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Identification and mapping of SNPs from ESTs in sunflower

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Abstract

More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from drought- and salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion–deletion polymorphism (SNP) variation in silico, had apparent tissue-specific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 × RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.

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References

  • Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  PubMed  CAS  Google Scholar 

  • Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730–2741

    Article  PubMed  CAS  Google Scholar 

  • Berry ST, Leon AJ, Hanfrey CC, Challis P, Burkholz A, Barnes SR, Rufener GK, Lee M, Caligari PDS (1995) Molecular marker analysis of Helianthus annuus L. 2. Construction of a RFLP linkage map for cultivated sunflower. Theor Appl Genet 91:195–199

    Article  CAS  Google Scholar 

  • Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci USA 101:15255–15260

    Article  PubMed  CAS  Google Scholar 

  • Burke JM, Rieseberg LH (2003) The fitness effects of transgenic disease resistance in wild sunflowers. Science 300:1250

    Article  PubMed  CAS  Google Scholar 

  • Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161:1257–1267

    PubMed  CAS  Google Scholar 

  • Burke JM, Lai Z, Salmaso M, Nakazato T, Tang S, Heesacker A, Knapp SJ, Rieseberg LH (2004) Comparative mapping and rapid karyotypic evolution in the genus Helianthus. Genetics 167:449–457

    Article  PubMed  CAS  Google Scholar 

  • Catala C, Rose JKC, Bennett AB (2000) Auxin-regulated genes encoding cell wall-modifying proteins are expressed during early tomato fruit growth. Plant Physiol 122:527–534

    Article  PubMed  CAS  Google Scholar 

  • Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz R, Ausubel FM, Davis RW, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203–207

    Article  PubMed  CAS  Google Scholar 

  • Clarke B, Lambrecht M, Rhee SY (2003) Arabidopsis genomic information for interpreting wheat EST sequences. Funct Integr Genomics 3:33–38

    PubMed  CAS  Google Scholar 

  • FAOSTAT (2004) Agricultural Production, Crops Primary Database

  • Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311–321

    PubMed  CAS  Google Scholar 

  • Fernandez P, Paniego N, Lew S, Hopp HE, Heinz RA (2003) Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project. BMC Genomics 4:40

    Article  PubMed  Google Scholar 

  • Gedil MA, Wye C, Berry ST, Seger B, Peleman J, Jones R, Leon A, Slabaugh MB, Knapp SJ (2001) An integrated RFLP–AFLP linkage map for cultivated sunflower. Genome 44:213–221

    Article  PubMed  CAS  Google Scholar 

  • Gentzbittel L, Vear F, Zhang YX, Berville A, Nicolas P (1995) Development of a consensus linkage RFLP map of cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 90:1079–1086

    Article  CAS  Google Scholar 

  • Gentzbittel L, Mestries E, Mouzeyar S, Mazeyrat F, Badaoui S, Vear F, de Labrouhe Tourvieille D, Nicolas P (1999) A composite map of expressed sequences and phenotypic traits of the sunflower (Helianthus annuus L) genome. Theor Appl Genet 99:218–234

    Article  CAS  Google Scholar 

  • Gentzbittel L, Abbott A, Galaud JP, Georgi L, Fabre F, Liboz T, Alibert G (2002) A bacterial artificial chromosome (BAC) library for sunflower, and identification of clones containing genes for putative transmembrane receptors. Mol Genet Genomics 266:979–987

    Article  PubMed  CAS  Google Scholar 

  • Giordano M, Oefner PJ, Underhill PA, Cavalli-Sforza L, Tosi R, Richiardi PM (1999) Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility. Genomics 56:247–253

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139–162

    Article  PubMed  CAS  Google Scholar 

  • Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA, Rieseberg LH (2004) Origin of extant domesticated sunflowers in eastern North America. Nature 430:201–205

    Article  PubMed  CAS  Google Scholar 

  • Heywood VH (1978) Flowering plants of the world. Prentice-Hall, Englewood Cliffs

    Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Jan CC, Vick BA, Miller JK, Kahler AL, Butler ETI (1998) Construction of a RFLP linkage map for cultivated sunflower. Theor Appl Genet 96:15–22

    Article  CAS  Google Scholar 

  • Kohler C, Merkle T, Neuhaus G (1999) Characterization of novel gene family of putative cyclic nucleotide and calmodulin-regulated ion channels in Arabidopsis thaliana. Plant J 18:97–104

    Article  PubMed  CAS  Google Scholar 

  • Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O‘Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678

    Article  PubMed  CAS  Google Scholar 

  • Kwok PY (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet 2:235–258

    Article  PubMed  CAS  Google Scholar 

  • Lai Z, Nakazato T, Salmaso M, Burke JM, Tang S, Knapp SJ, Rieseberg LH (2005) Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics (in press)

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Lexer C, Welch ME, Durphy JL, Rieseberg LH (2003) Natural selection for salt tolerance quantitative trait loci (QTLs) in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species. Mol Ecol 12:1225–1235

    Article  PubMed  CAS  Google Scholar 

  • Lexer C, Lai Z, Rieseberg LH (2004) Candidate gene polymorphisms associated with salt tolerance in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species. New Phytol 161:225–233

    Article  CAS  PubMed  Google Scholar 

  • Lunde CF, Morrow DJ, Roy LM, Walbot V (2003) Progress in maize gene discovery: a project update. Funct Integr Genomics 3:25–32

    PubMed  CAS  Google Scholar 

  • Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H, Deng XW (2002) Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14:2383–2398

    Article  PubMed  CAS  Google Scholar 

  • Maes T, Van de Steene N, Zethof J, Karimi M, D’Hauw M, Mares G, Van Montagu M, Gerats T (2001) Petunia AP2-like genes and their role in flower and seed development. Plant Cell 13:229–244

    Article  PubMed  CAS  Google Scholar 

  • Okamuro JK, Caster B, Villarroel R, Montagu MV, Jofuku KD (1997) The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc Natl Acad Sci USA 94:7076–7081

    Article  PubMed  CAS  Google Scholar 

  • Perez-Vich B, Fernandez-Martinez JM, Grondona M, Knapp SJ, Berry ST (2002) Stearoyl-ACP and oleoyl-PC desaturase genes cosegregate with quantitative trait loci underlying high stearic and high oleic acid mutant phenotypes in sunflower. Theor Appl Genet 104:338–349

    Article  PubMed  CAS  Google Scholar 

  • Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275–291

    Article  CAS  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  • Rieseberg LH, Choi H, Chan R, Spore C (1993) Genomic map of a diploid hybrid species. Heredity 70:285–293

    CAS  Google Scholar 

  • Rieseberg LH, Van Fossen C, Desrochers A (1995) Hybrid speciation accompanied by genomic reorganization in wild sunflowers. Nature 375:313–316

    Article  CAS  Google Scholar 

  • Rieseberg LH, Raymond O, Rosenthal DM, Lai Z, Livingstone K, Nakazato T, Durphy JL, Schwarzbach AE, Donovan LA, Lexer C (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301:1211–1216

    Article  PubMed  CAS  Google Scholar 

  • Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, van der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Barker BJ, Buell CR (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 131:419–429

    Article  PubMed  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

    Google Scholar 

  • Schnurr J, Shockey J, Browse J (2004) The acyl-CoA synthetase encoded by LACS2 is essential for cuticle development in Arabidopsis. Plant Cell 16:629–642

    Article  PubMed  CAS  Google Scholar 

  • Seiler GJ (1991) Registration of 13-downy mildew tolerant interspecific sunflower germplasm lines derived from wild annual species. Crop Sci 31:1714–1716

    Google Scholar 

  • Shoemaker RC, Specht JE (1995) Integration of the soybean molecular and classical genetic-linkage groups. Crop Sci 35:436–446

    Article  CAS  Google Scholar 

  • Slabaugh MB, Yu JK, Tang SX, Heesacker A, Hu X, Lu GH, Bidney D, Han F, Knapp SJ (2003) Haplotyping and mapping a large cluster of downy mildew resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms. Plant Biotechnol J 3:167–185

    Article  Google Scholar 

  • Snow AA, Pilson D, Rieseberg LH, Paulsen M, Pleskac N, Reagon MR, Wolf DE (2003) A Bt transgene reduces herbivory and enhances fecundity in wild sunflowers. Ecol Appl 13:279–286

    Article  Google Scholar 

  • Spiegelman JI, Mindrinos MN, Fankhauser C, Richards D, Lutes J, Chory J, Oefner PJ (2000) Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography. Plant Cell 12:2485–2498

    Article  PubMed  CAS  Google Scholar 

  • Tamborindeguy E, Ben C, Liboz T, Gentzbittel L (2004) Sequence evaluation of four specific cDNA libraries for developmental genomics of sunflower. Mol Gen Genomics 271:367–375

    Article  CAS  Google Scholar 

  • Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124–1452

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M, Lander ES (1998) Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082

    Article  PubMed  CAS  Google Scholar 

  • White PJ (1997) The regulation of K+ influx into roots of rye (Secale cereale L.) seedings by negative feedback via the K+ flux from shoot to root in the phloem. J Exp Bot 48:2063–2073

    Article  CAS  Google Scholar 

  • Wright SI, Bi XX, Schroeder SG, Yamasaki M, Doebly JF, McMullen MD, Gaut BS (2005) The effects of artifical selection on the maize genome. Science 308:1310–1314

    Article  PubMed  CAS  Google Scholar 

  • Xiao WZ, Oefner PJ (2001) Denaturing high-performance liquid chromatography: a review. Hum Mutat 17:439–474

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, Tang S, Slabaugh MB, Heesacker A, Cole G, Herring M, Soper J, Han F, Chu WC, Webb DM, Thompson L, Edwards KJ, Berry S, Leon AJ, Grondona M, Olungu C, Maes N, Knapp SL (2003) Towards a saturated molecular genetic linkage map for cultivated sunflower. Crop Sci 43:367–387

    Article  CAS  Google Scholar 

  • Zhang WK, Wang YJ, Luo GZ, Zhang JS, He CY, Wu XL, Gai JY, Chen SY (2004) QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet 108:1131–1139

    Article  PubMed  CAS  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Gregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    PubMed  CAS  Google Scholar 

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Acknowledgements

We thank Alex Kozik for processing and CAP3 assembly of the ESTs and Nolan Kane for editorial suggestions. We thank two anonymous reviewers for constructive suggestions on an earlier draft of the manuscript. We are grateful for the Center for Genomics and Bioinformatics at Indiana University for access to the DHPLC. Both the Center for Genomics and Bioinformatics and the Indiana Genomics Initiative provided funding for equipment used in this project. This research was supported by grant 2000-04922 from the United States Department of Agriculture and grant DBI0421630 from the United States National Science Foundation to LHR and grant NRI 2001-35301-09971 from the United States Department of Agriculture to KL.

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Authors and Affiliations

  1. Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA

    Z. Lai, Y. Zou, J. Andrews & L. H. Rieseberg

  2. Department of Biology, Trinity University, San Antonio, TX, 78212, USA

    K. Livingstone

  3. Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA

    S. A. Church

  4. Center for Applied Genetic Technologies, Department of Crop and Soil Science, University of Georgia, Athens, Georgia, 30602, USA

    S. J. Knapp

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  1. Z. Lai
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  2. K. Livingstone
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  3. Y. Zou
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  6. J. Andrews
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  7. L. H. Rieseberg
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Correspondence to Z. Lai.

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Communicated by R. Bernardo

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Lai, Z., Livingstone, K., Zou, Y. et al. Identification and mapping of SNPs from ESTs in sunflower. Theor Appl Genet 111, 1532–1544 (2005). https://doi.org/10.1007/s00122-005-0082-4

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