SSRs and INDELs mined from the sunflower EST database

Abundance, polymorphisms, and cross-taxa utility

Adam Heesacker, Venkata K. Kishore, Wenxiang Gao, Shunxue Tang, Judith M. Kolkman, Alan Gingle, Marta Matvienko, Alexander Kozik, Richard W Michelmore, Zhao Lai, Loren H. Rieseberg, Steven J. Knapp

Research output: Contribution to journalArticle

96 Citations (Scopus)

Abstract

Simple sequence repeats (SSRs) are abundant and frequently highly polymorphic in transcribed sequences and widely targeted for marker development in eukaryotes. Sunflower (Helianthus annuus) transcript assemblies were built and mined to identify SSRs and insertions-deletions (INDELs) for marker development, comparative mapping, and other genomics applications in sunflower. We describe the spectrum and frequency of SSRs identified in the sunflower EST database, a catalog of 16,643 EST-SSRs, a collection of 484 EST-SSR and 43 EST-INDEL markers developed from common sunflower ESTs, polymorphisms of the markers among the parents of several intraspecific and interspecific mapping populations, and the transferability of the markers to closely and distantly related species in the Compositae. Of 17,904 unigenes in the transcript assembly, 1,956 (10.9%) harbored one or more SSRs with repeat counts of n ≥ 5. EST-SSR markers were 1.6-fold more polymorphic among exotic than elite genotypes and 0.7-fold less polymorphic than non-genic SSR markers. Of 466 EST-SSR or INDEL markers screened for cross-species amplification and polymorphisms, 413 (88.6%) amplified alleles from one or more wild species (H. argophyllus, H. tuberosus, H. anomalus, H. paradoxus, and H. deserticola), whereas 69 (14.8%) amplified alleles from safflower (Carthamus tinctorius) and 67 (14.4%) amplified alleles from lettuce (Lactuca sativa); hence, only a fraction were transferable to distantly related genera in the Compositae, whereas most were transferable to wild relatives of H. annuus. Several thousand additional SSRs were identified in the EST database and supply a wealth of templates for EST-SSR marker development in sunflower.

Original languageEnglish (US)
Pages (from-to)1021-1029
Number of pages9
JournalTheoretical And Applied Genetics
Volume117
Issue number7
DOIs
StatePublished - Nov 2008

Fingerprint

Helianthus
Insertional Mutagenesis
Expressed Sequence Tags
Microsatellite Repeats
Helianthus annuus
genetic polymorphism
Databases
microsatellite repeats
Carthamus tinctorius
Lettuce
Asteraceae
Alleles
alleles
unigenes
wild relatives
Lactuca sativa
Genomics
Eukaryota
lettuce
eukaryotic cells

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Biotechnology

Cite this

Heesacker, A., Kishore, V. K., Gao, W., Tang, S., Kolkman, J. M., Gingle, A., ... Knapp, S. J. (2008). SSRs and INDELs mined from the sunflower EST database: Abundance, polymorphisms, and cross-taxa utility. Theoretical And Applied Genetics, 117(7), 1021-1029. https://doi.org/10.1007/s00122-008-0841-0

SSRs and INDELs mined from the sunflower EST database : Abundance, polymorphisms, and cross-taxa utility. / Heesacker, Adam; Kishore, Venkata K.; Gao, Wenxiang; Tang, Shunxue; Kolkman, Judith M.; Gingle, Alan; Matvienko, Marta; Kozik, Alexander; Michelmore, Richard W; Lai, Zhao; Rieseberg, Loren H.; Knapp, Steven J.

In: Theoretical And Applied Genetics, Vol. 117, No. 7, 11.2008, p. 1021-1029.

Research output: Contribution to journalArticle

Heesacker, A, Kishore, VK, Gao, W, Tang, S, Kolkman, JM, Gingle, A, Matvienko, M, Kozik, A, Michelmore, RW, Lai, Z, Rieseberg, LH & Knapp, SJ 2008, 'SSRs and INDELs mined from the sunflower EST database: Abundance, polymorphisms, and cross-taxa utility', Theoretical And Applied Genetics, vol. 117, no. 7, pp. 1021-1029. https://doi.org/10.1007/s00122-008-0841-0
Heesacker, Adam ; Kishore, Venkata K. ; Gao, Wenxiang ; Tang, Shunxue ; Kolkman, Judith M. ; Gingle, Alan ; Matvienko, Marta ; Kozik, Alexander ; Michelmore, Richard W ; Lai, Zhao ; Rieseberg, Loren H. ; Knapp, Steven J. / SSRs and INDELs mined from the sunflower EST database : Abundance, polymorphisms, and cross-taxa utility. In: Theoretical And Applied Genetics. 2008 ; Vol. 117, No. 7. pp. 1021-1029.
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