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.