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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids

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Author(s):
Serang, Oliver [1, 2] ; Mollinari, Marcelo [3] ; Franco Garcia, Antonio Augusto [3]
Total Authors: 3
Affiliation:
[1] Harvard Univ, Sch Med, Dept Neurobiol, Boston, MA 02115 - USA
[2] Childrens Hosp Boston, Dept Pathol, Boston, MA - USA
[3] Univ Sao Paulo ESALQ, Dept Genet, Sao Paulo - Brazil
Total Affiliations: 3
Document type: Journal article
Source: PLoS One; v. 7, n. 2 FEB 17 2012.
Web of Science Citations: 41
Abstract

The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species. (AU)

FAPESP's process: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
Grantee:Anete Pereira de Souza
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
FAPESP's process: 08/54402-4 - Development of a model to build genetic maps in autopolyploides, with applications in sugarcane
Grantee:Marcelo Mollinari
Support Opportunities: Scholarships in Brazil - Doctorate