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

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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.

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Acknowledgments

This research was supported by grants from the National Science Foundation Plant Genome Program (No. 0421630) and United States Department of Agriculture Plant Genome Program (No. 2000-04292) to S.J.K, R.W.M, and L.H.R, and Advanta Seeds, Pioneer Hi-Bred International, Syngenta, and the Paul C. Berger Endowment to S.J.K.

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Authors and Affiliations

  1. Center for Applied Genetic Technologies, The University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA

    Adam Heesacker, Wenxiang Gao, Shunxue Tang, Alan Gingle & Steven J. Knapp

  2. Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA

    Venkata K. Kishore & Judith M. Kolkman

  3. Department of Plant Science and Genome Center, University of California, Davis, CA, 95616, USA

    Marta Matvienko, Alexander Kozik & Richard M. Michelmore

  4. Department of Biology, Indiana University, Bloomington, IN, 47405, USA

    Zhao Lai & Loren H. Rieseberg

  5. Department of Botany, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Loren H. Rieseberg

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  1. Adam Heesacker
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  2. Venkata K. Kishore
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  10. Zhao Lai
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Correspondence to Steven J. Knapp.

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Communicated by M. Sorrells.

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122_2008_841_MOESM1_ESM.xls

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

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

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

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)

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Heesacker, A., Kishore, V.K., Gao, W. et al. SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 117, 1021–1029 (2008). https://doi.org/10.1007/s00122-008-0841-0

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