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

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 languageEnglish (US)
Article numbere51360
JournalPLoS One
Volume7
Issue number12
DOIs
StatePublished - Dec 19 2012

Fingerprint

Helianthus
Polymorphism
Helianthus annuus
Genes
genetic polymorphism
Genome
genome
genome assembly
unigenes
Oilseeds
oilseeds
Genetic Association Studies
inbred lines
Population
quantitative trait loci
genes
genomics
testing

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Bowers, J. E., Nambeesan, S., Corbi, J., Barker, M. S., Rieseberg, L. H., Knapp, S. J., & Burke, J. M. (2012). Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms. PLoS One, 7(12), [e51360]. https://doi.org/10.1371/journal.pone.0051360

Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms. / Bowers, John E.; Nambeesan, Savithri; Corbi, Jonathan; Barker, Michael S; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.

In: PLoS One, Vol. 7, No. 12, e51360, 19.12.2012.

Research output: Contribution to journalArticle

Bowers, John E. ; Nambeesan, Savithri ; Corbi, Jonathan ; Barker, Michael S ; Rieseberg, Loren H. ; Knapp, Steven J. ; Burke, John M. / Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms. In: PLoS One. 2012 ; Vol. 7, No. 12.
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