Comparative analysis of genetic structure of ukrainian paddlefish (Polyodon spathula) populations
DOI:
https://doi.org/10.31548/bio2018.03.025Abstract
The issue of preserving of genetic diversity of valuable fish species broodstock became particularly relevant in the modern conditions of aquaculture. Acipenseriformes are the representatives of valuable species of fish, including paddlefish (Polyodon spathula), which is widely reared in fish farms as a biomeliorator in ponds and for production of valuable sturgeon products.
One of the main causes that may affect the reduction of genetic diversity in the artificial paddlefish populations is the low number of individuals for the broodstocks formation, lack of the genetic control and targeted selection in reproduction of this species. The main requirement for the conservation of biodiversity of aquaculture objects is the application of such methods and approaches, which allow assessing the genetic polymorphism of the populations with a high level of probability.
At present stage of molecular genetics research, microsatellite DNA markers are one of the main and most effective approaches of studying the population genetic structure. Microsatellites allow identifying the allelic variants, studying paternal linkage between individuals and establishing the genetic linkage between broodstocks from different farms.
The investigation of paddlefish microsatellite DNA allows analyzing the genetic processes occurring in artificial populations of this species of fish, in order to preserve the genetic diversity and reproduce the offspring with desired genotypes under artificial conditions.
The purpose of our research was to carry out the comparative analysis of the genetic structure of paddlefish (Polyodon spathula) of Ukrainian populations by microsatellite DNA markers.
As the result of the study, we established the peculiarities of the genetic structure of artificial paddlefish populations. The general similarity of genetic profiles was found by the investigated microsatellite DNA loci.
The population from Kherson region was the most polymorphous and the number of identified alleles for that population was 25 allele variants. The population from Chernihiv region was the least polymorphous, the 21 allele variants were identified for this population. For the population from Vinnytsia region 22 allele variants were identified.
Based on the obtained data of the level of genetic variability, the maximum mean number of alleles per locus (Na) at 6,25 was recorded for the population from Kherson region, and the minimum mean Na at 5,25 was calculated for the population from Chernihiv region. The analysis of the heterozygosity of Ukrainian paddlefish populations showed that for Kherson population the mean observed heterozigosity (Ho) was 0,742, whereas the expected heterozygosity according to the Hardy-Weinberg equilibrium (He) was 0,618. For Chernihiv population, the mean values of Ho and He were 0,757 and 0,638, respectively. For Vinnytsia population, the average value of Ho (0,691) was also over He (0,602).
In general, we have established the predominance of the average value of observed heterozygosity (Ho = 0,730) over the expected heterozygosity (He = 0,619) for three populations of paddlefish. In addition, it was determined that predominance of Ho value was significant for Kherson population at locus Psp26 (p <0,001), for Chernihiv population at loci Psp12 (p <0,05) and Psp28 (p <0,01) and for Vinnytsia population at locus Psp28 (p<0,05). There was also established a significant shortage of heterozygous genotypes at locus Psp21 (p <0,05) for Kherson population and at locus Psp26 (p <0,001) for Vinnytsia population.
In accordance with the criterion of fixation index (Fis), the maximum predominance of heterozygous genotypes was observed at locus Psp28 for Vinnytsia paddlefish population (Fis = –0,493), while the maximum lack of heterozygous genotypes was established at locus Psp21 for Chernihiv population (Fis = 0,169).
The average values of fixation index Fis for all analyzed microsatellite loci ranged from Fis = –0,176 (Chernihiv population) to Fis = –0,129 (Vinnytsia population). The Fis value shows the predominance of heterozygous genotypes in the studied groups of fish, indicating the genetic polymorphism in artificial populations of paddlefish at this stage of reproduction under aquaculture conditions.
The polymorphism degree evaluation for investigated DNA-markers was measured by using polymorphism information content (PIC) value. In the context of populations, the minimum PIC index (0,305) was observed at locus Psp21 (Kherson population), the maximum PIC value calculated for this population was 0,753 at locus Psp26. In Chernihiv population index PIC ranged from 0,482 (Psp21) to 0,661 (Psp28), while for Vinnytsia population, this value varied from 0,340 (Psp21) to 0,670 (Psp26).
The average values of PIC index ranged from 0,550 (Vinnytsia population) to 0,581 (Chernihiv population) and, in general, for all populations, PIC index was 0,569. This result indicated the analyzed DNA-markers are polymorphic (PIC> 0,550).
The average level of probability of excluding (PE) for each of the studied populations slightly differed and ranged from 0,487 to 0,594 in the Vinnytsia and Kherson populations, respectively. The high PE value was recorded for locus Psp28 (1,000) for Kherson and Vinnytsia populations, which is explained by the presence of only heterozygous genotypes (100 %) in the investigated specimens of paddlefish at the locus. The low PE value was found for locus Psp21, which was at 0,069 (Kherson region), 0,096 (Vinnytsia region) and 0,153 (Chernihiv region), indicated that, generally, this locus was the least informative in the study of the genetic structure of artificial populations of paddlefish.
The average value of the combined probability of exclusion (CPE) for three paddlefish populations was 0,912, indicating the informative level at 91,2 % of the investigated microsatellite DNA-markers panel. In order to increase the accuracy of DNA analysis of paddlefish, the further expanding of the informative microsatellite DNA loci panel is required.
Thus, the obtained results show the predominance of heterozygous genotypes in the investigated groups of fish with the informative level at 91,2 % (CPE = 0,912), indicating the preservation of genetic polymorphism in artificial populations of paddlefish at this stage of reproduction under aquaculture conditions.
References
Tretiak, O.M., Tarasiuk S.I. (2011) Analiz henetychnoi struktury hrup veslonosa za okremymy henetyko-biokhimichnymy systemamy. Rybohospodarska nauka Ukrainy, 1, 50-57.
Mims, S. (2001) Aquaculture of Paddlefish in the United States Aquat. Living Resour, 14, 391−398.
https://doi.org/10.1016/S0990-7440(01)01137-8
Pikitch E., Doukakis P., Lauck I., P. Chakraborty, D.L. Erickson (2005) Status, trends and management of sturgeon and paddlefish fisheries. Fish Fish, 6, 233-265. https://doi.org/10.1111/j.1467-2979.2005.00190.x
Tretiak O.M. (2010) Systema naukovo obgruntovanoho rozvytku akvakultury veslonosa v Ukraini. Rybohospodarska nauka Ukrainy, 2, 3–25.
Kurtа K.M., Malysheva O.O., Grishyn B.O., Getia A.A., Babenko V.I. Shynkarenko L.M., Spyrydonov V. H. (2017) Identyfikatsiia alelnykh variantiv mikrosatelitnoi DNK veslonosa (Polyodon spathula). Bioresursy i pryrodokorystuvannia Ukrainy, T. 9, 5-6. Dostup za posylanniam. http://journals.nubip.edu.ua/index.php/Bio/article/view/9590
Kaczmarczyk D. Luczynski M., Kolman R. (2008) Assemblage of spawning pairs of farmed American paddlefish based on their individual genetic profiles – a new tool in managing of the broodstock`s gene pool. Summary document of Aquaculture Eurupe, 36-37.
Tymoshkyna N.N. Vodolazhskyy D.Y., Usatov A.V. (2010) Molekulyarno-henetycheskye markery v yssledovanyy vnutry-y mezhvydovoho polymorfyzma osetrovykh ryb (Acipenseriformes). Эkolohycheskaya henetyka, V.8 (1), 12–24.
Chistiakov D.A., Hellemans B., Volckaert F.A.M. (2006) Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics. Aquaculture. № 255 (1-4). 1-29. https://doi.org/10.1016/j.aquaculture.2005.11.031
Muhina Zh. M. Dubina E.V Molekulyarnyie markeryi i ih ispolzovanie v selektsionno-geneticheskih issledovaniyah / Zh. M. Muhina, // Nauchnyiy zhurnal KubGAU. 2011. 66. 97-107.
Нeist E.J, Mustapha A. (2008) Genetic Structure in Paddlefish Inferred from DNA Microsatellite Loci. Transactions of the American Fisheries Society, 137, iss. 3, 909–915.
Wirgin I. I., Stabile J. E., Waldman J. R. (1997) Molecular analysis in the conservation of sturgeons and paddlefish. Environmental Biology of Fishes. 48(1), 385-398. https://doi.org/10.1023/A:1007306911163
Dudu A, Suciu R., Parashiv M., Georgescu S.E., Costache M., Berrebi P. (2011) Nuklear Markers of Danube Sturgeons Hibridization. Melecular Sciences, 12, 6796-6809.
May B., Krueger C.C., Kincaid H.L. (1997) Genetic variation at microsatellite loci in sturgeon: primers sequence homology in Acipenser and Scaphirhynchus. Canadian Journal of Fisheries and Aquatic Sciences, 54, 1542–1547. https://doi.org/10.1139/f97-061
Kaczmarczyk D., Kohlmann K., Kersten P., Luczynski M. (2007) Polymorphism of microsatellite loci – a tool in studying biodiversity of paddlefish aquaculture broodstock. Environmental Biotechnology, 3, 44–48.
Zheng, X., Schneider, K., Lowe, J. D., Gomelsky, B., Mims, S. D., Bu, S. (2014). Genetic structure among four populations of paddlefish, Polyodon spathula (Actinopterygii: Acipenseriformes: Polyodontidae), based on disomic microsatellite markers. Acta Ichthyol. Piscat. 44 (3): 213–219.
https://doi.org/10.3750/AIP2014.44.3.05
Carter M. J., Milton I. D. (1993) An inexpensive and simple method for DNA purifications on silica particles. Nucleic Acids Res, 21, 1044—1046. https://doi.org/10.1093/nar/21.4.1044
Kurta Kh.M. Malysheva O.O., Spyrydonov V.H. (2017) Optymizatsiia umov polimeraznoi lantsiuhovoi reaktsii dlia doslidzhennia mikrosatelitnoi DNK veslonosa (Polyodon spathula). Biolohiia tvaryn, 19, № 2, 56-63.
Wright S. (1951) The genetical structure of populations. Ann. Eugethcs 15: 323-354.
Kalinowski S.T., M.L. Taper, T.C. Marshall (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 5, 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Marshall T.C. et al (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol.ecol, 639-655. https://doi.org/10.1046/j.1365-294x.1998.00374.x
Peakall R., Smouse P.E. (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
Downloads
Published
Issue
Section
License
Relationship between right holders and users shall be governed by the terms of the license Creative Commons Attribution – non-commercial – Distribution On Same Conditions 4.0 international (CC BY-NC-SA 4.0):https://creativecommons.org/licenses/by-nc-sa/4.0/deed.uk
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
