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Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

Published online by Cambridge University Press:  12 February 2007

Hao Gang-Ping ,
Wu Zhong-Yi ,
Chen Mao-Sheng ,
Cao Ming-Qing ,
Dominique Brunel ,
Georges Pelletier ,
Huang Cong-Lin  and
Yang Qing
Hao Gang-Ping
Affiliation:
Beijing Agro-Biotechnology Research Center, Beijing 100089, China College of Life Science, Nanjing Agricutural University, Nanjing 210095, China
Wu Zhong-Yi
Affiliation:
Beijing Agro-Biotechnology Research Center, Beijing 100089, China
Chen Mao-Sheng
Affiliation:
Beijing Agro-Biotechnology Research Center, Beijing 100089, China College of Life Science, Nanjing Agricutural University, Nanjing 210095, China
Cao Ming-Qing
Affiliation:
Beijing Agro-Biotechnology Research Center, Beijing 100089, China
Dominique Brunel
Affiliation:
Station de Génétique et Amélioration des Plantes, INRA, F-78026, Versailles, France
Georges Pelletier
Affiliation:
Station de Génétique et Amélioration des Plantes, INRA, F-78026, Versailles, France
Huang Cong-Lin*
Affiliation:
Beijing Agro-Biotechnology Research Center, Beijing 100089, China
Yang Qing*
Affiliation:
College of Life Science, Nanjing Agricutural University, Nanjing 210095, China
*
*Corresponding author. E-mail: huangconglin@hotmail.com or qyang19@njau.edu.cn
*Corresponding author. E-mail: huangconglin@hotmail.com or qyang19@njau.edu.cn
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Abstract

The levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

Keywords

CBF4 genesingle nucleotide polymorphismdrought tolerance
Type
Research Article
Information
Chinese Journal of Agricultural Biotechnology , Volume 1 , Issue 3 , December 2004 , pp. 181 - 190
Copyright
Copyright © China Agricultural University and Cambridge University Press 2004

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References

Bastide, B, Sipes, D, Hann, J and Ting, IP (1993) Effect of severe water stress on aspects of crassulacean acid metabolism in Xerosicyos. Plant Physiology 103, 4 1089–1096.CrossRefGoogle ScholarPubMed
Batley, J, Barker, G, O'Sullivan, H, Edwards, KJ and Edwards, D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology 132(1): 84–91.CrossRefGoogle ScholarPubMed
Bensen, JT, Langefeld, CD, Hawkins, GA, Green, LE, Mychaleckyj, JC and Brewer, CS et al. (2003) Nucleotide variation, haplotype structure, and association with end-stage renal disease of the human interleukin-1 gene cluster. Genomics 82(2): 194–217.CrossRefGoogle ScholarPubMed
Borevitz, JO and Nordborg, M (2003) The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiology 132,2718–725.CrossRefGoogle Scholar
Brookes, AJ (1999) The essence of SNPs. Gene 234,2177–186.CrossRefGoogle ScholarPubMed
Cargill, M, Altshuler, D, Ireland, J, Sklar, P, Ardlie, K and Patil, N et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genetics 22(3): 231–238.CrossRefGoogle ScholarPubMed
Ching, A, Caldwell, KS, Jung, M, Dolan, M, Smith, OS and Tingey, S et al. (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3, 1–14.CrossRefGoogle ScholarPubMed
Doyle, JJ and Doyle, JL (1987) Isolation of DNA from fresh plant tissue. Focus 12, 13–15.Google Scholar
Gao, JY, Hu, RH and Lu, Z (1984) A study on drought resistant indexes during seeding stage of rice. Scientia Agriculture Sinica 4, 41–46 (in Chinese with English abstract).Google Scholar
Guo, PZ (1993) Introduction to Population Genetics. Beijing, Agricultural Press. pp. 298–332.Google Scholar
Haake, V, Cook, D, Riechmann, JL, Pineda, O, Thomashow, MF and Zhang, JZ (2002) Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiology 130(2): 639–648.CrossRefGoogle ScholarPubMed
Halushka, MK, Fan, JB, Bentley, K, Hsie, L, Shen, N and Weder, A et al. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nature Genetics 22(3): 239–247.CrossRefGoogle ScholarPubMed
Hanfstingl, U, Berry, A, Kellogg, EA, Costa, JT 3rd, Rudiger, W and Ausubel, FM (1994) Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection. Genetics 138 3811–828.CrossRefGoogle ScholarPubMed
Innan, H, Tajima, F, Terauchi, R and Miyashita, NT (1996) Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics 143(4): 1761–1770.CrossRefGoogle ScholarPubMed
International SNP Map Working Group (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 6822928–930.CrossRefGoogle Scholar
Kawabe, A and Miyashita, NT (1999) DNA variation in the basic chitinase locus ( ChiB ) region of the wild plant Arabidopsis thaliana. Genetics 153(3): 1445–1453.CrossRefGoogle ScholarPubMed
Kawabe, A, Innan, H, Terauchi, R and Miyashita, NT (1997) Nucleotide polymorphism in the acidic chitinase locus ( ChiA ) region of the wild plant Arabidopsis thaliana. Molecular Biology and Evolution 14(12): 1303–1315.CrossRefGoogle ScholarPubMed
Kruglyak, L (1997) The use of a genetic map of biallelic markers in linkage studies. Nature Genetics 17, 121–24.CrossRefGoogle ScholarPubMed
Le Corre, V, Roux, F and Reboud, X (2002) DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Molecular Biology and Evolution 19, 81261–1271.CrossRefGoogle ScholarPubMed
Li, SJ, Wang, HC and Yu, WY (1983) Effect of drought on cell membrane of maize leaf. Acta Phytophysiologica Sinica 9, 223–229 in Chinese with English abstract.Google Scholar
McKhann, HI, Camilleri, C, Berard, A, Bataillon, T, David, JL and Reboud, X et al. (2004) Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant Journal 38(1): 193–202.CrossRefGoogle ScholarPubMed
Mauricio, R, Stahl, EA, Korves, T, Tian, D, Kreitman, M and Bergelson, J (2003) Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics 163(2): 735–746.CrossRefGoogle ScholarPubMed
Mullikin, JC, Hunt, SE, Cole, CG, Mortimore, BJ, Rice, CM and Burton, J et al. (2000) An SNP map of human chromosome 22. Nature 407(6803): 516–520.CrossRefGoogle ScholarPubMed
Nasu, S, Suzuki, J, Ohta, R, Hasegawa, K, Yui, R and Kitazawa, N et al. (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice ( Oryza sativa, Oryza rufipogon ) and establishment of SNP markers. DNA Research 9(5): 163–171.CrossRefGoogle ScholarPubMed
Purugganan, MD and Suddith, JI (1998) Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function. Proceedings of the National Academy of Sciences of the USA 95(14): 8130–8134.CrossRefGoogle ScholarPubMed
Rozas, J and Rozas, R (1999) DnaSP version 3: an intergrated program for molecular population genetics and molecular population analysis. Bioinformatics 15(2): 174–175.CrossRefGoogle Scholar
Sharbel, TF, Haubold, B, Mitchell-Olds, T (2000) Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Molecular Ecology 9(12): 2109–2118.CrossRefGoogle ScholarPubMed
Shepard, KA and Purugganan, MD (2003) Molecular population genetics of the Arabidopsis CLAVATA2 region: the genomic scale of variation and selection in a selfing species. Genetics 163(3): 1083–1095.CrossRefGoogle Scholar
Tajima, F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3): 585–595.CrossRefGoogle ScholarPubMed
Tenaillon, MI, Sawkins, MC, Long, AD, Gaut, RL, Doebley, JF and Gaut, BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize ( Zea mays ssp. Mays L.). Proceedings of the National Academy of Sciences of the USA 98(16): 9161–9166.CrossRefGoogle ScholarPubMed
Ullrich, H, Lattig, K, Brennicke, A and Knoop, V (1997) Mitochondrial DNA variations and nuclear RFLPs reflect different genetic similarities among 23 Arabidopsis thaliana ecotypes. Plant Molecular Biology 33(1): 37–45.CrossRefGoogle ScholarPubMed
Voryell, VH, Jessen, H, Schupp, JM, Webb, D and Keim, P (1999) Allele-specific hybridization markers for soybean. Theoretical and Applied Genetics 101, 1291–1298.Google Scholar
Wang, DG, Fan, JB, Siao, CJ, Berno, A, Young, P and Sapolsky, R et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280(5366): 1077–1082.CrossRefGoogle ScholarPubMed
Zhu, YL, Song, QJ, Hyten, DL, Van Tassell, CP, Matukumalli, LK and Grimm, DR et al. (2003) Single-nucleotide polymorphisms in soybean. Genetics 163(3): 1123–1134CrossRefGoogle ScholarPubMed