GenAPoPop software
Thereby, to provide a user-friendly solution to compute the specific corpus of population genetic indices needed to analyse partially clonal and selfed polysomic populations, we developed and packaged a new portable, multi-operating system, working by itself with no dependency software, named GenAPoPop (standing for Genetic Analyses of Polyploid Populations).
GenAPoPop is written combining python, fortran and html with a graphical user interface coded in Qt. The binary executables for Windows, Linux and MacOS are provided under the terms of a CC-BY-NC-SA license, version 4, and can be downloaded athttps://forgemia.inra.fr/solenn.stoeckel/genapopop1.0/. The idea of this software is to relieve the users of all scripting tasks, and simplify as much as possible the infile formatting. To this aim, GenAPoPop uses a graphical interface organized in a comprehensive workflow (Fig. 1). This software was also designed to complement the previously cited softwares that can be used easily using GenAPoPop dataset export feature.
It enables analysing genotypic dataset with confident allele dosage of autopolyploid species in which we can neglect double-reduction. Double-reductions in auto- and allopolypoloids result from multivalent pairing among homologous chromosomes, when two or more sister chromatids segregate in a same gamete (Wu et al. 2001, Huang et al. 2019, Jiang et al. 2021, Ferreira de Carvalho et al. 2021). The main consequence of double-reduction for population genetics is to increase the probability of identity-by-descent when compared to random chromosome segregation model (Hardy 2016). For example, an autotetraploid individual typedABCD can produce AA , BB , CC , DDgametes when double-reduction happens. Without double-reduction, onlyAB , AC , AD , BC , BD , CD gametes are produced.
Users should thus be warned that GenAPoPop doesn’t consider yet for double-reductio as it assumes a random chromosome segregation model (Muller 1914). This model considers that gametes originate from any combination of homologous chromosomes, thus excluding that two sister chromatids segregate in a same gamete. This is the most commonly observed case in polyploids (Wu et al. 2001). GenAPoPop ignorespure random chromatid segregation model where chromatids randomly segregate into gamete resulting in a rate of double-reduction of 1/7 for tetrasomic inheritance (Haldane 1930) and complete and partial equational segregation model where whole arms of sister chromatids are exchanged by recombination into different chromosomes, resulting in a rate of double-reduction of 1/6 when complete equational segregation occurs (Mather 1935, Huang et al. 2019).
Each packaged version of GenAPoPop is tested on X64 cpu systems (including server cpu Intel Xeon E5-2650 v3, AMD Threadripper 3970X and AMD Ryzen 7 5800u) with a Linux Debian-based distribution and Microsoft Windows 10 and 11 uptodate versions; The MacOS version is currently tested on a MacOS Big Sur, Intel version.