Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms

John E. Bowers; Savithri Nambeesan; Jonathan Corbi; Michael S. Barker; Loren H. Rieseberg; Steven J. Knapp; John M. Burke

doi:10.1371/journal.pone.0051360

Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms

John E. Bowers, Savithri Nambeesan, Jonathan Corbi, Michael S. Barker, Loren H. Rieseberg, Steven J. Knapp, John M. Burke

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Abstract

The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.

Original language	English (US)
Article number	e51360
Journal	PloS one
Volume	7
Issue number	12
DOIs	https://doi.org/10.1371/journal.pone.0051360
State	Published - Dec 19 2012

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abstract = "The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.",

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AU - Barker, Michael S.

AU - Rieseberg, Loren H.

AU - Knapp, Steven J.

AU - Burke, John M.

N1 - Funding Information: This study was supported in part by funding from commercial sources (Syngenta and Biogemma). This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

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N2 - The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.

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Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms

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