin. Res. 116, 14-20.
Moradi M.H., Farahani A.H. and Nejati-Javaremi A. (2017). Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information. Iranian J. Anim. Sci. 48, 39-49.
Ohta T. and Kimura M. (1971). Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics. 68, 571-579.
Prieur V., Clarke S.M., Brito L.F., McEwan J.C., Lee M.A., Brauning R., Dodds K.G. and Auvray B. (2017). Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps. BMC Genet. 18, 68-75.
Pudovkin A., Zaykin D. and Hedgecock D. (1996). On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics. 144, 383-387.
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., Maller J., Sklar P., De Bakker P.I. and Daly M.J. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575.
Qanbari S., Pimentel E., Tetens J., Thaller G., Lichtner P., Sharifi A. and Simianer H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. 41, 346-356.
Rashidi A., Almasi M. and Sattaei Mokhtari M. (2018). Inbreeding effects on lamb pre-weaning growth traits and survival in three Iranian sheep breeds. J. Livest. Sci. Technol. 6, 47-56.
Rochus C.M. and Johansson A.M. (2017). Estimation of genetic diversity in Gute sheep: Pedigree and microsatellite analyses of an ancient Swedish breed. Hereditas. 154, 4-10.
Rodríguez-Ramilo S.T., Fernández J., Toro M.A., Hernández D. and Villanueva B. (2015). Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population. PLoS One. 10, e0124157.
Sved J. (1971). Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2, 125-141.
Tahmoorespur M. and Sheikhloo M. (2011). Pedigree analysis of the closed nucleus of Iranian Baluchi sheep. Small Rumin. Res. 99, 1-6.
Uimari P. and Tapio M. (2011). Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J. Anim. Sci. 89, 609-614.
Vajed Ebrahimi M.T., Mohammadabadi M. and Esmailizadeh A. (2017). Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran. Arch. Anim. Breed. 60, 183-189.
VanRaden P.M. (2008). Efficient methods to compute genomic predictions. J. Dairy Sci. 91, 4414-4423.
Vozzi P., Marcondes C., Bezerra L. and Lôbo R. (2007). Pedigree analyses in the breeding program for nellore cattle. Embrapa Amazônia Oriental-Artigo em Periódico Indexado. 6(4), 1044-1050.
Wang J. (2005). Estimation of effective population sizes from data on genetic markers. Philos. T. R. Soc. B. 360, 1395-1409.
Waples R.S. (1989). A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics. 121, 379-391.
Waples R.S. (1991). Genetic methods for estimating the effective size of cetacean populations. Rep. Int. Whal. Comm. 13, 279-300.
Waples R.S. and Do C. (2008). LDNE: A program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8, 753-756.
Weir B. and Hill W.G. (1980). Effect of mating structure on variation in linkage disequilibrium. Genetics. 95, 477-488.
Wright S. (1922). Coefficients of inbreeding and relationship. Am. Nat. 56, 330-338.
Wright S. (1948). Encyclopaedia Britannica. University of Chicago Press, Chicago, Illinois.
Yang J., Lee S.H., Goddard M.E. and Visscher P.M. (2011). GCTA: A tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76-82.
Yazdi M., Engström G., Näsholm A., Johansson K., Jorjani H. and Liljedah L.E. (1997). Genetic parameters for lamb weight at different ages and wool production in Baluchi sheep. Anim. Sci. 65, 247-255.
Zeder M.A. (1999). Animal domestication in the Zagros: A review of past and current research. Paléorient. 25(2), 11-25.
Zhang Q., Calus M.P., Guldbrandtsen B., Lund M.S. and Sahana G. (2015). Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genet. 16, 88-98.
Zhao F., Wang G., Zeng T., Wei C., Zhang L., Wang H., Zhang S., Liu R., Liu Z. and Du L. (2014). Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livest. Sci. 170, 22-29.
Zhdanova O.L. and Pudovkin A.I. (2008). Nb_HetEx: A program to estimate the effective number of breeders. J. Hered. 99, 694-695.
