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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.)

A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids

Full text
Author(s):
Pereira, Guilherme S. [1, 2] ; Garcia, Antonio Augusto F. [1] ; Margarido, Gabriel R. A. [1]
Total Authors: 3
Affiliation:
[1] Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Genet, Ave Padua Dias 11, BR-13400970 Piracicaba - Brazil
[2] North Carolina State Univ, Bioinformat Res Ctr, 1 Lampe Dr, Campus Box 7566, Raleigh, NC 27607 - USA
Total Affiliations: 2
Document type: Journal article
Source: BMC Bioinformatics; v. 19, NOV 1 2018.
Web of Science Citations: 4
Abstract

BackgroundGenotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage.ResultsVCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SuperMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the Tassel-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species.ConclusionsWe demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data. (AU)

FAPESP's process: 12/25236-4 - Comparative QTL mapping and genomic synteny between sweet sorghum and sugarcane
Grantee:Guilherme da Silva Pereira
Support Opportunities: Scholarships in Brazil - Doctorate
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: 15/22993-7 - Transcriptomics for the identification of commercially important genes in sugarcane
Grantee:Gabriel Rodrigues Alves Margarido
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants