Genotype calling in tetraploid species from bi-allelic marker data using mixture models

Abstract

BackgroundAutomated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).ResultsWe present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.ConclusionsWe have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.

The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map

“…SNPs were initially filtered so that the average of their total signal intensity (the sum of the X and Y allele signal intensities) over all samples was greater than 0.2. The marker intensities were converted into allele dosages using the fitTetra package for R (Voorrips et al 2011). Changes to the default settings of the saveMarkerModels function of fitTetra were as follows: p.threshold was decreased from 0.99 to 0.95; peak.threshold was increased from 0.85 to 0.99; and sd.target was set to 0.04, where p.threshold is the minimum P-value required to assign a genotype to a sample; peak.threshold is the maximum allowed fraction of the scored samples that are in one peak; and sd.target is used to specify the maximum nonpenalized SD of the fit on a transformed scale (Voorrips et al 2011).…”

A maximum-likelihood estimation of pairwise relatedness for autopolyploids

“…For example, there are three types of partial heterozygotes (that is, A i A i A i A j , A i A i A i A j and A i A j A j A j ) if two alleles (A i and A j ) are present in an ambiguous genotype. Although some methods are able to determine tetraploid genotype (that is, Xu et al, 2002;Pfeiffer et al, 2011;Serang et al, 2012;Voorrips et al, 2011;Uitdewilligen et al, 2013), additional instrument or software may be required.…”

Genetic mapping in polyploids

“…However, there have also been a number of genotyping tools that have been put into the public domain. One of the first of these to be released was fitTetra (Voorrips et al, 2011), a freely-available R package (R Core Team, 2016) designed to assign genotypes to autotetraploids that were genotyped on either Illumina's Infinium or Affymetrix's Axiom arrays. fitTetra fits mixture models to bi-allelic SNP intensity ratios either under the constraint of Hardy-Weinberg equilibrium within the population, or as an unconstrained fit, using an expectation-maximisation (EM) algorithm in fitting.…”