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

Autor(es)

Pereira, Guilherme S. ^{[1, 2]} ; Garcia, Antonio Augusto F. ^[1] ; Margarido, Gabriel R. A. ^[1]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: BMC Bioinformatics; v. 19, NOV 1 2018.
• Citações Web of Science: 4

Resumo

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)

• Processo FAPESP: 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
• Beneficiário: Anete Pereira de Souza
• Linha de fomento: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 15/22993-7 - Transcriptômica para identificação de genes de interesse comercial em cana-de-açúcar
• Beneficiário: Gabriel Rodrigues Alves Margarido
• Linha de fomento: Auxílio à Pesquisa - Programa BIOEN - Apoio a Jovens Pesquisadores
• Processo FAPESP: 12/25236-4 - Mapeamento comparativo de QTLs e sintenia genômica entre sorgo sacarino e cana-de-açúcar
• Beneficiário: Guilherme da Silva Pereira
• Linha de fomento: Bolsas no Brasil - Doutorado