Genome organisation and retrotransposon driven molecular evolution of the endosperm Hardness (Ha) locus in Triticum aestivum cv Glenlea

Molecular Genetics and Genomics

Volumn 280, Issue 6, 2008, Pages 467-481

  Ragupathy, Raja ^a,b   Cloutier, Sylvie ^a  

^a Cereal Research Centre   (Canada)

^b UNIVERSITY OF MANITOBA   (Canada)

Author keywords

BAC; Chromosomal deletion; Hardness locus; Triticum aestivum

Indexed keywords

ARTICLE; CHROMOSOME DELETION; CONTROLLED STUDY; ENDOSPERM; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENOME; GENOTYPE; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; WHEAT;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; MODELS, GENETIC; MUTAGENESIS, INSERTIONAL; RETROELEMENTS; SEEDS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRITICUM;

TRITICUM AESTIVUM;

EID: 56349098077     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0380-z     Document Type: Article

References (54)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410
2. OD Anderson C Rausch O Moullet ES Lagudah 2003 The wheat D-genome HMW-glutenin locus: BAC sequencing, gene distribution, and retrotransposon clusters Funct Integr Genomics 3 56 68
3. B Beecher A Bettge E Smidansky MJ Giroux 2002 Expression of wild-type Pinb sequence in transgenic wheat complements a hard phenotype Theor Appl Genet 105 870 877
4. JL Bennetzen 2005 Transposable elements, gene creation and genome rearrangement in flowering plants Curr Opin Genet Dev 15 621 627
5. M Bhave CF Morris 2008 Molecular genetics of puroindolines and related genes: regulation of expression, membrane binding properties and applications Plant Mol Biol 66 221 231
6. M Bhave CF Morris 2008 Molecular genetics of puroindolines and related genes: allelic diversity in wheat and other grasses Plant Mol Biol 66 205 219
7. R Brodie RL Roper C Upton 2004 JDOTTER: a java interface to multiple dotplots generated by dotter Bioinformatics 20 279 281
8. SA Brooks L Huang BS Gill JP Fellers 2002 Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance Genome 45 963 972
9. S Brunner K Fengler M Morgante S Tingey A Rafalski 2005 Evolution of DNA sequence non homologies among maize inbreds Plant Cell 17 343 360
10. N Chantret A Cenci F Sabot OD Anderson J Dubcovsky 2004 Sequencing of the Triticum monococcum Hardness locus reveals good microcolinearity with rice Mol Genet Genomics 271 377 386
11. N Chantret J Salse F Sabot S Rahman A Bellec B Laubin I Dubois C Dossat P Sourdille P Joudrier M Gautier L Cattolico M Beckert S Aubourg J Weissenbach M Caboche M Bernard P Leroy B Chalhoub 2005 Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops) Plant Cell 17 1033 1045
12. KM Devos JKM Brown JL Bennetzen 2002 Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis Genome Res 12 1075 1079
13. KM Devos J Ma AC Pontaroli LH Pratt JL Bennetzen 2005 Analysis and mapping of randomly chosen bacterial artificial chromosomes clones from hexaploid bread wheat Proc Natl Acad Sci USA 102 19243 19248
14. L Dubreil S Meliande H Chiron JP Compoint L Quillien G Branlard D Marion 1998 Effect of puroindolines on the bread making properties of wheat flour Cereal Chem 75 222 229
15. B Ewing L Hillier MC Wendl G Green 1998 Base-calling of automated sequencer traces using phred. I. accuracy assessment Genome Res 8 175 185
16. MD Gale KM Devos 1998 Comparative genetics in the grasses Proc Natl Acad Sci USA 95 1971 1974
17. MF Gautier ME Aleman A Guirao D Marion P Joudrier 1994 Triticum aestivum puroindolines, two basic cystine-rich seed proteins: cDNA sequence analysis and developmental gene expression Plant Mol Biol 25 43 57
18. MF Gautier P Cosson A Guirao R Alary P Joudrier 2000 Puroindoline genes are highly conserved in diploid ancestor wheats and related species but absent in tetraploid Triticum species Plant Sci 153 81 91
19. D Gordon C Abajian P Green 1998 Consed: a graphical tool for sequence finishing Genome Res 8 195 202
20. P Greenwell JD Schofeld 1986 A starch granule protein associated with endosperm softness in wheat Cereal Chem 63 379 380
21. YQ Gu J Salse D Coleman-Derr A Dupin C Crossman GR Lazo N Huo H Belcram C Ravel G Charmet M Charles OD Anderson B Chalhoub 2006 Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes Genetics 174 1493 1504
22. AC Hogg T Sripo B Beecher JM Martin MJ Giroux 2004 Wheat puroindolines interact to form friabilin and control wheat grain hardness Theor Appl Genet 108 1089 1097
23. S Huang A Sirikhachornkit X Su J Faris B Gill R Haselkorn P Gornicki 2002 Genes encoding plastiod acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat Proc Natl Acad Sci USA 99 8133 8138
24. E Isidore B Scherrer B Chalhoub C Feuillet B Keller 2005 Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels Genome Res 15 526 536
25. CJ Jolly G Glenn S Rahman 1996 GSP-1 genes are linked to the grain hardness locus (Ha) on wheat chromosome 5D Proc Natl Acad Sci USA 93 2408 2413
26. J Jurka 2000 Repbase update: a database and an electronic journal of repetitive elements Trends Genet 16 418 420
27. BA Kronmiller RP Wise 2008 TEnest:automated chronological annotation and visualization of nested plant transposable elements Plant Physiol 146 45 59
28. Law CN, Young CF, Brown JWS, Snape JW, Worland AJ (1978) The study of grain protein control in wheat using whole chromosome substitution lines. In: Seed protein improvement by nuclear techniques. International atomic energy agency, Vienna, pp 483-502
29. W Li P Zhang JP Fellers B Friebe BS Gill 2004 Sequence composition, organization, and evolution of the core Triticeae genome Plant J 40 500 511
30. W Li L Huang BS Gill 2008 Recurrent deletions of puroindoline genes at the grain hardness locus in four independent lineages of polyploid wheat Plant Physiol 146 200 212
31. MC Luo C Thomas FM You J Hsiao S Ouyang CR Buell M Malandro PE McGuire OD Anderson J Dvorak 2003 High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labelling kit and sizing of restriction fragments by capillary electrophoresis Genomics 82 378 389
32. J Ma KM Devos JL Bennetzen 2004 Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice Genome Res 14 860 869
33. J Ma JL Bennetzen 2006 Recombination, rearrangement, reshuffling and divergence in a centromeric region of rice Proc Natl Acad Sci USA 103 383 388
34. JM Martin FD Meyer ED Smidansky H Wanjugi AE Blechl MJ Giroux 2006 Complementation of the pina (null) allele with the wild type Pina sequence restores a soft phenotype in transgenic wheat Theor Appl Genet 113 1563 1570
35. Mattern JM, Morris R, Schmidt JW, Johnson VA (1973) Location of genes for kernel properties in wheat cultivar Cheyenne using chromosome substitution lines. In: Sears ER, Sears LMS (eds) Proc of the 4th international wheat genetics symposium. University of Missouri, Columbia, pp 703-707
36. CF Morris 2002 Puroindolines: the molecular genetic basis of wheat grain hardness Plant Mol Biol 48 633 647
37. CF Morris OM Lukow CE Perron 1998 Grain hardness, dough mixing and pan bread performance among wheats differing in puroindoline hardness mutation Cereal Foods World 43 533
38. SD Nilmalgoda S Cloutier AZ Walichnowski 2003 Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers Genome 46 870 878
39. OE) high molecular weight glutenin subunit Theor Appl Genet 116 283 296
40. S Rahman JC Jolly JH Skerritt A Wallosheck 1994 Cloning of a wheat 15-kDa grain softness protein. GSP is a mixture of puroindoline-like polypeptides Eur J Biochem 223 917 925
41. K Sakata Y Nagamura H Numa BA Antonio H Nagasaki A Idonuma W Watanabe Y Shimizu I Horiuchi T Matsumoto T Sasaki K Higo 2002 RiceGAAS: an automated annotation system and database for rice genome sequence Nucleic Acids Res 30 98 102
42. D Sandhu KS Gill 2002 Gene-containing regions of the wheat and the other genomes Plant Physiol 128 803 811
43. P SanMiguel BS Gaut A Tikhonov Y Nakajima JL Bennetzen 1998 The paleontology of intergene retrotransposons of maize Nature Genet 20 43 45
44. C Soderlund I Longden R Mott 1997 FPC: a system for building contigs from restriction fingerprinted clones Bioinformatics 13 523 535
45. ELL Sonnhammer R Durbin 1996 A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis Gene 167 1 10
46. P Sourdille MR Perretant G Charmet P Leroy MF Gautier P Joudrier JC Nelson ME Sorrells M Bernard 1996 Linkage between RFLP markers and genes affecting kernel hardness in wheat Theor Appl Genet 93 580 586
47. TA Tatusova TL Madden 1999 BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences FEMS Microbiol Lett 174 247 250
48. G Tranquilli D Lijavetzky G Muzzi J Dubcovsky 1999 Genetic and physical characterization of grain texture-related loci in diploid wheat Mol Gen Genet 262 846 850
49. C Vitte O Panaud 2005 LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model Cytogenet Genome Res 110 91 107
50. C Vitte T Ishii F Lamy DS Brar O Panaud 2004 Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.) Molecular Gen Genomics 272 504 511
51. Wessler SR (2006) Eukaryotic transposable elements: teaching old genomes new tricks. In: Lynn Helena Caporale (Ed) The implicit genome. Oxford University Press, NY, pp 138-162
52. T Wicker DE Matthews B Keller 2002 TREP: A database for Triticeae repetitive elements Trends Plant Sci 7 561 562
53. T Wicker F Sabot A Huna-Van JL Bennetzen P Copy B Chalhoub A Flavell P Leroy M Morgante O Panaud E Paux P SanMiguel AH Schulman 2007 A unified classification system for eukaryotic transposable elements Nature Rev Genet 8 973 982
54. Z Xu H Wang 2007 LTR_ FINDER: an efficient tool for the prediction of full-length LTR retrotransposons Nucleic Acids Res 35 W265 W268