Journal of Marine Science and Technology

Journal of Marine Science and Technology

Determining the genetic diversity and inbreeding coefficient of cultured Anzeh (Luciobarbus esocinus) population using fluorescently labeled microsatellite markers

Articles in Press

Document Type : Original Manuscript

Authors
Malek Silavi 1, 2
Ebrahim Rajabzadeh Ghatrami 1
Samira Nazemroaya 3
1 Department of Fisheries, Faculty of Marine Natural Resources, Khorramshahr University of Marine Sciences and Technology, Khorramshahr, Iran.
2 Native Fish Breeding Center of Khuzestan General Directorates for Fisheries, Ahvaz, Iran.
3 South Iran Aquaculture Research Institute, Iranian Fisheries Scientific Research Institute, Agricultural Research, Education, and Extension Organization, Ahvaz, Iran
10.22113/jmst.2024.447140.2587
Abstract
Abstract
In this study, the genetic diversity and inbreeding coefficient of the Anzeh fish population in three distinct geographical regions were investigated and estimated in ten gene loci using fluorescently labeled microsatellite markers. Sampling was conducted with 20 adult Anzeh fish (male and female), 10 one-year-old fish and 10 two-year-old young from Breeding Center of Khuzestan General Directorates fisheries, 20 fish from the Karkeh, and the Dez Dams. Among 33 private alleles in all populations, BC-49 and BC-39 loci exhibited the most five alleles. The highest (11) and lowest (2) number of private alleles were found in Male cultured and wild (Dez and Karkheh) populations. The minimum and maximum Shannon diversity index were 1.169 and 1.650 in Karkheh and one-year-old cultured populations. The mean F index was calculated as 0.018 in all populations. The mean inbreeding coefficient of Fis was 0.0059 in all Loci. Negative numbers were obtained in five loci and the Fis ranged from 0.123 to 0.289 in the rest of the loci, which indicates low inbreeding in populations. The two-year-old cultured population was in Hardy-Weinberg equilibrium at all loci. However, one-year-old breeding, Karkheh, and Dez population in one locus, and Male and Female cultured broodstocks in two and six loci showed a significant deviation from the Hardy-Weinberg equilibrium (p<0.05). The AMOVA based on FST illustrated 13% and 78% of the diversity between and within the population, respectively. The calculated FST (0.126) showed a meaningful moderate genetic distance among the populations (p<0.05). According to the FST matrix, the lowest genetic distance (0.038) was observed between the two-year-old cultured and Dez populations. The highest genetic distance was found at 0.185 between the Female cultured and Karkheh populations. These results showed that the populations of Anzeh have high genetic diversity in Khuzestan, and very little inbreeding was observed in the populations.
 
 
INTRODUCTION
Knowledge of the amount of genetic diversity among individuals of a species is one of the valuable goals of stock management and breeding, so population genetic studies or molecular ecology of economically valuable fish are very necessary to protect their population and maintain sustainable fishing. One of the requirements of broodstock management in hatcheries is to estimate the genetic dependency among them. With genetic monitoring, it is possible to estimate the genetic diversity during many generations of aquatic breeders and provide important information about the efficiency of reproduction management.
 
MATERIAL AND METHODS
In this study, the genetic diversity and inbreeding coefficient of the Anzeh fish population in three distinct geographical regions were investigated and estimated in ten gene loci using fluorescently labeled microsatellite markers. Sampling was conducted with 20 adult Anzeh fish (equal ratio of male and female), 10 one-year-old fish and 10 two-year-old young from Native Fish Breeding Center of Khuzestan General Directorates for fisheries, 10 fish from the Karkeh, and 10 fish from the Dez lakes behind Dams.
 
RESULTS
Among 33 private alleles in all populations, BC-49 and BC-39 loci exhibited the most five alleles. The highest (11) and lowest (2) number of private alleles were found in Male cultured and wild (Dez and Karkheh) populations. The BC-47 locus had two private alleles exclusively in the one-year-old population.. The mean observed (Ho) and expected (He) heterozygosity in all populations were calculated as 0.667 and 0.681, respectively. The minimum and maximum Shannon diversity index were 1.169 and 1.650 in Karkheh and one-year-old cultured populations, respectively. The mean F index was calculated as 0.018 in all populations. The mean inbreeding coefficient of Fis was 0.0059 in all Loci. Negative numbers were obtained in five loci and the Fis ranged from 0.123 to 0.289 in the rest of the loci, which indicates low inbreeding in populations. The two-year-old cultured population was in Hardy-Weinberg equilibrium at all loci. However, one-year-old breeding, Karkheh, and Dez population in one locus, and Male and Female cultured broodstocks in two and six loci showed a significant deviation from the Hardy-Weinberg equilibrium (p<0.05). The AMOVA based on FST illustrated 13% and 78% of the diversity between and within the population, respectively. The calculated FST (0.126) showed a meaningful moderate genetic distance among the populations (p<0.05). According to the FST matrix, the lowest genetic distance (0.038) was observed between the two-year-old cultured and Dez populations. The highest genetic distance was found at 0.185 between the Female cultured and Karkheh populations.
 
DISCUSSION AND CONCLUSION
These results showed that the populations of Anzeh have high genetic diversity in Khuzestan, and very little inbreeding was observed in the populations.
Since there are no main factors influencing natural selection in wild aquatic populations (such as food competition, pressure from fishermen, environmental conditions, etc.) It will be in such a situation, that the phenomenon of "inbreeding" causes an increase in the percentage of malformations in the produced fish and, as a result, reduces production efficiency. In fact, due to the small population of breeding fish and the possibility of their close kinship, strengthening the possibility of "inbreeding" is always in a potential form. Inbreeding or the phenomenon of inbreeding, the genotypic structure of the population is determined not only by the allelic frequencies and the forces affecting the allelic frequency (mutation, migration, deviation, and drift or random mating) but also by the mating system. As a result of inbreeding, the genetic purity is increased, and the amount of impurity is also reduced compared to random mating conditions. The phenomenon of inbreeding occurs in natural and cultivated societies due to inbreeding and positive selective mating, when phenotypic.
Keywords
Anzeh
Microsatellite markers
inbreeding
genetic diversity
Hardy-Weinberg Equilibrium

Subjects

Abdul-Muneer, P. M. 2014. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies", Genetics Research International, vol. 2014, Article ID 691759, 11 pages, 2014. DOI: 10.1155/2014/691759
Alam, S. and Islamb, Sh., 2005. Population genetic structure of Catla catla (Hamilton) revealed by microsatellite DNA markers. Aquaculture, 246, pp. 151–160. DOI:10.1016/j. aquaculture.2005.02.012
Alarcon, J.A; Magoulas, A.; Georgakopoulos, T., Zouros, E. and Alvarez, M.C., 2004. Genetic comparison of wild and cultivated European populations of the gilthead sea bream (Sparus aurata). Aquaculture, 230, 65–80. DOI:10.1016/S0044-8486(03)00434-4
Alavi, S. M. H., 2008. Fish spermatology: implications for aquaculture management. Fish spermatology, pp.397-460.
Bataillon T. M., David J. L. and Schoen D. J. 1996. Neutral genetic markers and conservation: simulated germplasm collections. Genetics, 144, pp.409-417. DOI: 10.1093/genetics/ 144.1. 409
Beardmore, J.A., Mair, G.C. and Lewis, R.I., 1997. Biodiversity in aquatic systems in relation to aquaculture. Aquaculture. Reserch, 28, 829-839, DOI: 10.104 6/j.1365-2109.1997.00 947.x.
Bekkevold, D., Hansen, M. M. and Loeschcke, V., 2002. Male reproductive competition in spawning aggregations of cod (Gadus morhua, L.). Molecular Ecology, 11(1), pp.91-102. DOI: 10.1046/ j.0962-1083 .2001 .01424.x.
Bjorklund, M., Aho, T. and Larsson, L.C., 2007. Genetic differentiation in pikeperch (Sander lucioperca): the relative importance of gene flow, drift and common history, Journal of fish Biology., 71, pp. 264–278. DOI: 10.1111 /j.1095- 8649.2007.01609.x
Brighitte, J., Hansen, M. and Loeschcker, V., 2005. Microsatellite DNA analysis of northern pike (Esox lucius) populations: insights into the genetic structure and demographic history of a genetically departures species. Biology Journal of Linnean Society, 84, pp.1-11. DOI: 10.1111/j.1095-8312.2005.00416.x
Brown, B., Wang, H.P., Li, L., Givens, C. and Wallet, G., 2007. Yellow perch strain evaluation I: Genetic variance of six broodstock populations. Aquaculture, 271, pp. 142-151. DOI: 10.1016/j.aquaculture .2007 .06.022
Carvalho, G.R. and Hauser, L., 1998. Advances in the molecular analysis of fish population structure. Italian Journal of Zoology, 65(S1), 21-33. DOI: 10.1080/11250009809386791.
Charlesworth, D. and Willis, J.H., 2009. The genetics of inbreeding depression. Nature reviews genetics, 10(11), pp.783-796. DOI: 10. 1038/nrg2664
Chistiakov, D.A., Hellemans, B. and Volckaert, F.A.M., 2006. Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics. Aquaculture, 255, pp.1– 29. DOI: 10.1016/j.a quaculture.2005.11.031
Ciftci, Y. and Okumus, I. 2002. Fish Population Genetics and Applications of molecular Markers to Fisheries and Aquaculture: I- Basic Principles of Fish Ppoulation genetics. Turkish Journal of Fisheries and Aquatic Science, 2, pp. 145-155. Corpus ID: 27490529
Dahle, G., Jørstad, K.E., Rusaas, H.E. and Otterå, H., 2006. Genetic characteristics of broodstock collected from four Norwegian coastal cod (Gadus morhua) populations. ICES Journal of Marine Science, 63(2), pp.209-215. https://doi.org/10.1016/j.icesjms. 2005.10.015
DeWoody, J. A. and Avise, J. C., 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Journal of fish biology, 56(3), pp.461-473. DOI: 10.1111/j.1095-8649.2000.tb00748.x
Dorak, T., 2005. Basic population genetics. www.dorak.info/genetics/popgen.html
Earl, D.A. and VonHoldt, B.M., 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation genetics resources, 4, pp.359-361. http://dx.doi.org/10.1007/s12686-011-9548-7
Epperson, B.K., 2003. Geographical Genetics. Princeton: Princeton University Press. Princeton and Oxford, Book ISBN: 0-691-08668-0
Falush, D., Stephens, M. and Pritchard, J.K., 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164(4), pp.1567-1587. https://doi.org/10.1093/genetics/164.4.1567
Frankham, R., 2008. Genetic adaptation to captivity in species conservation programs. Molecular Ecology 17, pp.325-333. DOI: 10.1111/j.1365-294X.2007.03399.x.
Gagiotti, O.E., Lange, O., Rassman, K. and Gliddon, C., 1999. A comparision of two indirect methods for estimating average levels of gene flow using microsatellite data. Molecular Ecology, 8, pp. 1513-1520. DOI: 10.1046/j. 1365-294x.1999.00730.x
Gjedrem, T. and Baranski, M., 2009. The success of selective breeding in aquaculture. In Selective Breeding in Aquaculture: An Introduction (pp. 13-23). Springer, Dordrecht. DOI:10.1007/978-90-481-2773-3
Hakansson, J. and Jensen, P., 2005. Behavioural and morphological variation between captive populations of red junglefowl (Gallus gallus) possible implications for conservation. Biological Conservation 122, pp.431-439. DOI:10.1016/j.biocon.2004.09.004
Hallerman, E M. 2004. Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, Maryland, 458 p. DOI: 10. 1111/j.1467-2979.2004.00145_3.x
Hansen, M.M., Nielsen, E.E., Ruzzante, D.E., Bouza, C. and Mensberg, K.L.D., 2000. Genetic monitoring of supportive breeding in brown trout (Salmo trutta L.) using microsatellite DNA markers. Canadian Journal of  Fish Aquaculture Scintific. 57, pp. 2130– 2139. DOI:10.1139/cjfas-57-10-2130
Hartl, D.L. and Clark, A. G., 1997. Principles of Population Genetics, 3nd edn. Sinauer Associates, Inc, Sunderland.  Translated to Persian by M.A. Hashemzadeh Saqarlou, Naqsh Mehr Publications,
Hashemzadeh-saghaerlu, I. 2005. Pupolation genetics: principles and applications for fisheries scientists by translation. Naqsh Mehr Publications, Tehran, (In Persian).
Hedrick, P.W., 2011. Genetics of populations. Jones & Bartlett Publishers.
Karaminasab, M., Hosseinnia, Z., Kolangi Miandare, H. and Shabany, A., 2014. Genetic diversity of Barbus grypus in the Karkheh River in Khuzestan Province and cultured fish studied using a microsatellite marker. Genetic Engineering and Biosafety Journal, 3(2), pp. 114-123. (In Persian)
Kashiri, H., Shabani, A. and Shabanpoor, B., 2012. Genetic diversity of caspian roach (Rutilus rutilus caspicus) in gharesou and gomishan regions using microsatellite. Iranian Journal of Biology, 25(1), pp.139-147. (In Persian)
Kearse M., Moir R., Wilson A., Stones S, Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., 2012. An integrated and extendable desktop software platform for the organization and analysis of sequence data” Bioinformatics, Volume 28, Issue 12, June 2012, Pages 1647–1649, DOI: 10.1093/bioinformatics /bt199
Leclerc, D., Wirth T.H. and Bernatchez, L., 2000. Isolation and characterization of microsatellites in yellow perch (Perca favesens), and cross-species amplification within the family Percidae. Molocoly. Ecologicaly. Notes, 9, pp. 995-997. DOI: 10.1046/j.1365-294x.2000.00939-3.x
Li, D., Kang, D., Yin, Q., Sun, X. and Liang, L., 2007. Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinus carpio       L.) populations. Journal of genetics and Genomics, 34(11), pp. 984-993. DOI: 10.1016/S1673-8527(07)60111-8   
Lin, S.J., Defossez, P.A. and Guarente, L., 2000. Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae. Science, 289(5487), pp.2126-2128. DOI: 10.1126/ science.289.5487.2126
Liu, Z. J. and Cordes, J. F. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238, pp. 1-37. DOI: 10.1016/j.aquaculture.2004.05.027
Longwu, G., Cuiyun, L., Guangxiang, T., Chao, L. and Wei, X., 2012. Development and characterization of twenty microsatellite markers for the endangered fish Luciobarbus capito. Conservation genetics resources, 4(4), pp. 865-867. DOI:10.1007/s12686-012-9660-3
Lundrigan, T. A., Reist, J. D., Ferguson, M. M., 2005. Microsatellite genetic ariation within and among Arctic charr (Salvelinus alpines) from aquaculture and natural populations in North America. Aquaculture, 244, 63-75. DOI:10.1016/j.aquaculture.2004.11.027
May, B. and Krueger, e.e. (1990) "Use of allozyme data for population analysis". In Whitmore, D.H., ed. Electrophoretic and Isoelectric Focusing Techniques in Fisheries Management. Boston: CRC Press, pp. 71-157.
Naghavian S, Hasani S, Ahani Azar M, Khanahmad AR, Sagh DA and Mamizade NB, 2013. Genetic diversity in Shirvan Kordi sheep using microsatellite markers and compared to estimation of inbreeding coefficient using pedigree. Animal Science Researches, 24, pp. 93-105. (In Persian).
Nei, M., 1972. Genetic distance between populations. The American Naturalist, 106(949), pp.283-292. https://doi.org/10.1 086/282771
Ohta, T. 1982. Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proceedings of the National Academy of Sciences, 79, pp.1940-1944. doi: 10.1073/pnas.79.6.1940
Oosterhout C.V., Hutchinson W.F., Wills D.P.M. and Shipley P. 2004. Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, pp.535-538.
Peakall, R. and Smouse, P.E. 2006. Genalex 6: genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, pp.288-295. doi.org/10.1111/j.1471-8286.2005.01155.x
Reilly, A., Elliott, N.G., Grewe, P.M., Clabby, C., Powell, R. and Ward, R.D., 1999. Genetic differentiation between Tasmanian Cultured Atlantic salmon (Salmo salar L.) and their ancestral Canadian population: comparison of microsatellite DNA and allozyme and mitochondrial DNA variation. Aquaculture, 173(1-4), pp. 459-469. DOI: 10.1016/S00 44-8486(98)00476-1
Rezaei, M., Shabani, A., Shabanpour, B. and Kashiri, H., 2010. Study of genetic structure of Rutilus frisii kutum in Golestan province coastal waters using microsatellite markers. Iranian Scientific Fisheries Journal, 19(3), pp. 151-156. DOR: 20.1001.1.16807073.2012.14.2.15.7. (In Persian)
Rezvani Gilkolaei, S., Salari Aliabdi, M. A., Savari, A., Zolgharnein, H. and Nabavi, S. M. B. 2009. Investigation on genetic structure of Cobia (Rachycentron canadum) using microsatellite markers. Iranian Scientific Fisheries Journal, 18(3), pp.61-69. (In Persian)
Rousset, F. 2004. Genetic structure and selection in subdivided populations Princeton. Princeto University Press. DOI: 10 .1515/ 9781400847242
Skaala, Ø., Høyheim, B., Glover, K. A. and Dahle, G. 2004. Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L): allelic diversity and identification of individuals. Aquaculture, 240, pp. 131-143. DOI: 10.1016/j. 2004.07.009
Stankiewicz, K., Vasquez, K. and Baums, I., 2020. The Delta K method alone is not sufficient to determine best clustering solutions for Bayesian analysis of population genetic structure in empirical data sets. Authorea Preprints. DOI: 10.22541/au.158817808.87389369
Tautz, D., 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic acids research, 17(16), pp.6463-6471. DIO: 10.1093/ nar/17.16.6463
Tessier, N., Bernatchez, L. and Wright, J. M., 1997. Population structure and impact of supportive breeding inferred from mitochondrial and microsatellite DNA analyses in land‐locked Atlantic salmon Salmo salar L. Molecular Ecology, 6(8), pp.735-750. DOI: 10.1046/j.1365-294X. 1997.00244.x
Viard, F., Justy, F. and Jarne, P., 1997. Population dynamics inferred from temporal variation at microsatellite loci in the selfing snail Bulinus truncatus. Genetics, 14, pp. 6973- 6982. DOI: 10.1093/genetics/146.3.973
Wang, C., Yu, X. and Tong, J. 2007. Microsatellite diversity and population genetic structure of redfin culture (Culter erythropterus) in fragmented lakes of the Yangtze river. Hydrobiologia, 586, pp. 321-329 DOI: 10.1007/s10750-007-0702-x
Wright, S., 1949. The genetical structure of populations. Annals of eugenics, 15(1), pp.323-354. https://doi.org/10.1111/j.1469-1809.1949.tb 02451.x
Wirth, T.H., Saint-Laurent, V. and Bernatchez, L., 1999. Isolation and characterization of microsatellites in walleye (Stizostedion vitreum), and crossspecies amplification within the family Percidae. Molecular Ecology, 8, pp. 1960-1962. DOI: 10.1046/j.1365-294x. 1999. 00778-3.x
Journal of Marine Science and Technology

Articles in Press, Accepted Manuscript
Available Online from 13 January 2025

  • Receive Date 07 April 2024
  • Revise Date 01 July 2024
  • Accept Date 03 September 2024
  • Publish Date 13 January 2025