Genetic characterization of Garra rufa (Heckel, 1843) populations in Tigris Basin, Iran using microsatellite markers

Hamed Kolangi Miandare, Ghasem Askari, Ali Shabany, Hamid Reza Rezaei

Abstract

The isolation-by-distance theory states that the genetic differentiation between individuals raised by increasing geographic distance. Therefore, this study tested this hypothesis for Garra rufa, a freshwater fish species of Iranian inland waters, from six rivers located at the different distances in Tirgis basin. For this purpose, eight variable microsatellite loci were applied to identify geographic-based population structure of G. rufa. From 240 fish of six populations, 102 alleles were found with a mean number of 11.625 to 13.250 alleles. Heterozygosity was ranged 0.567-0.638 in six studied populations. Moreover, a significant deviations from Hardy-Weinberg were found in the studied populations. Unweight pair group analysis indicated that the six studied populations could be divided into four major clusters. The results revealed a fairly high level of genetic variation in the microsatellite loci within six studied populations. Wright’s fixation index (Fst) ranged between 0.013-0.044 indicating little genetic differentiation between populations. Within this range, however, we found a strong positive relation between Fst and geographical distance lending support to the isolation-by-distance theory.

Keywords

Genetic diversity, Microsatellite, Doctor fish, Tigris Basin, Iran.

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References

Abbas K., Zhou X.Y., Li Y., Gao Z.X., Wang W.M. (2010). Microsatellite diversity and population genetic structure of yellowcheek, Elopichthys bambusa (Cyprinidae) in the Yangtze River. Biochemical Systematics and Ecology, 38: 806-812.

Avise J.C. (2000). Phylogeography the history and formation of species. Harward University Press, Cambridge. 447 p.

Bassam B.J., Caetano-Anolles G., Gresshoff G.M. (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry, 84: 680-683.

Bergh M.O., Getz W.M. (1989). Stability and harvesting of competing populations with genetic variation in life history strategy. Theoretical Population Biology, 113: 939-965.

Bhassu S., Yusoff K., Panandam J.M., Embong W.K., Oyyan S., Tan S.G. (2004). The genetic structure of Oreochromis spp. (Tilapia) populations in Malaysia as revealed by microsatellite DNA analysis. Biochemical Genetics, 42: 217-229.

Borrell Y.J., Bernardo D., Blanco G., Vazquez E., Sanchez J.A. (2008). Spatial and temporal variation of genetic diversity and estimation of effective population sizes in Atlantic salmon (Salmo salar, L.) populations from Asturias (Northern Spain) using microsatellites. Conservation Genetics, 9: 807-819.

Castric V., Bernatchez L., Belkhir K., Bonhomme F. (2002). Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses. Heredity, 89: 27-35.

Chen L., Li Q., Yang J. (2008). Microsatellite genetic variation in wild and hatchery populations of the sea cucumber (Apostichopus Japonicus Selenka) from northern China. Aquaculture Research, 39: 1541-1549.

Crooijmans R.P.M.A., Bierbooms V.A.F., Komen J., Van der poal J.J., Groenen M.A.M. (1997). Microsatellite markers in common carp (Cyprinus carpio L.). Animal Genetics, 28: 129-134.

Cruz P., Ibarra F.M., Galinda S., Mendoza C. (2005). Isolation of microsatellite loci in green abalone (Haliotis fulgens) and cross-species amplification in two other North American red (Haliotis rufescens) and pink (Haliotis corrugata) abalones. Molecular Ecology Notes, 5: 857-859.

Cornuet J.M., Luikart G. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144: 2001-2014.

Cui J.Z., Shen X.Y., Yang G.P., Gong Q.L., Gu Q.Q. (2005). Characterization of microsatellite DNAs in Takifugu rubripes genome and their utilization in the genetic diversity analysis of T. rubripes and T. pseudommus. Aquaculture, 250: 129-137.

Dewoody J.A., Avise J.C. (2000). Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Fish Biology, 56: 461-473.

Diz P.A., Presa P. (2009). The genetic diversity pattern of Mytilus alloprovincialis in Galician Rías (NW Iberian estuaries). Aquaculture, 287: 278-285.

Durna S., Bardakci F., Degerli N. (2010). Genetic diversity of Garra rufa Heckel, 1843 (Teleostei: Cyprinidae) in Anatolia. Biochemical Systematics and Ecology, 38: 83-92.

Excoffier L., Laval G., Schneider S. (2005). Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1: 47-50.

Garcia DeLeon F.J., Dallas J.F., Chatain B., Canonne M., Versini J.J., Bonhomme F. (1995). Development and use of microsatellite markers in sea bass, Dicentrarchus labrax (Linneaus 1758) (Perciformes: Serranidae). Molecular Marine Biology, 4: 62-68.

Gopalakrishnan A., Musammilu K.K., Basheer V.S., John L., Padmakumar K.G., Lal K.K., Lakra W.S. (2009). Low genetic differentiation in the populations of the Malabar carp Labeo dussumieri as revealed by allozymes, microsatellites and RAPD. Asian Fisheries Science, 22: 359-391.

Grassi F., Imazio S., Gomarasca S., Citterio S., Aina R., Sgorbati S., Sala F., Patrignani G., Labra M. (2004). Population structure and genetic variation within Valeriana wallrothii Kreyer in relation to different ecological locations. Plant Science, 166: 1437-1441.

Hillis D.M., Mortiz C., Mable B. (1996). Molecular systematics. 2nd ed., Sinauer Associates Sunderland. 655 p.

Hinten M.A., Harriss G.F., Rossetto M., Bravestock P.R. (2003). Genetic variation and island biogeography: Microsatellite and mitochondrial DNA variation in island populations of the Australian bush rat, Rattus fuscipes greyii. Conservation Genetics, 4: 759-778.

Israel J., Cordes J.F., Blumberg M.A., May B. (2004). Geographic pattern of genetic differentiation among collections of green sturgeon. North American Journal of Fisheries Management, 24: 922-931.

Kanapen D., Taylor M., Blust R., Verheyen T. (2006). Isolation and characterization of polymorphic microsatellite loci in the gudgeon, Gobio gobio (Cyprinidae). Molecular Ecology Notes, 6: 387-389.

Keivany Y., Nezamoleslami A., Dorafshan S., Eagderi S. (2015). Length-weight and length-length relationships in populations of Garra rufa from different rivers and basins of Iran. International Journal of Aquatic Biology, 3(6): 409-413.

Kim W., Lee Y., Bang I.C. (2007). Isolation and characterization of polymorphic microsatellite markers for the endangered Korean freshwater fish Hemibarbus mylodon. Molecular Ecology Notes, 7: 516-518.

Koskinen M.T., Piironen J., Primmer C.R. (2001). Interpopulation genetic divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation. Conservation Genetics, 2: 133-143.

Koskinen M.T., Piironen J., Sundell P., Primmer C.R. (2002). Spatiotemporal evolutionary relationships and genetic assessment of stocking effects in grayling (Thymallus thymallus, Salmonidae). Ecology Letters, 5: 193-205.

Li J., Wang G., Bai Z. (2009). Genetic variability in four wild and two farmed stocks of the Chinese freshwater pearl mussel (Hyriopsis cuminggii) estimated by microsatellite DNA. Aquaculture, 287: 286-291.

Liu F., Xia J.H., Bai Z.H., Fu J.J., Li J.L., Yue G.H. (2009). High genetic diversity and substantial population differentiation in grass carp (Ctenopharyngodon idella) revealed by microsatellite analysis. Aquaculture, 297: 51-56.

Lucentini L., Palomba A., Lancioni H., Gigliarelli L., Sgaravizzi G., Natali M., Panara F. (2009). Temporal changes and effective population size of an Italian isolated and supportive-breeding managed northern pike (Esox lucius) population. Fisheries Research, 96:139-147.

Mandal A., Rao D., Karuppaiah D., Gopalakrishnan A., Pozhoth J., Samraj Y.C.T., Doyle R.W. (2012). Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India. Gene, 491: 149-157.

Maremi S., Kenji K., Nadezhda Z., Aoi N., Tomoki O., Takafumi N., Vladimir B., Koji N. (2005). Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study. Marine Biotechnology, 7: 13-728.

Matura R., Sharma S., Barat A., Pande V., Mahanta P. (2012). Development and characterization of microsatellite markers in Garra gotyla (Family: Cyprinidae, Pisces). Molecular Ecology Research, 12: 185-189.

Mousavi-Sabet H., Eagderi S. (2016). Garra lorestanensis, a new cave fish from the Tigris River drainage with remarks on the subterranean fishes in Iran (Teleostei: Cyprinidae). FishTaxa, (2016) 1: 45-54.

Nagarajan M., Haniffa M.A., Gopalakrishnan A., Basheer V.S., Muneer A. (2006). Genetic variability of Channa punctatus populations using randomly amplified polymorphic DNA. Aquaculture Research, 37: 1151-1155.

Neff B.D., Gross M.R. (2001). Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution, 55: 1717-1733.

Nei M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89: 583-590.

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

Primmer C.R., Veselov A.J., Zubchenko A., Poututkin A., Bakhmet I., Koskinen M.T. (2006). Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia. Molecular Ecology, 15: 653-666.

Quan Y.C., Sun X.W., Liang L.G. (2007). Development of microsatellite markers for southern catfish (Silurus meriaionalis) and cross-species amplification in northern sheatfish (Silurus soldatovi). Molecular Ecology Nots, 7: 223-226.

Rice W.R. (1989). Analyzing tables of statistical test. Evolution, 43: 223-225.

Jouladeh-Roudbar A., Vatandoust S., Eagder, S., Jafari-Kenari S., Mousavi-Sabet H. (2015). Freshwater fishes of Iran; an updated checklist. AACL Bioflux, 8(6): 855-909.

Ruzafa A.P., Wangüemert M.W., Lenfant P., Marcos C., Charton J.G. (2006). Effects of fishing protection on the genetic structure of fish populations. Biological Conservation, 129: 244-255.

Shao Z.J., Zhao N., Zhu B., Zhou F.L., Chang J.G. (2002). Application of microsatellite primers developed from shovelnose sturgeon in Chinese sturgeon. Acta Hydrobiologyca Siniea, 26: 577-584.

Slatkin M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139: 457-462.

Smýkal P., Hýbl M., Corander J., Jarkovský J., Flavell A.J., Griga M. (2008). Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theoretical and Applied Genetics, 17: 413-424.

Ündar L., Akpinar M.A., Yanikoğlu A. (1990). Doctor fish and psoriasis. Lancet 335: 470-471.

Wang Y., Fu D., Xia J. (2012). The genetic diversity of the noble scallop (Chlamys nobilis, Reeve 1852) in China assessed using five microsatellite markers. Marine Genomics, 9: 63-67.

Wright S. (1978). Evolution and the genetics of population’s variability within and among natural populations. 2nd ed., University of Chicago Press, Chicago.

Yalçin-Özdilek S. (2007). Possible threat for Middle East inland water: An exotic and invasive species, Pterygoplichthys disjunctivus (Weber, 1991) in Asi River, Turkey (Pisces: Loricariidae). Journal of Fisheries and Aquatic Science, 24: 303-306.

Yeh F.C., Yang R.C., Boyle T. (1999). POPGENE version 1.3.1. Microsoft Window-bases free ware for population Genetic Analysis. Retrieved from http://www.uallberta.ca/fyeh. On: 11September 2014.

Yue G. H., Li Y., Lim L.C. Orban L. (2004). Monitoring the genetic diversity of three Asian arowana (Scleropages formosus) captive stocks using AFLP and microsatellites. Aquaculture, 237: 89-102.

Zhuo X., Liang R., Chen Y., Huang G., Yu D., Zou J. (2012). Genetic characterization of northern snakehead (Channa argus) populations in China using microsatellite markers. Biochemical Systematics and Ecology, 43: 25-31.

Zoller S., Lutzoni F., Scheidegger C. (1999). Genetic variation within and among populations of the threatened liken lobaria pulmonaira in Switzerland and implications for its conversation. Molecular Ecology, 8: 2049-2059.

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