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An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.)

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Abstract

With the aim to study variability in genes involved in ecological adaptations, we have analysed sequence polymorphisms of eight unique genes putatively involved in drought response by isolation and analysis of allelic sequences in eight inbred lines of sunflower of different origin and phenotypic characters and showing different drought response in terms of leaf relative water content (RWC). First, gene sequences were amplified by PCR on genomic DNA from a highly inbred line and their products were directly sequenced. In the absence of single nucleotide polymorphisms, the gene was considered as unique. Then, the same PCR reaction was performed on genomic DNAs of eight inbred lines to isolate allelic variants to be compared. The eight selected genes encode a dehydrin, a heat shock protein, a non-specific lipid transfer protein, a z-carotene desaturase, a drought-responsive-element-binding protein, a NAC-domain transcription regulator, an auxin-binding protein, and an ABA responsive-C5 protein. Nucleotide diversity per synonymous and non-synonymous sites was calculated for each gene sequence. The π a/π s ratio range was usually very low, indicating strong purifying selection, though with locus-to-locus differences. As far as non-coding regions, the intron showed a larger variability than the other regions only in the case of the dehydrin gene. In the other genes tested, in which one or more introns occur, variability in the introns was similar or even lower than in the other regions. On the contrary, 3′-UTRs were usually more variable than the coding regions. Linkage disequilibrium in the selected genes decayed on average within 1,000 bp, with large variation among genes. A pairwise comparison between genetic distances calculated on the eight genes and the difference in RWC showed a significant correlation in the first phases of drought stress. The results are discussed in relation to the function of analysed genes, i.e. involved in gene regulation and signal transduction, or encoding enzymes and defence proteins.

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References

  • Almoguera C, Jordano J (1992) Developmental and environmental concurrent expression of sunflower dry-seed-stored low-molecular-weight heat-shock protein and Lea mRNAs. Plant Mol Biol 19:781–792

    Article  PubMed  CAS  Google Scholar 

  • Bakker EG, Toomajian C, Kreitman M, Bergelson J (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis thaliana. Plant Cell 18:1803–1818

    Article  PubMed  CAS  Google Scholar 

  • Bakker EG, Traw MB, Toomajian C, Kreitman M, Bergelson J (2008) Low levels of polymorphism in genes that control the activation of defence response in Arabidopsis thaliana. Genetics 178:2031–2043

    Article  PubMed  CAS  Google Scholar 

  • Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140:783–796

    PubMed  CAS  Google Scholar 

  • Burke JM, Knapp SJ, Rieseberg LH (2005) Genetic consequences of selection during the evolution of cultivated sunflower. Genetics 171:1933–1940

    Article  PubMed  CAS  Google Scholar 

  • Carranco R, Almoguera C, Jordano J (1997) A plant small heat shock protein gene expressed during zygotic embryogenesis but noninducible by heat stress. J Biol Chem 272:27470–27475

    Article  PubMed  CAS  Google Scholar 

  • Close TJ (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97:795–803

    Article  CAS  Google Scholar 

  • Conti A, Pancaldi S, Fambrini M, Michelotti V, Bonora A, Salvini M, Pugliesi C (2004) A deficiency at the gene coding for zeta-carotene desaturase characterizes the sunflower non dormant-1 mutant. Plant Cell Physiol 45:445–455

    Article  PubMed  CAS  Google Scholar 

  • Cronn R, Brothers M, Klier K, Bretting PK, Wendel JF (1997) Allozyme variation in domesticated annual sunflower and its wild relatives. Theor Appl Genet 95:532–545

    Article  Google Scholar 

  • Cummings MP, Clegg MT (1998) Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci USA 95:5637–5642

    Article  PubMed  CAS  Google Scholar 

  • David KM, Couch D, Braun N, Brown S, Grosclaude J, Perrot-Rechenmann C (2007) The auxin-binding protein 1 is essential for the control of cell cycle. Plant J 50:197–206

    Article  PubMed  CAS  Google Scholar 

  • De Oliveira Carvalho A, Moreira Gomes V (2007) Role of plant lipid transfer proteins in plant cell physiology—a concise review. Peptides 28:1144–1153

    Article  Google Scholar 

  • Diaz-Martin J, Almoguera C, Prieto-Dapena P, Espinosa JM, Jordano J (2005) Functional interaction between two transcription factors involved in the developmental regulation of a small heat stress protein gene promoter. Plant Physiol 139:1483–1494

    Article  PubMed  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1989) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Feder ME, Mitchell-Olds T (2003) Evolutionary and ecological functional genomics. Nat Rev Genet 4:649–655

    Article  Google Scholar 

  • Felsenstein J (1989) PHYLIP-phylogeny inference package (Version 3.2). Cladistics 5:164–166

    Google Scholar 

  • Giordani T, Natali L, D’Ercole A, Pugliesi C, Fambrini M, Vernieri P, Vitagliano C, Cavallini A (1999) Expression of a dehydrin gene during embryo development and drought stress in ABA deficient mutants of sunflower (Helianthus annuus L.). Plant Mol Biol 39:739–748

    Article  PubMed  CAS  Google Scholar 

  • Giordani T, Natali L, Cavallini A (2003) Analysis of a dehydrin encoding gene and its phylogenetic utility in Helianthus. Theor Appl Genet 107:316–325

    Article  PubMed  CAS  Google Scholar 

  • Hare MP, Palumbi SR (2003) High intron sequence conservation across three mammalian orders suggests functional constraints. Mol Biol Evol 20:969–978

    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 

  • Haseneyer G, Ravel C, Dardevet M, Balfourier F, Sourdille P, Charmet G, Brunel D, Sauer S, Geiger HH, Graner A, Stracke S (2008) High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections. Theor Appl Genet 117:321–331

    Article  PubMed  CAS  Google Scholar 

  • Hass CG, Tang S, Leonard S, Miller JF, Traber MG, Miller JF, Knapp SJ (2006) Three non-allelic epistatically interacting methyltransferase mutations produce novel tocopherol (vitamin E) profiles in sunflower. Theor Appl Genet 113:767–782

    Article  PubMed  CAS  Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

    Article  Google Scholar 

  • Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S (2008) Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178:2217–2226

    Article  PubMed  CAS  Google Scholar 

  • Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291

    Article  PubMed  CAS  Google Scholar 

  • Kawabe A, Innan H, Terauchi R, Miyashita NT (1997) Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana. Mol Biol Evol 14:1303–1315

    PubMed  CAS  Google Scholar 

  • Kolkman JM, Slabaugh MB, Bruniard JM, Berry ST, Bushman SB, Olungu C, Maes N, Abratti G, Zambelli A, Miller JF, Leon A, Knapp SJ (2004) Acetohydroxyacid synthase mutations conferring resistance to imidazolinone or sulfonylurea herbicides in sunflower. Theor Appl Genet 109:1147–1159

    Article  PubMed  CAS  Google Scholar 

  • Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132

    Article  PubMed  CAS  Google Scholar 

  • Lin J-Z, Brown AHD, Clegg MT (2001) Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum). Proc Natl Acad Sci USA 98:531–536

    Article  PubMed  CAS  Google Scholar 

  • Liu X, Baird WV (2003) Differential expression of genes regulated in response to drought or salinity stress in sunflower. Crop Sci 43:678–687

    CAS  Google Scholar 

  • Liu X, Baird VW (2004) Identification of a novel gene, HaABRC5, from Helianthus annuus (Asteraceae) that is upregulated in response to drought, salinity, and abscisic acid. Am J Bot 91:184–191

    Article  CAS  Google Scholar 

  • Liu A, Burke JM (2006) Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 173:321–330

    Article  PubMed  CAS  Google Scholar 

  • Moriyama EN, Powell JR (1996) Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 13:261–277

    PubMed  CAS  Google Scholar 

  • Natali L, Giordani T, Cavallini A (2003) Sequence variability of a dehydrin gene within Helianthus annuus. Theor Appl Genet 106:811–818

    PubMed  CAS  Google Scholar 

  • Navari-Izzo F, Quartacci MF, Melfi D, Izzo R (1993) Lipid composition of plasma membrane isolated from sunflower seedlings grown under water-stress. Physiol Plant 87:508–514

    Article  CAS  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426

    PubMed  CAS  Google Scholar 

  • Ogata N, Alter HJ, Miller RH, Purcell RH (1991) Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc Natl Acad Sci USA 88:3392–3396

    Article  PubMed  CAS  Google Scholar 

  • Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, Kikuchi S (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10:239–247

    Article  PubMed  CAS  Google Scholar 

  • Ouvrard O, Cellier F, Ferrare K, Tousch D, Lamaze T, Dupuis J-M, Casse-Delbart F (1996) Identification and expression of water stress- and abscisic acid-regulated genes in a drought-tolerant sunflower genotype. Plant Mol Biol 31:819–829

    Article  PubMed  CAS  Google Scholar 

  • Rieseberg LH, Seiler GJ (1990) Molecular evidence and the origin and development of the domesticated sunflower (Helianthus annuus, Asteraceae). Econ Bot 44(Suppl):79–91

    Article  Google Scholar 

  • Roche J, Hewezi T, Bouniols A, Gentzbittel L (2007) Transcriptional profiles of primary metabolism and signal transduction-related genes in response to water stress in field-grown sunflower genotypes using a thematic cDNA microarray. Planta 226:601–617

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175

    Article  PubMed  CAS  Google Scholar 

  • Schuppert GF, Tang S, Slabaugh MB, Knapp SJ (2006) The sunflower high-oleic mutant Ol carries variable tandem repeats of FAD2-1, a seed-specific oleoyl-phosphatidyl choline desaturase. Mol Breed 17:241–256

    Article  CAS  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227

    Article  PubMed  CAS  Google Scholar 

  • Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100:158–170

    Article  PubMed  CAS  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed  CAS  Google Scholar 

  • Tang S, Knapp SJ (2003) Microsatellites uncover extraordinary diversity in native American land races and wild populations of cultivated sunflower. Theor Appl Genet 106:990–1003

    PubMed  CAS  Google Scholar 

  • Tang S, Hass CG, Knapp SJ (2006) Ty3/gypsy-like retrotransposon knockout of a 2-methyl-6-phytyl-1, 4-benzoquinone methyltransferase is non-lethal, uncovers a cryptic paralogous mutation, and produces novel tocopherol (vitamin E) profiles in sunflower. Theor Appl Genet 113:783–799

    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 

  • Vukich M, Schulman AH, Giordani T, Natali L, Kalendar R, Cavallini A (2009) Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers. Theor Appl Genet 119:1027–1038

    Article  PubMed  CAS  Google Scholar 

  • Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276

    Article  PubMed  CAS  Google Scholar 

  • Wilkins MR, Gasteiger E, Bairoch A, Sanchez J-C, Williams KL, Appel RD, Hochstrasser DF (1998) Protein identification and analysis tools in the ExPASy server. In: Link AJ (ed) Methods in molecular biology, 2-D proteome analysis protocols, vol 112. Humana Press Inc., Totowa, pp 531–552

    Chapter  Google Scholar 

  • Zhu B, Choi D-W, Fenton R, Close TJ (2000) Expression of the barley dehydrin multigene family and the development of freezing tolerance. Mol Gen Genet 264:145–153

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by PRIN-MIUR, Project “Variabilità di sequenza ed eterosi in piante coltivate”.

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Authors and Affiliations

  1. Genetics Section, Department of Crop Plant Biology, University of Pisa, Pisa, Italy

    T. Giordani, M. Buti, L. Natali, C. Pugliesi & A. Cavallini

  2. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, Udine, Italy

    F. Cattonaro & M. Morgante

  3. Department of Crop and Environmental Sciences, University of Udine, Udine, Italy

    M. Morgante

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  1. T. Giordani
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  2. M. Buti
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  4. C. Pugliesi
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  7. A. Cavallini
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Correspondence to A. Cavallini.

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Communicated by A. Bervillé.

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Giordani, T., Buti, M., Natali, L. et al. An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.). Theor Appl Genet 122, 1039–1049 (2011). https://doi.org/10.1007/s00122-010-1509-0

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  • DOI: https://doi.org/10.1007/s00122-010-1509-0

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