Genetic Variation within and between Three Iranian Goat Populations Using Nine Microsatellite Markers

Subject Areas : Camel

P. Gholizadeh ¹ , M.B. Montazer Torbati ² , A. Javanmard ³ , S. Alijani ⁴

1 - Department of Animal Science, Faculty of Agriculture, University of Birjand, Birjand, Iran
2 - Department of Animal Science, Faculty of Agriculture, University of Birjand, Birjand, Iran
3 - Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
4 - Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

Received: 2020-11-28 Accepted : 2021-05-15 Published : 2022-03-01

Keywords: genetic diversity, Conservation, Microsatellite markers, indigenous goat,

Abstract :

Genetic diversityis essential and mirrors for diversity pattern and population evolution. With this motivation, the aim here is to investigate genetic similarities of three indigenous goats of Iran: Azerbaijan (n=50), Sarbisheh (n=50), Busher (n=29) using 9 microsatellites markers. We extracted genomic DNA and then employed routine polymerase chain reaction (PCR) protocol for amplification of nine specific microsatellite markers. The experimental raw genotype was applied to generate summary of statistics for molecular diversity criteria. From the results, 8 microsatellites visualized satisfactory electrophoresis pattern and reasonable degree of polymorphism. The ILSTS004 (0.42) and BM415 (1.8) microsatellite markers indicated highest and lowest value for Shannon index. We obtain 57-67% range for observed heterozygosity value regarding to Azerbaijan and Sarbisheh goat, respectively. From these results it is clear the high genetic similarity was found between the Sarbisheh and Busher populations. Overall, bottleneck based evidence using IAM and SMM models demonstrated normal ‘L’-shaped distribution in investigated Azerbaijan and Sarbisheh goat. In conclusion, this analysis leads evidence for sufficient genetic variation within investigated goat.

References:

Abdelkader A.A., Ata N., Benyoucef M.T., Djaout A., Azzi N., Yilmaz O., Cemal I. and Gaouar S.B.S. (2017). New genetic identification and characterisation of 12 Algerian sheep breeds by microsatellite markers. Italian J. Anim. Sci. 17, 38-48. ‏

Abdelkader A.A., Yilmaz O., Ata N., Cemal I. and Gaouar S.B.S. (2019). Assessment of genetic diversity of Turkish and Algerian native sheep breeds. Acta Agric. Slovenica. 115, 5-14. ‏

Abdul-Muneer P.M. (2014). Application of microsatellite markers in conservation genetics and fisheries management: Recent advances in population structure analysis and conservation strategies-review article. Genet. Res. Int. 2014, 691759-691765.

Amos W., Saweer S.J., Feakes R.W. and Rubinsztein D.C. (1996). Microsatellites show mutational bias and heterozygote instability. Nat. Genet. 43, 390-391.

Askari N., Mohammadabadi M.R. and Baghizadeh A. (2011). ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian J. Biotechnol. 9, 222-229.

Barker J.S.F. (1994). A global protocol for determining genetic distances among domestic Livestock breeds. Pp. 501-508 in Proc. 5^th World Congr. Genet. Appl. Livest. Prod. Guelph, Ontario, Canada.

Botstein D., White R.L., Skolnick M. and Davis W. (1980). Construction of genetic linkage maps in man using restriction fragment length polymorphisms. Am. J. Human Genet. 32, 314-331.

Cherifi Y.A., Gaouar S.B.S., Guastamacchia R., El-Bahrawy K.A., Abushady A.M.A., Sharaf A.A., Harek D., Lacalandra G.M., Saidi-Mehtar N. and Ciani E. (2017). Weak genetic structure in northern African dromedary camels reflects their unique evolutionary history. PloS One. 1, e0168672.

Coombs J.A., Letcher B.H. and Nislow K.H. (2008). CREATE: A software to create input files from diploid genotypic data for 52 genetic software programs. Mol. Ecol. Resour. 8, 578-580. ‏

Crowford A.M., Kappes S.M., Paterson K.A., de Gotari M.J., Dodds K.G., Freking B.A., Stone R.T. and Beattie C.W. (1997). Microsatellite evolution: testing the ascertainment bias hypothesis. J. Mol. Evol. 46, 256-260.

De-Gortari M.J., Freking B.A., Cuthbertson R.P., Kappes S.M., Keele J.W., Stone R.T., Kreg A., Leymaster K.R., Dodds G.K., Allan M., Crawford A.M. and Beattie C.W. (1998). A second-generation linkage map of the sheep genome. Mamm. Genome. 9, 204-209. ‏

Dossybayev K., Orazymbetova Z., Mussayeva A., Saitou N., Zhapbasov R., Makhatov B. and Bekmanov B. (2019). Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis. Arch. Anim. Breed. 62, 305-311.

Dudu A., Popa G.O., Ghita E., Pelmus R., Lazar C., Costache M. and Georgescu S.E. (2020). Assessment of genetic diversity in main local sheep breeds from Romania using microsatellite markers. Arch. Anim. Breed. 63, 53-58.

Ebrahimi M., Taghi V., Mohammadreza M. and Ali E. (2017). Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran. Arch. Anim. Breed. 3,183.

Excoffier L. and Lischer H. (2010). ARLEQUIN suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10, 564-567.

FAO. (2004). Secondary Guidelines for Development of National Farm Animal Genetic Resources Management Plans. Measurement of Domestic Animal Diversity (MoDAD): Recommended Microsatellite Markers Initiative for Domestic Animal Diversity. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.

FAO. (2011). Guidelines for the Molecular Genetic Characterization of Animal Genetic Resources. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.

FAOSTAT. (2020). Database of the Food and Agricultural Organization (FAO) of the United Nations. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.

Glaubitz J.C. (2004). Convert: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes. 4, 309-310.

Goldstein D.B. and Schlotterer C. (1999). Microsatellites; Evolution and Application. Oxford University Press. Oxford, United Kingdom.

Greguła-Kania M., Karpinski M., Gruszecki M.T., Milewski S., Drozd L., Patkowski K., Czyżowski P., Goleman M., Tajchman K., Kondracki M., Wiercińska K. and Szymanowska A. (2015). Analysis of genetic diversity in newly created sheep populations and their maternal breeds. Sci. Ann. Polish Anim. Prod. 4, 21-29. ‏

Hristova D., Todorovska E., Vassilev D., Metodiev S., Popov I., Yablanski T. and Zhelyazkov E. (2014). Microsatellites based genetic diversity and population structure of seven Bulgarian indigenous sheep breeds. Int. J. Curr. Microbiol. Appl. Sci. 3, 569-581.

Hussain T., Musthafa M.M., Babar M., Shaheen M. and Marikar F. (2019). Molecular genetic diversity and relationship of indigenous sheep breeds of Pakistan based on nuclear microsatellite loci. ‏ Rev. Vet. 30, 54-58.

Jawasreh K.I., Mustafa I., Zuhair M.A., Abdel B.I. and Al Sukhni I. (2018). Genetic diversity and population structure of local and exotic sheep breeds in Jordan using microsatellites markers. Vet. World. 11, 2231-0916.

Jyotsana B., Jakhesaraa S., Prakashb V., Ranka D.N. and Vataliyac P.H. (2010). Genetic features of Patanwadi, Marwari and Dumba sheep breeds (India) inferred by microsatellite markers. Small Rumin. Res. 93, 57-60.

Karsli B.A., Demir E., Fidan H.G. and Karsli T. (2020). Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites. Arch. Anim. Breed. 63, 165-172.

Kdidi S., Calvo J.H., Gonzalez-Calvo L., Sassi M.B., Khorchani T. and Yahyaoui M.H. (2015). Genetic relationship and admixture in four Tunisian sheep breeds revealed by microsatellite markers. Small Rumin. Res. 131, 64-69. ‏

Kevorkian S.E.M., Georgescu S.E., Manea M.A., Zaulet M., Hermenean A.O. and Costache M. (2010). Genetic diversity using microsatellite markers in four Romanian autochthonous sheep breeds. Romanian Biotechnol. Lett. 15, 5059-5065. ‏

Kusza S., Dimov D., Nagy I., Bosze Z., Javor A. and Kukovics S. (2010). Microsatellite analysis to estimate genetic relationships among five Bulgarian sheep breeds. Genet. Mol. Biol. 33, 51-56.

Mahmoud A.H., Farah M.A., Alanazi K., Rady A., Salah M., Amor N. and Mohammed O. (2017). Genetic diversity among Sawakni, Berberi and Najdi sheep breeds in Saudi Arabia using microsatellites markers. African J. Biotechnol. 16, 171-178.

Manjari J.S., Kumari B.P., Ekambaram B., Reddy Y.R. and Amol T. (2018). Studies on genetic Variability in Nellore brown sheep using microsatellite Markers. Int. J. Livest. Res. 11, 149-157.

Miller B.A. and Lu C.D. (2019). Current status of global dairy goat production: An overview. Asian-Australasian J. Anim. Sci. 32(8), 1219-1232.

Mohankishore M., Punyakumari B., Suresh J., Bharathi G. and Amol J.T. (2019). Genetic diversity analysis of Macherla Brown Sheep using microsatellite markers. Int. J. Livest. Res. 9, 84-93.

Musthafa M.M., Aljummah R.S. and Alshaik M.A. (2012). Genetic diversity of Najdi sheep based on microsatellite analysis. African J. Biotechnol. 11, 14868-14876. ‏

Nei M. (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, USA.

Ocampo R., Cardona H. and Martinez R. (2016). Genetic diversity of Colombian sheep by microsatellite markers. Chilian J. Agric. Res. 76, 40-47. ‏

Peakall R. and Smouse P.E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 28, 2537-2539.

Piry S., Luikart G. and Cornuet J.M. (1999). Bottleneck: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Heridity. 90, 502-503.

Pritchard J.K., Stephens M. and Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics. 155, 945-959.

Qwabe S.O. (2011). Genetic and phenotypic characterization of the South African Namaqua Afrikaner sheep breed. MS Thesis. University of Pretoria, Pretoria, Africa.

Rahal O., Aissaoui C., Ata N., Yilmaz O., Cemal I., Ameur Ameur A. and Gaouar S.B.S. (2020). Genetic characterization of four Algerian cattle breeds using microsatellite markers. Anim. Biotechnol. 4, 1-9.

Samadi Shams S., Zununi Vahed S., Soltanzad F., Kafil V., Barzegari A., Atashpaz S. and Barar J. (2011). Highly effective DNA extraction method from fresh, frozen, dried and clotted blood samples. BioImpacts. 3, 183-187.

Tavakolian J. (2000). An Introduction to Genetic Resources of Native Farm Animals in Iran. Animal Science Genetic Research Institute Press. Tehran, Iran.

Tefiel H., Ata N., Chahbar M., Benyarou M., Fantazi K., Yilmaz O., Cemal I., Karaca O., Boudouma D. and Gaouar S.B.S. (2018). Genetic characterization of four Algerian goat breeds assessed by microsatellite markers. Small Rumin. Res. 160, 65-71.

Vahidi S.M.F., Faruque M.O., Kalahari A., Afraz F., Mousavi S.M., Boettcher P., Joost S., Han J.L., Colli L., Periasamy K., Negrini R. and Ajmone-Marsan P. (2016). Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep. Anim. Genet. 4, 463-470. ‏

Vahidi S.M.F., Tarang A.R., Naqvi A.N., Falahati Anbaran M., Boettcher P., Joost S., Colli L., Garcia J.F., Ajmone-Marsan P. (2014). Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Genet. Sel. Evol. 46(27), 20-27.

Yeh F.C., Yang R. and Boyle T. (1999). POPGENE. Microsoft Windows Based Freeware for Population Genetic Analysis. Release 1.31. University of Alberta, Edmonton, Canada.

Zenga X.C., Chen H.Y., Hui W.Q., Jia B., Du Y.C. and Tian Y.Z. (2010). Genetic diversity measures of 8 local sheep breeds in northwest of china for genetic resource conservation. Asian- Australasian J. Anim. 23, 1552-1556.

Zhang M., Peng W.F., Hu X.J., Zhao Y.X. and Yang J. (2018). Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin. Sci. Rep. 8, 11677-11684.

Zheng Z., Wang X., Li M., Li Y., Yang Z., Wang X., Pan X., Gong M., Zhang Y., Guo Y., Wang Y., Liu J., Cai Y., Chen Q., Okpeku M., Colli L., Cai D., Wang K., Huang S., Sonstegard T.S., Ali Esmailizadeh A., Zheng W., Zheng T., Xu Y., Xu N., Yang Y., Han J., Chen L., Lesur J., Daly K.G., Bradley D.G., Heller R., Zheng G., Wang W., Chen Y. and Jiang Y. (2020). The origin of domestication genes in goats. Sci. Adv. 6(21), 1-13.