Nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana and its molecular evolution analyses

Acta Genetica Sinica

Volumn 31, Issue 12, 2004, Pages 1415-1425

  Hao, Gang Ping ^a,b   Wu, Zhong Yi ^a   Cao, Ming Qing ^a   Pelletier, Georges ^c   Brunel, Dominique ^c   Huang, Cong Lin ^a   Yang, Qing ^b  

^a National Engineering Research Center of Vegetable   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

^c INRA 78026   (France)

Author keywords

Arabidopsis thaliana; CBF4; Nucleotide polymorphism

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CBF4; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; BALANCING SELECTION; CBF4 GENE; DNA POLYMORPHISM; DNA STRUCTURE; DROUGHT; GENE; GENE DELETION; GENE INDUCTION; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC VARIABILITY; HYPOTHESIS; INTRASPECIFIC NUCLEOTIDE POLYMORPHISM; MOLECULAR EVOLUTION; MUTATION; NATURAL SELECTION; NATURE POSITIVE SELECTION; NEUTRAL MUTATION HYPOTHESIS; NONHUMAN; NONSYNONYMOUS MUTATION; NUCLEOTIDE POLYMORPHISM; NUCLEOTIDE SEQUENCE; SELECTIVE PRESSURE; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; EVOLUTION, MOLECULAR; LINKAGE DISEQUILIBRIUM; NATURAL DISASTERS; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANS-ACTIVATORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; INSERTION SEQUENCES;

EID: 10844285349     PISSN: 03794172     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. Sharbel T F, Haubold B, Mitchell-Olds T. Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol Ecol, 2000, 9(12): 2109-2118.
2. ZHANG Zhi-Yong, LI De-Zhu. Molecular phylogeny of section Parrya of Pinus (pinaceae) based on chloroplast matK gene sequence data. Acta Botanica Sinica, 2004, 46(2): 171-179.
3. TU Li-Li, ZHANG Xian-Long, ZHU Long-Fu, NIE Yi-Chun, GUO Xiao-Ping. Origin, diversity and evolution of NBS-type disease resistance gene analogues in sea-island cotton (Gossypium barbadense L.). Acta Genetica Sinica, 2003, 30(11): 1071-1077.
4. Purugganan M D, Suddith J I. Molecular population genetics of floral homeotic loci: departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana. Genetics, 1999, 151: 839-848.
5. Kawabe A, Innan H, Terauchi R, Miyashita N T. Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana. Mol Biol Evol, 1997, 14(12): 1303-1315
6. Kawabe A, Miyashita N T. DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana. Genetics, 1999, 153: 1445-1453.
7. Kuittinen H, Aguadé M. Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana. Genetics, 2000, 155: 863-872.
8. Mauricio R, Stahl E A, Korves T, Tian D, Kreitman M, Bergelson J. Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics, 2003, 163(2): 735-746.
9. Le Corre V, Roux F, Reboud X. DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is consistent with local selection for flowering time. Mol Biol Evol, 2002, 19(8): 1261-1271.
10. Innan H, Tajima F, Terauchi R, Miyashita N T. Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics, 1996, 143: 1761-1770.
11. Hanfstingl U, Berry A, Kellogg E A, Costa-III J T, Rudiger W, Ausubel F M. Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics, 1994, 138(3): 811-828.
12. Haake V, Cook D, Riechmann J L, Pineda O, Thomashow M F, Zhang J Z. Transcription factor CBF4 Is a regulator of drought adaptation in Arabidopsis. Plant Physiol, 2002, 130: 639-648.
13. Doyle J J, Doyle J L. Isolation of DNA from fresh plant tissue. Focus, 1987, 12: 13 -15.
14. Rozas J, Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular population analysis. Bioinformatics, 1999, 15: 174-175
15. GUO Ping-Zhong. Introduction to population genetics. Beijing: Agricultural Press, 1993, 298-332.
16. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989, 123: 585-595.
17. Shepard K A, Purugganan M D. Molecular population genetics of the Arabidopsis CLAVATA2 region: the genomic scale of variation and selection in a selfing species. Genetics, 2003, 163: 1083-1095.
18. Nordborg M, Borevitz J O, Bergelson J, Berry C C, Chory J, Hagenblad J, Kreitman M, Maloof J N, Noyes T, Oefner P J, Stahl E A, Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet, 2002, 30(2): 190-193.
19. Wang D G, Fan J B, Siao C J, 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 M S, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson T J, Lander E S. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 1998, 280(5366): 1077-1082.
20. Ching A, Caldwell K S, Jung M, Dolan M, Smith O S, Tingey S, Morgante M, Rafalski A J. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics, 2002, 3: 1-14.
21. Zhu Y L, Song Q J, Hyten D L, van Tassell C P, Matukumalli L K, Grimm D R, Hyatt S M, Fickus E W, Young N D, Cregan P B. Single-nucleotide polymorphisms in soybean. Genetics, 2003, 163(3): 1123-1134.
22. Tenaillon M I, Sawkins M C, Anderson L K, Stack S M, Doebley J, Gaut B S. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. Mays L.). Proc Natl Acad Sci USA, 2001, 98: 9161-9166.
23. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res, 2002, 9(5): 163-171.
24. Batley J, Barker G, O' Sullivan H, Edwards K J, Edwards D. Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol, 2003, 132(1): 84-91.
25. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane C R, Lim E P, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley G Q, Lander E S. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet, 1999, 22(3): 231-238.
26. Jander G, Norris S R, Rounsley S D, Bush D F, Levin I M, Last R L. Arabidopsis map-based cloning in the post-genome era. Plant Physiol, 2002, 129(2): 440-450.
27. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register J C 3rd, Tingey S V, Rafalski A. Insertion-deletion polymorphisms in 3′- regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol, 2002, 48: 539-547.
28. Britten R J, Rowen L, Williams J, Cameron R A. Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA, 2003, 100(8): 4661-4665.
29. Hudson R R. Estimating the recombination parameter of finite population model without selection. Genet Res, 1987, 50: 245-250.