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Background  Sunflower belongs to the largest plant family on earth, the genomically poorly explored  Compositae . Downy mildew  Plasmopara halstedii  (Farlow) Berlese & 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  Pl   ARG   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  Pl   ARG   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 .    Results  A 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  Pl   ARG  .    Conclusions  This 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.

bmc genomics

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