Genassemblage 2.0 software as a tool for maintaining genetic variation in human dependent fish populations
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1
University of Warmia and Mazury in Olsztyn, Poland
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2
Stanisław Sakowicz Inland Fisheries Institute, Poland
Introduction
Maintaining high genetic variation, expressed as high heterozygosity and allelic diversity, is crucial for populations viability and their adaptation to environmental changes (Lacy 1997, Hansen et al. 2000, Hallerman 2003). Conserving genetic diversity in broodstocks is important for conservation of human-dependent fish species. If individuals are paired without knowledge of the genetic differences between them, they might be genetically similar, which would prevent optimal transfer of genetic variation from parental stock to their progeny.
Highly polymorphic fragments of DNA, such as microsatellites, can be used to prepare genetic profiles of fish that could be used for breeding. These profiles can be used to identify individuals that are as different as possible and assemble them in breeding pairs.
To help identify the best possible breeding pairs within and between breeding stocks and manage genetic variation of protected populations, Genassemblage 2.0 was constructed. The software is intended to be useful in the conservation of human dependent fish species, the maintenance of genetic variation in broodstock, the production of juveniles for fish farming, and for educational purposes.
Material and methods
Genassemblage 2.0 is a free-of-charge Windows-based program. It is an improved version of Genassemblage 1.0 (Kaczmarczyk 2015) with expanded functionality. Its installer and a detailed user guide can be downloaded from the author’s website. The software requires the use of MS Excel, version 2003 or newer.
Genassemblage 2.0 has four modules, which can be chosen by clicking on their respective bars. Two modules can be used to find optimal combinations of parents. The module “Select best breeding pair” was designed for breeding individuals. The user can decide how many pairs to include in the set of best pairs. The suitability of pairs for breeding is evaluated by simultaneously comparing heterozygosity and percentage of weak heterozygotes expected in the progeny, as well as the number of different alleles that will be inherited by their offspring. In version 2.0, we have added the “v index”, so that users can define the relative importance of the three indicators. The Genassemblage 2.0 user guide provides details of the calculations.
The module “Select individuals for group spawning” is new in Genassemblage 2.0 and was intended especially as a help in breeding of fish. It enable to find a group males and females that, when bred together, will contribute the highest genetic diversity to the progeny. After clicking on the bar of this module, the user can indicate how many males and females to include in this set. The Genassemblage 2.0 user guide provides details of the calculations.
An input file for Genassemblage 2.0 can be prepared in a MS Excel spreadsheet. Both modules described above use the same input file. It includes data such as the population group, the population name, the individual’s sex and tag number, and a list of alleles detected at investigated loci (Fig. 1).
To generate the results given below, we used the “Select best breeding pair” module and checked the fields for heterozygosity, percentage of weak heterozygotes and number of different alleles expected in the progeny. Using the v index, we defined the relative importance of the indicators as heterozygosity (0.40), share of “weak heterozygotes” (0.20) and number of different alleles (0.40). The number of pairs was set at four.
We used the “Select individuals for group spawning” module to identify a set of two males and two females that will contribute the highest allelic diversity to their progeny. In the window, we chose “Number of alleles” as the primary indicator.
Results
The results provided by the “Select best breeding pair” module are presented in four MS Excel sheets (Fig. 2A–D). They include the expected heterozygosity in the progeny of each pair (Fig. 2A), the number of alleles that will be inherited by progeny (Fig. 2B), the share of weak heterozygotes (Fig. 2C), and the results of the v index (Fig. 2D). Based on this index, pairs A07xC41, A14xB20, B05xC38 and C42xC40 were selected as optimal. The average heterozygosity for the progeny of this set is 0.630 vs 0.573 in all possible variants; the share of weak heterozygotes, 0.167 vs 0.317; and the average number of alleles, 21 vs 20. The χ2 value for the differences between the values of the indicators in the set of 4 pairs vs that of all possible pairs is 0.2413.
The “Select individuals for group spawning” module indicated that the optimal group includes males B05 and C41, and females A07 and C40 (Fig. 2E). Their progeny will inherit 29 alleles and their heterozygosity will be 0.593.
Conclusion
Genassemblage 2.0 identifies the set of parents that have the best values of genetic variation indicators. It indicates optimal sets of breeding pairs without using the same individuals more than once, thus reducing inbreeding risk. It can also select individuals for group breeding of fish to transfer the highest amount of genetic variation to the next generation. Thus, Genassemblage 2.0 can be used for fish farming and conservation of human dependent populations.
Acknowledgements
The present studies were carried out within the project No. 2014/15/B/NZ9/05240 granted by the National Science Centre (Poland) for years 2015-2019.
References
Hallerman E. 2003. Inbreeding. In: Population Genetics: Principles and Applications for Fisheries Scientists (Ed.) Hallerman E., pp. 215-239.
Hansen M.M., Villanueva B., Nielsen E.E., Bekkevold D. 2008. Investigating the genetics of populations. In: The Atlantic Salmon: Genetics, Conservation and Management (Eds) Verspoor E., Stradmeyer L., Nielsen J.L., pp. 86-114, Blackwell Publishing, UK.
Kaczmarczyk D. 2015. Genassemblage software, a tool for management of genetic diversity in human dependent population. Conserv. Gen. Res. 7: 49-51.
Lacy R.C. 1997. Importance of genetic variation to the viability of mammalian populations J. Mammal., pp. 320-335.
Keywords:
Bioinformatics tool,
assemblage breeding pairs,
conservation genetics,
Genetic Markers,
conservation
Conference:
XVI European Congress of Ichthyology, Lausanne, Switzerland, 2 Sep - 6 Sep, 2019.
Presentation Type:
Oral
Topic:
THREATS AND CONSERVATION
Citation:
Kaczmarczyk
D and
Wolnicki
J
(2019). Genassemblage 2.0 software as a tool for maintaining genetic variation in human dependent fish populations.
Front. Mar. Sci.
Conference Abstract:
XVI European Congress of Ichthyology.
doi: 10.3389/conf.fmars.2019.07.00164
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Received:
29 Jul 2019;
Published Online:
30 Jul 2019.
*
Correspondence:
Dr. Dariusz Kaczmarczyk, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland, d.kaczmarczyk@uwm.edu.pl