‘Gametes Simulator’: a multilocus genotype simulator to analyze genetic structure in outbreeding diploid species

Porta, Bettina; Fernández, Peter; Galván, Guillermo A.; Priano, Federico Condón

doi:10.1590/1984-70332020v20n1s9

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Crop Breeding and Applied Biotechnology

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SOFTWARE RELEASE • Crop Breed. Appl. Biotechnol. 20 (1) • Jan-Mar 2020 • https://doi.org/10.1590/1984-70332020v20n1s9 copy

‘Gametes Simulator’: a multilocus genotype simulator to analyze genetic structure in outbreeding diploid species

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Bulk sampling and subsequent DNA fingerprinting are applied to obtain estimated allelic frequency data and unveil population structure for outbreeding species. We developed ‘Gametes Simulator’, a routine to simulate gametes from allelic frequencies of unlinked loci, which enables the analysis of population structure through Bayesian analysis. Based on the allelic frequencies in the populations, the software simulates the alleles per population in the right proportions and assigns one allele per marker to each gamete following Mendel’s laws that govern gametogenesis.

Keywords:
Bulk sampling; unlinked loci; allelic frequencies.

Marker name	Allele name	Pop 1	Pop 2	Pop 3	Pop 4	Pop 5	...	Pop n
MK1	MK1a	0.33	0.10	0.40	0.50	0.25	…	Allelic frequency for MK1a in Pop n
MK1	MK1b	0.33	0	0.60	0.30	0.25	…	Allelic frequencyfor MK1b in Pop n
MK1	MK1c	0.33	0.70	0	0.20	0.25	…	Allelic frequency for MK1c in Pop n
…	…	…	…	…	…	…	…	Allelic frequency for .......... in Pop n
MK1	MK1i	0	0.20	0	0	0.25	…	Allelic frequency for MK1i in Pop n
MK2	MK2a	1.0		0.25	0.30		…	Allelic frequency for MK2a in Pop n
MK2	MK2b	0		0.60	0.10		…	Allelic frequency for MK2b in Pop n
MK2	MK2c	0		0.10	0.50		…	Allelic frequency for MK2c in Pop n
MK2	MK2d	0		0.05	0.10		…	Allelic frequency for MK2d in Pop n
MK3	MK3a	0.30	0.10	0.80	0.75	1.0	…	Allelic frequency for MK3a in Pop n
MK3	MK3b	0.70	0.90	0.20	0.25	0	…	Allelic frequency for MK3b in Pop n
MK4	MK4a	0.20	0.30	0.36	0.10	0.50	…	Allelic frequency for MK4a in Pop n
MK4	MK4b	0.60	0	0.14	0.20	0.25	…	Allelic frequency for MK4b in Pop n
MK4	MK4c	0.20	0.70	0.50	0.70	0.25	…	Allelic frequency for MK4c in Pop n
MKn	MKni	…	…	…	…	…	…	Allelic frequency for MKni in Pop n

Algorithm	Output	Homology with gametogenesis	Biological meaning
1. Takes the matrix of allelic frequencies per marker and per population as input.			The fraction of all chromosomes in the diploid population that carry each allele
2. Translates the genetic frequencies of each allele in each population into repeated alleles as many times as Af^# × Gs*	4th column in each marker Excel sheet in the file ‘First output of the software’		Real number of allele copies expected in a sample of gametes taken from each population Size of the sample: Gs*
3.Takes the output from 2 and sorts at random the alleles per marker within each population, allocating one allele randomly to each gamete	5th column in each marker Excel sheet in the file ‘First output of the software’	Random allocation of each allele per marker (locus) to each future gamete in the gametogenesis process (1st Mendel’s law) and independently among unlinked markers (2nd Mendel’s law). Also independent among populations because the allelic frequencies per population reported in the input matrix have no influence on one another	Genetic variability among gametes within populations determined by random and by the allelic frequencies present in each population
4.Multilocus haplotype assemblage (gamete genotype): takes the output from the previous step (5th column of each Excel marker sheet) and assembles it considering all the markers. Gametes Simulator does so by gathering the genetic information for each locus per gamete after the randomization process.	Final matrix that has the list of simulated gametes´ haplotypes in each population as rows and all the markers as columns	Chromatid assignment to each future gamete during anaphase II in meiosis II to give place to the gametes. The alleles present in each chromatid were determined previously by random recombination events (in prophase I) and the random alignment and splitting up of homologues (in metaphase I; anaphase I) and sister chromatids (in metaphase II; anaphase II) in meiosis I and II, respectively.	Multilocus haplotype of gametes belonging to a certain population

Crop Breeding and Applied Biotechnology Universidade Federal de Viçosa, Departamento de Fitotecnia, 36570-000 Viçosa - Minas Gerais/Brasil, Tel.: (55 31)3899-2611, Fax: (55 31)3899-2611 - Viçosa - MG - Brazil
E-mail: cbab@ufv.br

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[1] *E-mail:bporta@fagro.edu.uy