Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationship between a MITE insertion in exon 2 and variation in forage maize digestibility

BMC Genetics

Volumn 5, Issue , 2004, Pages

  Guillet Claude, Carine ^a,b   Birolleau Touchard, Christelle ^b   Manicacci, Domenica ^c   Rogowsky, Peter M ^c   Rigau, Joan ^d   Murigneux, Alain ^e   Martinant, Jean Pierre ^e   Barrière, Yves ^b  

^a UNIVERSITÉ LAVAL   (Canada)

^b CEMAGREF   (France)

^c CNRS   (France)

^d INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

^e Campus Universitaire des Cézeaux   (France)

Author keywords

[No Author keywords available]

Indexed keywords

LIGNIN; MESSENGER RNA; PEROXIDASE;

ARTICLE; CELL WALL; CONTROLLED STUDY; DIGESTION; ENZYME DEFICIENCY; EXON; FORAGE CROP; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE STRUCTURE; GENE TARGETING; GENETIC CODE; GENETIC DISTANCE; GENETIC IDENTIFICATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GERMPLASM; HAPLOTYPE; INBRED STRAIN; INTROGRESSION; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT BREEDING; PROTEIN FUNCTION; PROTEIN POLYMERIZATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; QUANTITATIVE TRAIT LOCUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SILENT GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSPOSON; ENZYMOLOGY; GENE EXPRESSION; GENETIC RECOMBINATION; GENETICS; INBREEDING; MAIZE; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; MUTATION;

ZEA MAYS;

BASE SEQUENCE; CELL WALL; DIGESTION; DNA TRANSPOSABLE ELEMENTS; EXONS; GENE EXPRESSION; GENETIC VARIATION; INBREEDING; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTATION; PEROXIDASES; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; ZEA MAYS;

EID: 15744393574     PISSN: 14712156     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2156-5-19     Document Type: Article

References (33)

1. Barrière Y, Guillet C, Gofnner D, Pichon M: Genetic Variation and Breeding Strategies for Improved Cell Wall Digestibility in Annual Forage Crops. A Review. Anim Res 2003, 52:193-228.
2. Boerjan W, Ralph J, Baucher M: Lignin biosynthesis. Annu Rev Plant Biol 2003, 54:519-546.
3. Boudet AM: Towards an understanding of the supramolecular organization of the lignified wall. The plant cell wall Edited by: J Rose. Blackwell publishing; 2003:155-182.
4. Blee KA, Choi JW, O'Connell AP, Schuch W, Lewis NG, Bolwell GP: A lignin-specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification. Phytochemistry 2003, 64:163-176.
5. Li Y, Kajita S, Kawai S, Katayama Y, Morohoshi N: Down-regulation of an anionic peroxidase in transgenic aspen and its effect on lignin characteristics. J Plant Res 2003, 116:175-182.
6. The Maize Genetics and Genomics Database [http://www.maizegdb.org]
7. de Obeso M, Caparros-Ruiz D, Vignols F, Puigdomenech P, Rigau J: Characterisation of maize peroxidases having differential patterns of mRNA accumulation in relation to lignifying tissues. Gene 2003, 309:23-33.
8. Roussel V, Gibelin C, Fontaine AS, Barrière Y: Genetic Analysis in Recombinant Inbred Lines of Early Dent Forage. II- QTL Mapping for Cell Wall Constituents and Cell Wall Digestibility from per se Value and Top Cross Experiments. Maydica 2002, 47:9-20.
9. Méchin V, Argillier O, Hébert Y, Guingo E, Moreau L, Charcosset A, Barrière Y: Genetic Analysis and QTL Mapping of Cell Wall Digestibility and Lignification in Silage Maize. Crop Sci 2001, 41:690-697.
10. Clark RM, Linton E, Messing J, Doebley JF: Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA 2004, 101:700-707.
11. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ: SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 2002, 3:19.
12. Buckler ES 4th, Thornsberry JM: Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 2002, 5:107-111.
13. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES 4th: Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 2001, 28:286-289.
14. Palaisa KA, Morgante M, Williams M, Rafalski A: Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 2003, 15:1795-1806.
15. Poke FS, Vaillancourt RE, C. Elliot R., Reid BR: Sequence variation in two lignin biosynthesis genes, cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD2). Mol Breed 2003, 12:107-118.
16. Wessler SR, Bureau TE, White SE: LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev 1995, 5:814-821.
17. Tajima F: Evolutionary relationship of DNA sequences in finite populations. Genetics 1983, 105:437-460.
18. Watterson GA: On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975, 7:256-276.
19. Li WH, Wu CI, Luo CC: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 1985, 2:150-174.
20. Grantham R: Amino acid difference formula to help explain protein evolution. Science 1974, 185:862-864.
21. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES 4th: Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 2001, 98:11479-11484.
22. Hudson RR, Kaplan NL: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 1985, 111:147-164.
23. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS: Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A 2001, 98:9161-9166.
24. Rafalski A: Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 2002, 5:94-100.
25. Rafalski A, Morgante M: Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 2004, 20:103-111.
26. Larkin PD, Park WD: Association of waxy gene single nucleotide polymorphism with starch characteristic in rice (Oriza sativa L.). Mol Breed 2003, 12:335-339.
27. Selinger DA, Chandler VL: Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize. Proc Natl Acad Sci USA 1999, 96:15007-15012.
28. Spell ML, Baran G, Wessler SR: An RFLP adjacent to the maize waxy gene has the structure of a transposable element. Mol Gen Genet 1988, 211:364-366.
29. Marita JM, Vermerris W, Ralph J, Hatfield RD: Variations in the cell wall composition of maize brown midrib mutants. J Agric Food Chem 2003, 51:1313-1321.
30. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
31. Aufrére J, Michalet-Doreau B: In vivo digestibility and prediction of digestibility of some by-products. ECC Seminar Belgique; 1983.
32. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
33. Sokal RR, Rohlf FJ: Biometry. Edited by: Ed W H Freeman. San Francisco; 1981.