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

Background: Automated 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). Results: We 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 i...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Roeland E. Voorrips, Gerrit Gort, Ben Vosman
• Keywords: Biometrics, BMCBI 2011, Hardy Weinberg Equilibrium, Mixture Models, Potato Varieties