Theoretical and Applied Genetics

, Volume 117, Issue 7, pp 1021–1029

SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility

Authors

  • Adam Heesacker
    • Center for Applied Genetic TechnologiesThe University of Georgia
  • Venkata K. Kishore
    • Department of Crop and Soil ScienceOregon State University
  • Wenxiang Gao
    • Center for Applied Genetic TechnologiesThe University of Georgia
  • Shunxue Tang
    • Center for Applied Genetic TechnologiesThe University of Georgia
  • Judith M. Kolkman
    • Department of Crop and Soil ScienceOregon State University
  • Alan Gingle
    • Center for Applied Genetic TechnologiesThe University of Georgia
  • Marta Matvienko
    • Department of Plant Science and Genome CenterUniversity of California
  • Alexander Kozik
    • Department of Plant Science and Genome CenterUniversity of California
  • Richard M. Michelmore
    • Department of Plant Science and Genome CenterUniversity of California
  • Zhao Lai
    • Department of BiologyIndiana University
  • Loren H. Rieseberg
    • Department of BiologyIndiana University
    • Department of BotanyThe University of British Columbia
    • Center for Applied Genetic TechnologiesThe University of Georgia
Original Paper

DOI: 10.1007/s00122-008-0841-0

Cite this article as:
Heesacker, A., Kishore, V.K., Gao, W. et al. Theor Appl Genet (2008) 117: 1021. doi:10.1007/s00122-008-0841-0

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.

Supplementary material

122_2008_841_MOESM1_ESM.xls (2.8 mb)
Supplemental Table 1 SSR motifs, repeat counts, reference sequences, and other supporting data for 16,643 dinucleotide, trinucleotide, and tetranucleotide repeats identified in an assembly of 89,225 sunflower ESTs downloaded from GenBank dbEST on 8-25-2005 (XLS 2900 kb)
122_2008_841_MOESM2_ESM.xls (144 kb)
Supplemental Table 2 DNA marker, EST, and contig names, DNA marker types, and putative functions for SNP, SSR, and INDEL markers (HT1-HT1058) developed from sunflower ESTs (XLS 144 kb)
122_2008_841_MOESM3_ESM.xls (208 kb)
Supplemental Table 3 SSR motifs and repeat counts, Compositae Genome Program Database (CGPdb) reference sequence identifiers, primer sequences, and annealing temperatures for 527 sunflower EST-SSR and INDEL markers (XLS 208 kb)
122_2008_841_MOESM4_ESM.xls (505 kb)
Supplemental Table 4 EST-SSR and INDEL marker allele lengths (bp) and heterozygosities among common and wild sunflower, lettuce, prickly lettuce, and safflower germplasm accessions (XLS 505 kb)

Copyright information

© Springer-Verlag 2008