Nucleotide diversity and molecular evolution of the WAG-2 gene in common wheat (Triticum aestivumL) and its relatives

Genetics and Molecular Biology

Volumn 34, Issue 4, 2011, Pages 606-615

  Wei, Orgnameshuhong ^a,b   Peng, Zhengsong ^a,b   Zhou, Yonghong ^a   Yang, Zaijun ^b   Wu, Kai ^b   Ouyang, Zhongming ^b  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b CHINA WEST NORMAL UNIVERSITY   (China)

Author keywords

Copy number variation; Genetic diversity; Molecular evolution; Triticum; WAG 2

Indexed keywords

ALLELE; ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DIPLOIDY; EXON; GENE FUNCTION; GENE IDENTIFICATION; GENE ISOLATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; HEXAPLOIDY; INTRON; MADS3 GENE; MOLECULAR CLONING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLANT GENE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; TETRAPLOIDY; WAG 1 GENE; WAG 2 GENE; WHEAT; ZMM2 GENE;

EID: 82355168975     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572011000400013     Document Type: Article

References (56)

1. Altschul SF, Gish W, Miller W,Myers EW and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 1215:403-410.
2. Batley J, Mogg R, Edwards D, O'Sullivan H and Edwards KJ (2003) A high-throughout SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Mol Breeding 11:111-120.
3. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register III JC, Tingey SV and Rafalski A (2002) Insertion-deletion polymorphisms in 3 regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539-547.
4. Brown WM, Prager EM, Wang A and Wilson AC (1982) Mito-chondrial DNA sequences of primates, tempo and mode of evolution. J Mol Evol 18:225-239.
5. Buckler IV ES, Thornsberry JM and Kresovich S (2001) Molecular diversity, structure and domestication of grasses. Genet Res 77:213-218.
6. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, et al. (1999) Characterization of single nucleotide polymorphisms in coding regions of human genes. Nat Genet 22:231-238.
7. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M and Rafalski AJ (2002) SNP frequency, haplo-type structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3:19-33.
8. Ciaffi M, Paolacci AR, D'Aloisio E, Tanzarella OA and Porceddu E (2005) Identification and characterization of gene sequences expressed in wheat spikelets at the heading stage. Gene 346:221-230.
9. Clarke KR and Gorley RN (2001) PRIMER v. 5: User Manual/Tutorial. PRIMER-E Ltd, Plymouth, pp 91-92.
10. Doebley J (1992) Molecular systematics and crop evolution. In: Soltis DE, Soltis PS and Doyle JJ (eds) Molecular Systematics of Plants. Chapman & Hall, New York, pp 202-222.
11. Doyle JJ and Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15.
12. Feuillet C, Penger A, Gellner K, Mast A and Keller B (2001) Molecular evolution of receptor-like kinase genes in hexaploid wheat. Independent evolution of orthologs after polyploi-dization and mechanisms of local rearrangements at para-logous loci. Plant Physiol 125:1304-1313.
13. Galtier N, Gouy M and Gautier C (1996) SEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548.
14. Gaut BS (1998) Molecular clocks and nucleotide substitution rates in higher plants. Evol. Biol 30:93-120.
15. Gojobori T, Li WH and Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360-369.
16. Grob GBJ, Gravendeel B and Eurlings MCM (2004) Potential phylogenetic utility of the nuclear FLORICAULA/LEAFY second intron: Comparison with three chloroplast DNA regions in Amorphophallus (Araceae). Mol Phylogenet Evol 30:13-23.
17. Gu YQ, Coleman-Derr D, Kong XY and Anderson OD (2004) Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four Triticeae genomes. Plant Physiol 135:459-470.
18. Hama E, Takumi S, Ogihara Y and Murai K (2004) Pistillody is caused by alterations to the class-B MADS-box gene expression pattern in alloplasmic wheats. Planta 218:712-720.
19. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R and Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploidy wheat. Proc Natl Acad Sci USA 99:8133-8138.
20. Hayashi K, Hashimoto N, Daigen M and Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212-1220.
21. Kang HG, Noh YS, Chung YY, Costa MA, An K, An G(1995) Phenotypic alterations of petal and sepal by ectopic expression of a rice MADS-box gene in tobacco. Plant Mol Biol 29:1-10.
22. Li WH, Wu CI and Luo CC(1984) Nonrandomnessofpoint mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58-71.
23. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E, Sklar P, et al. (2000) Large-scale discovery and genotyping of single nucleotide polymorphisms in the mouse. Nat Genet 24:381-386.
24. Martin AP and Burg TM (2002) Perils of paralogy: Using HSP70 genes for inferring organismal phylogenies. Syst Biol 51:570-587.
25. Meguro A, Takumi S, Ogihara Y and Murai K (2003) WAG, a wheat AGAMOUS homolog, is associated with development of pistil-like stamens in alloplasmic wheats. Sex Plant Reprod 15:221-230.
26. Mena M, Ambrose BA, Meeley RB, Briggs SP, Yanofsky MF and Schmidt RJ (1996) Diversification of C-function activity in maize flower development. Science 274:1537-1540.
27. Mizumoto K, Hatano H, Hirabayashi C, Murai K and Takumi S (2009) Altered expression of wheat AINTEGUMENTA homolog, WANT-1, in pistil and pistil-like transformed stamen of an alloplasmic line with Aegilops crassa cytoplasm. Dev Genes Evol 219:175-187.
28. Murai K, Murai R, Takumi S and Ogihara Y (1998) Cloning and characterization of cDNAs corresponding to the wheat MADS-box genes. Proc 9th Int Wheat Genet Symp 1:89-94.
29. Murai K, Takumi S, Koga H and Ogihara Y (2002) Pistillody, homeotic transformation of stamens into pistil-like structures, caused by nuclear-cytoplasm interaction in wheat. Plant J 29:169-181.
30. Murai K, Miyamae M, Kato H, Takumi S and Ogihara Y (2003) WAP1, a wheat APETALA1 homolog, plays a central role in the phase transition from vegetative to reproductive growth. Plant Cell Physiol 44:1255-1265.
31. Nicholas KB and Nicholas HBJ (1997) GeneDoc: A tool for editing and annotating multiple sequence alignments. Embnew News 4:1-4.
32. Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39:197-218.
33. Nielsen R and Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
34. Ogihara Y, Mochida K, Nemoto Y, Murai K, Yamazaki Y, Shin I T and Kohara Y (2003) Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J 33:1001-1011.
35. Paolacci AR, Tanzarella OA, Porceddu E, Varotto S and Ciaffi M (2007) Molecular and phylogenetic analysis of MADS-box genes of MIKC type and chromosome location of SEP-like genes in wheat (Triticum aestivum L.). Mol Genet Genomics 278:689-708.
36. Petersen G, Seberg O, Yde M and Berthelsen K (2006) Phylogen-etic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum). Mol Phylogenet Evol 39:70-82.
37. Purugganan MD, Rounsley SD, Schmidt RJ and Yanofsky MF (1995) Molecular evolution of flower development: Diversification of plant MADS-box regulatory gene family. Genetics 140:345-356.
38. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94-100.
39. Rosenberg MS, Subramanian S and Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol 20:988-993.
40. Rozas J, Sanchez-Delbarrio J.C, Messeguer X and Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
41. Saitou N and Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
42. Shimada S, Ogawa T, Kitagawa S, Suzuki T, Ikari C, Shitsukawa N, Abe T, Kawahigashi H, Kikuchi R, Handa H, et al. (2009) A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULL-like gene, VRN1, is upstream of FLOWERING LOCUS T. Plant J 58:668-681.
43. Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchell-Olds T and Weisshaar B (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13:1250-1257.
44. Shitsukawa N, Tahira C, Kassai KI, Hirabayashi C, Shimizu T, Takumi S, Mochida K, Kwaura K, Ogihara Y and Murai K (2007) Genetic and epigenetic alteration among three homo-eologous genes of a class E MADS-box gene in hexaploid wheat. Plant Cell 19:1723-1737.
45. Soltics DE, Soltics PS and Tate JA (2003) Advances in the study of polyploidy since plant speciation. New Phytol 161:173-191.
46. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293:489-493.
47. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
48. Tamura K and Nei M (1993) Estimation of the number of nucleo-tide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526.
49. Tamura K, Nei M and Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030-11035.
50. Tamura K, Dudley J,Nei M and KumarS (2007) MEGA4: Molecular Evolutionary Genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
51. Theissen G, Kim JT and Saedler H (1996) Classification and phy-logeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes. J Mol Evol 43:484-516.
52. Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTALW: 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.
53. Vision TJ, Brown DG and Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290:2114-2117.
54. Yamaguchi T, Lee DY, Miyao A, Hirochika H, An G and Hirano H-Y (2006) Functional diversification of the two C-class MADS box genes OSMADS3 and OSMADS58 in Oryza sativa. Plant Cell 18:15-28.
55. Zhao T, Ni Z, Dai Y, Yao Y, Nie X and Sun Q (2006b) Characterization and expression of 42 MADS-box genes in wheat (Triticum aestivum L.). Mol Gen Genom 276:334-350.
56. Zhao XY, Cheng ZJ and Zhang XS (2006) Overexpression of TaMADS1, a SEPALLATA-like gene in wheat, causes early flowering and the abnormal development of floral organs in Arabidopsis. Planta 223:698-707.