Nucleotide diversity and linkage disequilibrium in antioxidant genes of Brachypodium distachyon

Plant Science

Volumn 197, Issue , 2012, Pages 122-129

  Luo, Na ^a,b,c   Yu, Xiaoqing ^c   Liu, Jianxiu ^a   Jiang, Yiwei ^c  

^a INSTITUTE OF BOTANY   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

^c PURDUE UNIVERSITY   (United States)

Author keywords

Antioxidant gene; Brachypodium distachyon; Drought stress; Linkage disequilibrium; Nucleotide diversity

Indexed keywords

ANTIOXIDANT; CATALASE; OXIDOREDUCTASE; PEROXIDASE; PLANT DNA; VEGETABLE PROTEIN;

ARTICLE; BRACHYPODIUM; DNA SEQUENCE; DROUGHT; ENZYMOLOGY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGICAL STRESS; PHYSIOLOGY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

ANTIOXIDANTS; BASE SEQUENCE; BRACHYPODIUM; CATALASE; DNA, PLANT; DROUGHTS; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; PEROXIDASE; PHYLOGENY; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; STRESS, PHYSIOLOGICAL;

BRACHYPODIUM; BRACHYPODIUM DISTACHYON; POACEAE;

EID: 84867598831     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2012.09.010     Document Type: Article

References (48)

1. Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002, 7:405-410.
2. Asada K. The water-water cycle in chloroplasts: scavenging of active oxygen and dissipation of excess photons. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1999, 50:601-639.
3. Møller I.M., Jensen P.E., Hansson A. Oxidative modifications to cellular components in plants. Annu. Rev. Plant Biol. 2007, 58:459-481.
4. Li F., Wu Q.Y., Duan M., Dong X.C., Li B., Meng Q.W. Transgenic tomato plants overexpressing chloroplastic monodehydroascorbate reductase are resistant to salt- and PEG-induced osmotic stress. Photosynthetica 2012, 50:120-128.
5. Yin L., Wang S., Eltayeb A.E., Uddin M.I., Yamamoto Y., Tsuji W., Takeuchi Y., Tanaka K. Overexpression of dehydroascorbate reductase, but not monodehydroascorbate reductase, confers tolerance to aluminum stress in transgenic tobacco. Planta 2010, 23:609-621.
6. Gaber A., Yoshimura K., Yamamoto T., Yabuta Y., Takeda T., Miyasaka H., Nakano Y., Shigeoka S. Glutathione peroxidase-like protein of Synechocystis PCC 6803 confers tolerance to oxidative and environmental stresses in transgenic Arabidopsis. Physiol. Plant. 2006, 128:251-262.
7. Roxas V.P., Smith R.K., Allen E.R., Allen R.D. Overexpression of glutathione S-transferase/glutathione peroxidase enhances the growth of transgenic tobacco seedlings during stress. Nat. Biotechnol. 1997, 15:988-991.
8. Kwak S.-S., Lim S., Tang L., Kwon S.-Y., Lee H.-S. Enhanced tolerance of transgenic crops expressing both superoxide dismutase and ascorbate peroxidase in chloroplasts to multiple environmental stress. Salinity and Water Stress 2009, 197-203. Springer Science, The Netherlands. M. Ashral, M. Ozturk, H.R. Athar (Eds.).
9. Li Y-J., Hai R-L., Du X-H., Jiang X-N., Lu H. Over-expression of a Populus peroxisomal ascorbate peroxidase (PpAPX) gene in tobacco plants enhances stress tolerance. Plant Breed. 2009, 128:404-410.
10. Yu J., Buckler E.S. Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 2006, 17:155-160.
11. Kim S., Plagnol V., Hu T.T., Toomajian C., Clark R.M., Ossowski S., Ecker J.R., Weigel D., Nordborg M. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 2007, 39:1151-1155.
12. Remington D.L., Thornsberry J.M., Matsuoka Y., Wilson L.M., Whitt S.R., Doebley J., Kresovich S., Goodman M.M., Bucker E.S. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:11479-11484.
13. Kristie A.M., Caicedo A.L., Polato N.R., Olsen K.M., McCouch S., Purugganan M.D. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 2007, 177:2223-2232.
14. Caldwell K.S., Russell J., Langridge P., Powell W. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 2006, 172:557-567.
15. Somers D.J., Banks T., DePauw R., Fox S., Clarke J., Pozniak C., McCartney C. Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 2007, 50:557-567.
16. Li Y., Haseneyer G., Schön C.C., Ankerst D., Korzun V., Wilde P., Bauer E. High level of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response. BMC Plant Biol. 2011, 11:6.
17. Hamblin M.T., Mitchell S.E., White G.M., Gallego J., Kukatla R., Wing R.A., Paterson A.H., Kresovich S. Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diversity sample of sorghum bicolor. Genetics 2004, 167:471-483.
18. Liu A., Burke J.M. Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 2006, 173:321-330.
19. Xing Y., Frei U., Schejbel B., Asp T., Lübberstedt T. Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biol. 2007, 7:43.
20. Brazauskas G., Pasakinskiene I., Asp T., Lubberstedt T. Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot morphology. Plant Sci. 2010, 179:194-201.
21. Alice F., Lenk I., Petersen K., Jensen C.S., Nielsen K.K., Schejbel B., Andersen J.R., Lübberstedt T. Nucleotide diversity and linkage disequilibrium of nine genes with putative effects on flowering time in perennial ryegrass (Lolium perenne L.). Plant Sci. 2011, 180:228-237.
22. Olson M.S., Robertson A.L., Takebayashi N., Silim S., Schroeder W.R., Tiffin P. Nucleotide diversity and linkage disequilibrium in Balsam Poplar (Populus balsamifera). New Phytol. 2010, 186:526-536.
23. Liu S., Jiang Y. Identification of differentially expressed genes under drought stress in perennial ryegrass. Physiol. Plant. 2010, 139:375-387.
24. González-Martínez S.C., Ersoz E., Brown G.R., Wheeler N.C., Neale D.B. DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 2006, 172:1915-1926.
25. Draper J., Mur L.A.J., Jenkins G., Ghosh-Biswas G.C., Bablak P., Hasterok R., Routledge A.P.M. Brachypodium distachyon: a new model system for functional genomics in grasses. Plant Physiol. 2001, 127:1539-1555.
26. Kellogg E.A. Evolutionary history of the grasses. Plant Physiol. 2001, 125:1198-1205.
27. Garvin D.F., Gu Y.Q., Hasterok S.P., Hazen G., Jenkins T.C., Mockler L.A., Mur J., Vogel J.P. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Plant Genome 2008, 48:69-84.
28. Ozdemir B.S., Hernandez P., Filiz E., Budak H. Brachypodium genomics. Int. J. Plant Genomics 2008, 1-7.
29. Vogel J.P., Tuna M., Budak H., Huo N., Gu Y., Steinwand M.A. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol. 2009, 9:88.
30. Vogel J.P., Garvin D.F., Mockler T.C., Schmutz J., Rokhsar D., Bevan M.W., et al. (The International Brachypodium Initiative), genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768.
31. Mur L.A.J., Allainguillaume J., Catala'n P., Hasterok R., Jenkins G., Lesniewska K., Thomas I., Vogel J. Exploiting the Brachypodium tool box in cereal and grass research. New Phytol. 2011, 191:334-347.
32. Luo N., Liu J., Yu X., Jiang Y. Natural variation of drought response in Brachypodium distachyon. Physiol. Plant. 2011, 141:19-29.
33. Doyle J.J., Doyle J.L. Isolation of plant DNA from fresh tissue. Focus 1990, 12:13-15.
34. Rozas J., Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 1999, 15:174-175.
35. Watterson G.A. On the number of segregating sites on genetical models without recombination. Theor. Popul. Biol. 1975, 7:256-276.
36. Nei M. Molecular Evolutionary Genetics 1987, Columbia University Press, New York.
37. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
38. Hill W.G., Robertson A. Linkage disequilibrium in finite populations. Theor. Appl. Genet. (Der Ziichter) 1968, 38:226-231.
39. Bradbury P.J., Zhang Z., Kroon D.E., Casstevens T.M., Ramdoss Y., Buckler E.S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23:2633-2635.
40. Yamasaki M., Schroeder S., Sanchez-Villeda H., Gaut B., McMullen M.D. Empirical analysis of selection screens for domestication and improvement loci in maize by extended DNA sequencing. Plant Genome 2008, 1:33-43.
41. Krutovsky K.V., Neal D.B. Nucleotide diversity and linkage disequilibrium in cold-hardiness-and wood quality-related candidate genes in Douglas Fir. Genetics 2005, 171:2029-2041.
42. Lin Y., Hwang S.Y., Hsu P.Y., Chiang Y.C., Huang C., Wang C., Lin T.P. Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana. BMC Plant Biol. 2008, 8:16.
43. Li W.H. Rates and patterns of nucleotide substitutions. Molecular Evolution 1997, Sinauer Associates, Sunderland, pp. 177-213.
44. Garris A.J., McCouch S.R., Kresovich S. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 2003, 165:759-769.
45. Flint-Garcia S.A., Thornsberry J.M., Buckler E.S. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 2003, 54:357-374.
46. Zhu C., Gore M., Buckler E.S., Yu J. Status and prospects of association mapping in plants. Plant Genome 2008, 1:5-20.
47. Nordborg M. Linkage disequilibrium gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 2000, 154:923-929.
48. Buckler E.S., Thornsberry J.M., Kresovich S. Molecular diversity, structure and domestication of grasses. Genetic Res. Cambridge 2001, 77:213-218.