Management of Genetic Variation in the Gamete Bank of the Endangered Lake Minnow Eupallasella percnurus, Using Genassemblage 2.2 Software

Abstract

The management of genetic resources deposited in gene banks requires knowledge of the genetic profiles of the gamete donors and bioinformatics tools to process this information. In this work, we show how to use Genassemblage 2.2 software in managing the genetic variation deposited in a bank of cryopreserved semen. Our demonstration was based on the leuciscid fish species, lake minnow Eupallasella percnurus, which is designated as endangered in Poland. The semen samples (n = 192) were taken from four Polish lake minnow populations and frozen in the gene bank. Fin clips were taken and DNA extracted. Across 13 investigated microsatellite loci, 21-53 alleles were identified in each population and 66 in the entire group of samples. The module "Management of genetic variation in gamete bank" of Genassemblage 2.2 software was used to find the set of samples that will preserve 100% of the detected allelic diversity in the next generation. Our results showed that a small group of 4-19 semen samples was enough to transfer all alleles detected across this set of samples. We, therefore, recommend Genassemblage 2.2 as a convenient tool for the detection of genetic differences between donors, the construction of optimal sets of samples for conservation of genetic variation, and for managing genetic variation deposited in gamete banks. Consequently, it can be used in breeding human-dependent populations and to optimize the use of genetic diversity in samples in the gamete banks. It can be especially useful for conserving populations of species characterized by low genetic variation, such as the lake minnow.