BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflowerReport as inadecuate




BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 14:628

Plant genomics

Abstract

BackgroundSunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii Farlow Berlese and de Toni is one of the major diseases of cultivated sunflower Helianthus annuus L

In the search for new sources of downy mildew resistance, the locus PlARG on linkage group 1 LG1 originating from H. argophyllus is promising since it confers resistance against all known races of the pathogen. However, the mapping resolution in the PlARG region is hampered by significantly suppressed recombination and by limited availability of polymorphic markers. Here we examined a strategy developed for the enrichment of molecular markers linked to this specific genomic region. We combined bulked segregant analysis BSA with next-generation sequencing NGS and de novo assembly of the sunflower transcriptome for single nucleotide polymorphism SNP discovery in a sequence resource combining reads originating from two sunflower species, H. annuus and H. argophyllus.

ResultsA computational pipeline developed for SNP calling and pattern detection identified 219 candidate genes. For a proof of concept, 42 resistance gene-like sequences were subjected to experimental SNP validation. Using a high-resolution mapping population, 12 SNP markers were mapped to LG1. We successfully verified candidate sequences either co-segregating with or closely flanking PlARG.

ConclusionsThis study is the first successful example to improve bulked segregant analysis with de novo transcriptome assembly using next generation sequencing. The BSTA pipeline we developed provides a useful guide for similar studies in other non-model organisms. Our results demonstrate this method is an efficient way to enrich molecular markers and to identify candidate genes in a specific mapping interval.

KeywordsBulked segregant transcriptome analysis 454 next-generation sequencing Marker enrichment pipeline De novo transcriptome assembly Resistance gene candidates Helianthus argophyllus Helianthus annuus Sunflower Plasmopara halstedii PlARG Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-628 contains supplementary material, which is available to authorized users.

Maren Livaja, Yu Wang contributed equally to this work.

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Author: Maren Livaja - Yu Wang - Silke Wieckhorst - Grit Haseneyer - Michael Seidel - Volker Hahn - Steven J Knapp - Stefan Taudi

Source: https://link.springer.com/







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