Analysis of the Efficiency for the Pig-Tailing Technique to Dissect the Molecular Parameters Based on Microsatellite Markers: Camels (Camelus dromedaries) as Model

محورهای موضوعی : Camel

M. Bitaraf Sani ¹ , N. Asadzadeh ² , R. Nahavandi ³ , Z. Roudbari ⁴ , S.A. Rafat ⁵ , A. Mirjalili ⁶ , A. Javanmard ⁷

1 - Department of Animal Science, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research Education and Extension Organization (AREEO), Yazd, Iran
2 - Department of Animal Science, Animal Science Research Institute of Iran (ASRI), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
3 - Department of Animal Science, Animal Science Research Institute of Iran (ASRI), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
4 - Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran
5 - Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
6 - Department of Soil Conservation and Watershed Management, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research Education and Extension Organization (AREEO), Yazd, Iran
7 - Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

تاریخ دریافت : 1401/02/24 تاریخ پذیرش : 1401/05/26 تاریخ انتشار : 1402/09/10

کلید واژه: genetic diversity, polymorphism, camel, alleles, pig-tailing,

چکیده مقاله :

Microsatellite markers historically have been one of the most popular tools for assessing the genetic diversity of livestock due to their nature and polymorphism with their motifs. A challenging problem that arises in this domain is the occurrence of errors in the genotyping process. Additionally, errors in genotyping and allele size determination occur when the genotype determined by the molecular technique does not match the actual genotype in the individual's genome. Furthermore, errors have a direct impact on the ability to differentiate between individuals in a population, and incorrect conclusions and mislead breeders in decisions. With this motivation, the present report aims to evaluate the efficiency of the pig-tailing technique on the parameters of molecular differentiation based on microsatellites in a population of camels. For this purpose, a total of 20 unrelated camel individuals from different regions of Yazd province were collected, and then genomic DNA was extracted using routine salting out methods. Then, five microsatellite polymorphic sites were selected according to Food and Agriculture Organization (FAO), and two groups of common primers and pig-tailed primers (GTTTCTT nucleotide sequence added to 5' reverse primer) were fluorescently candidates for in-population differentiation and diversity. Clustering and principal component analysis (PCA) was performed using the R Package (version 4.2.0), MEGA, and PRCOMP package under the R environment. Interestingly, the results of genotyping showed that the pig-tailing technique tends to reduce the false band patterns (stutter) and also significantly reduce the chance of error in di-motif microsatellite type. On this basis, we can conclude that the pig-tailing strategy in microsatellite genotyping in camel’s genetic diversity, seems to be a suitable method.

منابع و مأخذ:

Almathen F., Charruau P., Mohandesan E., Mwacharo J.M., Orozco-terWengel P., Pitt D., Abdussamad A.M., Uerpmann M., Uerpmann H.P. and De Cupere B. (2016). Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary. Proc. Natl. Acad. Sci. 113, 6707-6712

Arthofer W., Heussler C., Krapf P., Schlick-Steiner B.C. and Steiner F.M. (2018). Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing. Fly. 12(1), 13-22.

Ballard L.W., Adams P.S., Bao Y., Bartley D., Bintzler D., Kasch L., Petukhova L. and Rosato C. (2002). Strategies for genotyping: Effectiveness of tailing primers to increase accuracy in short tandem repeat determinations. J. Biomol Technol.  13, 20-29.

Bouvet R., Verdier M.C., El Baroudi Y., Galibert M.D., David V., Schutz S., Tron C. and Pharm F. (2020). An easy and fast multiplex pharmacogenetics assay to simultaneously analyze 9 genetic polymorphisms involved in response variability of anticancer drugs. Int. J. Mol. Sci. 21, 2-12.

Brookes C., Bright J.A., Harbison S. and Buckleton J. (2011). Characterizing stutter in forensic STR multiplexes. Forensic science international. Genetics. 6, 58-63.

Brownlow R.J., Dawson D.A., Horsburgh G.J., Bell J.J. and Fish J.D. (2008). A method for genotype validation and primer assessment in heterozygote-deficient species, as demonstrated in the prosobranch mollusc Hydrobia ulvae. BMC Genet. 9, 1-5.

Cherifi Y.A., Gaouar S.B., Guastamacchia R., El-Bahrawy K.A., Abushady A.M., Sharaf A.A., Harek D., Lacalandra G.M., Saïdi-Mehtar N. and Ciani E. (2017). Weak genetic structure in northern African dromedary camels reflects their unique evolutionary history. PLoS One. 12(1), e0168672.

Geng R.Q., Chang H., Yang Z.P., Sun W., Wang L.P., Lu S.X., Tsunoda K. and Ren Z.J. (2003). Study on origin and phylogeny status of Hu sheep. Asian-Australasian J. Anim. Sci. 16, 743-747.

Ghasemi Meymandi M., Mohammadabadi M.R. and Esmailizadeh A.K. (2015). Genetic variation of camels in the North of Kerman province using microsatellite markers. Anim. Prod. Res. 4, 35-45.

Guerouali A. and Acharbane R. (2004). Camel Genetic Resources in Morocco. Pp. 1-5 in Semin. Camelidis, Sousse, Tunisia.

Guliye A.Y., Noor I.M., Bebe B.O. and Kosgey I.S. (2007). Role of camels (Camelus dromedaries) in the traditional lifestyle of Somali pastoralists in northern Kenya. Outlook Agric. 36(1), 29-34.

Hale M.L., Burg T.M. and Steeves T.E. (2012). Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals Per Population Is Enough to Accurately Estimate Allele Frequencies. PLoS One. 7, e45170.

Hassanin A., Delsuc F., Ropiquet A., Hammer C., Jansen van Vuuren B., Matthee C. and Couloux A. (2012). Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335(1), 32-50.

Hedayat-Evrigh N., Khalkhali-Evrigh R., Vahedi V., Pourasad K. and Sharifi R.S. (2018). Genetic diversity and population structure of old world camelids (Camelus dromedaries and Camelus bactrianus) in Iran using mitochondrial DNA. J. Vet. Med. 24(3), 467-471.

Mahmoud M.A., Alshaikh R.S., Aljumaah O.B., Mohammed M. (2012). Genetic variability of camel (Camelus dromedarius) populations in Saudi Arabia based on microsatellites analysis. African J. Biotechnol. 11, 11173-11180.

Mariasegaram M., Pullenayegum S., Jahabar Ali M., Shah R.S., Penedo M.C., Wernery U. and Sasse J. (2002). Isolation and characterization of eight microsatellite markers in Camelus dromedarius and cross-species amplification in Camelus bactrianus and Lama pacos. Anim. Genet. 33, 385-387.

Mburu D.N., Ochieng J.W., Kuria S.G., Jianlin H., Kaufmann B.B., Rege B.J. and Honotte O. (2003). Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: Implications for their classification. Anim. Genet. 34, 26-32.

Mohandesan E., Fitak R.R., Corander J., Yadamsuren A., Chuluunbat B., Abdelhadi O.A., Raziq P.N., Stalder G., Walzer C., Faye B. AND Burge P.A. (2017). Mitogenome sequencing in the genus camelus reveals evidence for purifying selection and long-term divergence between wild and domestic bactrian camels. Sci. Rep. 7, 9970-.9982.

Musthafa M.M. (2015). A review of microsatellite marker usage in the assessment of genetic diversity of Camelus. Iranian J. Appl. Anim. Sci. 5(1), 1-4.

Proskuryakova A., Kulemzina A., Perelman P., Makunin A., Larkin D., Farré M. and Beklemisheva V. (2017). X Chromosome evolution in Cetartiodactyla. Genes. 8(9), 2-16.

Rout P.K., Joshi M.B., Mandal A., Laloe D., Singh L. and Thangaraj K. (2008). Microsatellite-based phylogeny of Indian domestic goats. BMC Genet. 9, 1-11.

Schulz U., Minguez Y., Checa M.L., Gorcia-Atance P., Dunner S., Gercia D. and Canon J. (2005). The majorero camel (Camelus dromedarius) breed. Anim. Genet. Res. Inf. 36, 61-71.

Shirk R.Y., Glenn T.C., Chang S.M. and Hamrick J.L. (2013). Development and characterization of microsatellite primers in Geraniaceae (Geranium carolinianum) with 454 sequencing. Appl. Plant Sci. 1(8), 1-3.