High resolution melting analysis for the detection of EMS induced mutations in wheat SbeIIa genes

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Botticella, Ermelinda ^a   Sestili, Francesco ^a   Hernandez Lopez, Antonio ^b   Phillips, Andrew ^b   Lafiandra, Domenico ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

^b ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRITICUM AESTIVUM;

1,4 ALPHA GLUCAN BRANCHING ENZYME; AMYLOSE; MESYLIC ACID ETHYL ESTER; PLANT DNA; VEGETABLE PROTEIN;

ALLELE; ARTICLE; BIOLOGY; DNA SEQUENCE; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENE TARGETING; GENETICS; GENOTYPE; METHODOLOGY; MOLECULAR GENETICS; MUTATION; SINGLE NUCLEOTIDE POLYMORPHISM; WHEAT;

1,4-ALPHA-GLUCAN BRANCHING ENZYME; ALLELES; AMYLOSE; COMPUTATIONAL BIOLOGY; DNA, PLANT; ETHYL METHANESULFONATE; GENE EXPRESSION REGULATION, PLANT; GENE TARGETING; GENOTYPE; MOLECULAR SEQUENCE DATA; MUTATION; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; TRITICUM;

EID: 80755143074     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-156     Document Type: Article

References (59)

1. Soh HN, Sisson MJ, Turner M. Effect of starch granule size distribution and elevated amylose content on durum dough rheology and spaghetti cooking quality. Cereal Chem 2006, 83:513-519.
2. Waring S. Functionality of resistant starch in food applications. 2005, , http://eu.foodinnovation.com/pdfs/functresist.pdf
3. Chanvrier H, Appelqvist IAM, Bird AR, Gilbert E, Htoon A, Li Z, Lillford PJ, Lopez-Rubi A, Morell MK, Topping DL. Processing of novel elevated amylose wheats: functional properties and starch digestibility of extruded products. J Agric Food Chem 2007, 55:10248-10257. 10.1021/jf0718650, 18001033.
4. Sajilata MG, Singhal RS, Kulkarni PR. Resistant starch: a review. Compr Rev Food Sci Food Safety 2006, 5:5-17.
5. Freire A, Podczeck F, Veiga F, Sousa J. Starch-based coatings for colon-specific delivery. Part II: Physicochemical properties and in vitro drug release from high amylose maize starch films. Eur J Pharm Biopharm 2009, 72:587-594. 10.1016/j.ejpb.2009.02.010, 19264128.
6. Ball SG, Morell MK. From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. Ann Rev Plant Biol 2003, 54:207-233.
7. Stone B, Morell MK. Carbohydrate. Wheat, Chemistry and Technology 2009, 299-362. AACC International St. Paul MN, Khan K, Shewry PR, 4.
8. Yamamori M, Endo TR. Variation of starch granule proteins and chromosome mapping of their coding genes in common wheat. Theor Appl Genet 1996, 93:275-281.
9. Sestili F, Botticella E, Bedo Z, Phillips A, Lafiandra D. Production of novel allelic variation for genes involved in starch biosynthesis through mutagenesis. Mol Breeding 2010, 25:145-154.
10. Yamamori M, Fujita S, Hayakawa K, Matsuki J, Yasui T. Genetic elimination of a starch granule protein, SGP-1, of wheat generates an altered starch with apparent high amylose. Theor App Genet 2000, 101:21-29.
11. Lafiandra D, Sestili F, D'Ovidio R, Janni M, Botticella E, Ferrazzano G, Silvestri M, Ranieri R, DeAmbrogio E. Approaches for the modification of starch composition in durum wheat. Cereal Chem 2010, 87(1):28-34.
12. Regina A, Kosar-Hashemi B, Li Z, Rampling L, Cmiel M, Gianibelli MC, Konik-Rose C, Larroque O, Rahman S, Morell MK. Multiple isoforms of starch branching enzyme-I in wheat: lack of the major Sbe-I isoform does not alter starch phenotype. Funct Plant Biol 2004, 31:591-601.
13. Rahman S, Regina A, Li Z, Mukai Y, Yamamoto M, Kosar-Hashemi B, Abrahams S, Morell MK. Comparison of starch-branching enzyme genes reveals evolutionary relationships among isoforms. Characterization of a gene for starch-branching enzyme IIa from the wheat genome donor. Aegilops tauschii Plant Physiol 2001, 125:1314-24.
14. Regina A, Kosar-Hashemi B, Li Z, Pedler A, Mukai Y, Yamamoto M, Gale K, Sharp PJ, Morell MK, Rahman S. Starch branching enzyme IIb in wheat is expressed at low levels in. the endosperm compared to other cereals and encoded at a non-syntenic locus. Planta 2005, 222:899-909. 10.1007/s00425-005-0032-z, 16172866.
15. Regina A, Bird A, Topping D, Freeman S, Barsby T, Kosar-Hashemi B, Rahman S, Morell MK. High-amylose wheats generated by RNA interference improves indices of large-bowel health in rats. Proc Nat Acad Sci USA 2006, 103:3546-3551. 10.1073/pnas.0510737103, 1450120, 16537443.
16. Sestili F, Janni M, Doherty A, Botticella E, D'Ovidio R, Masci S, Jones H, Lafiandra D. Increasing the amylose content of durum wheat through silencing of the SBEIIa genes. BMC Plant Biol 2010, 10:144. 10.1186/1471-2229-10-144, 3095290, 20626919.
17. McCallum CM, Comai L, Greene EA, Henikoff S. Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol 2000, 123:439-442. 10.1104/pp.123.2.439, 1539256, 10859174.
18. Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D. A reverse genetic, non transgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 2005, 23:75-81. 10.1038/nbt1043, 15580263.
19. Uauy C, Paraiso F, Colasuonno P, Tran RK, Tsai H, Berardi S, Comai L, Dubcovsky J. A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheats. BMC Plant Biol 2009, 9:115. 10.1186/1471-2229-9-115, 2748083, 19712486.
20. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003, 49:853-860. 10.1373/49.6.853, 12765979.
21. Dong C, Vincent K, Sharp S. Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor. BMC Plant Biol 2009, 9:143. 10.1186/1471-2229-9-143, 2794869, 19958559.
22. Gady ALF, Hermans FWK, Van de Wal MHBJ, Van Loo EN, Visser RGF, Bachem CWB. Implementation of two high through-put techniques in a novel application, detecting point mutations in large EMS mutated plant populations. Plant Methods 2009, 5:13. 10.1186/1746-4811-5-13, 2763861, 19811648.
23. Joppa LR, Williams ND. Langdon durum disomic substitution lines and aneuploid analysis in tetraploid wheat. Genome 1988, 30:222-228.
24. Rakszegi M, Kisgyorgy BN, Tearall K, Shewry PR, Lang L, Phillips A, Bedo Z. Diversity of agronomic and morphological traits in a mutant population of bread wheat studied in the Healthgrain program. Euphytica 2010, 174:409-421.
25. Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31:3812-3814. 10.1093/nar/gkg509, 168916, 12824425.
26. Kuriki T, Stewart DC, Preiss J. Construction of chimeric enzymes out of maize endosperm branching enzymes I and II activity and properties. J Biol Chem 1997, 272:2899-2904.
27. Abad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, Jeiger JH. The x-ray crystallographic structure of Escherichia coli branching enzyme. J Biol Chem 2002, 277:42164-42170. 10.1074/jbc.M205746200, 12196524.
28. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40. 10.1186/1471-2105-9-40, 2245901, 18215316.
29. Lal S, Choi J, Curtis Hannah L. The AG dinucleotide terminating introns is important but not always required for pre-mRNA splicing in the maize endosperm. Plant Physiol 1999, 120(1):65-72. 10.1104/pp.120.1.65, 59270, 10318684.
30. Brown JWS. Arabidopsis intron mutations and pre-mRNA splicing. Plant J 1996, 10:771-780. 10.1046/j.1365-313X.1996.10050771.x, 8953241.
31. Smith CJW, Chu TT, Nadal-Ginard B. Scanning and competition between AGs are involved in 39 splice site selection in mammalian introns. Mol Cell Biol 1993, 13:4939-4952. 360135, 8336728.
32. Yamamori M, Nakamura T, Kuroda A. Variations in the content of starch-granule bound protein among several Japanese cultivars of common wheat (Triticum aestivum L). Euphytica 1992, 64:215-219.
33. Urbano M, Margiotta B, Colaprico G, Lafiandra D. Waxy protein in diploid, tetraploid and hexaploid wheats. Plant Breeding 2002, 121:1-5.
34. Svensson B. Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity and stability. Plant Mol Biol 25:141-157.
35. Hong S, Mikkelsen R, Preiss J. Analysis of the amino terminus of maize branching enzyme II by polymerase chain reaction random mutagenesis. Arch Biochem Biophys 2001, 386:62-68. 10.1006/abbi.2000.2179, 11361001.
36. Parry MAJ, Madgwick PJ, Bayon C, Tearall K, Lopez AH, Baudo M, Rakszegi M, Hamada W, Al-Yassin A, Ouabbou H, Labhilili H, Phillips A. Mutation discovery for crop improvement. J Exp Bot 2009, 60:2817-2825. 10.1093/jxb/erp189, 19516074.
37. Hofinger BJ, Jing HC, Hammond KE, Kanyuka K. High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley. Theor Appl Genet 2009, 119:851-865. 10.1007/s00122-009-1094-2, 19578831.
38. Reed GH, Wittwer CT. Sensitivity and specificity of single nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 2004, 50:1748-1754. 10.1373/clinchem.2003.029751, 15308590.
39. Cai XL, Wang ZY, Zhang JL, Hong MM. Aberrant splicing of intron 1 leads to the heterogeneous 5' UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 1998, 14:459-465. 10.1046/j.1365-313X.1998.00126.x, 9670561.
40. Henikoff S, Comai L. Single-nucleotide mutations for plant functional genomics. Ann Rev Plant Biol 2003, 54:375-401.
41. Saito M, Nakamura T. Two point mutations identified in emmer wheat generate null Wx-A1 alleles. Theor Appl Genet 2005, 110:276-282. 10.1007/s00122-004-1830-6, 15592661.
42. Patron NJ, Smith AM, Fahy BF, Hylton CM, Naldrett MJ, Rossnagel BG, Denyer K. The altered pattern of amylose accumulation in the endosperm of low-amylose barley cultivars is attributable to a single mutant allele of granule-bound starch synthase I with a deletion in the 5'-non-coding region. Plant Physiol 2002, 130:190-198. 10.1104/pp.005454, 166552, 12226499.
43. Zhu YF, Li YW, Chen Y. Generation and characterization of a high molecular weight glutenin 1Bx14-deficient mutant in common wheat. Plant Breeding 2005, 124:421-427.
44. Frischmeyer PA, Dietz HC. Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet 1998, 8:1893-1900.
45. Maquat LE. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 2004, 5:89-99.
46. Jofuku KD, Schipper RD, Goldberg RB. A frameshift mutation prevents Kunitz trypsin inhibitor mRNA accumulation in soybean embryos. Plant Cell 1989, 1:427-435. 159774, 2562563.
47. Dehesh K, Franci C, Parks BM, Seeley KA, Short TW, Tepperman JM, Quail PH. Arabidopsis HY8 locus encodes phytochrome A. Plant Cell 1993, 5:1081-1088. 160342, 8400877.
48. Marchant A, Bennett MJ. The Arabidopsis AUX1 gene: a model system to study mRNA processing in plants. Plant Mol Biol 1998, 36:463-471. 10.1023/A:1005961303167, 9484486.
49. Isshiki M, Yamamoto Y, Satoh H, Shimamoto K. Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol 2001, 125:1388-1395. 10.1104/pp.125.3.1388, 65617, 11244118.
50. Miura H, Sugawara A. Dosage effect of Waxy genes on amylose synthesis in wheat. Theor Appl Genet 1996, 93(7):1066-1070.
51. Konik-Rose C, Thistleton J, Chanvrier H, Tan I, Halley P, Gidley M, Kosar-Hashemi B, Wang H, Larroque O, Ikea J, McMaugh S, Regina A, Rahman S, Morell M, Li Z. Effects of starch synthase IIa gene dosage on grain, protein and starch in endosperm of wheat. Theor Appl Genet 2007, 115:1053-1065. 10.1007/s00122-007-0631-0, 17721773.
52. McClearly BV, Solah V, Gibson TS. Quantitative measurement of total starch in cereal flours and products. J Cereal Sci 1994, 20:51-58.
53. Nakamura T, Yamamori M, Hirano H, Hidaka S, Nagamine T. Production of waxy (amylose-free) wheats. Mol Gen Genet 1995, 248:253-259. 10.1007/BF02191591, 7565586.
54. Tai TH, Tanksley SD. A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 1991, 8:297-303.
55. Laudencia-Chingcuanco DL, Stamova BS, You FM, Lazo GR, Beckles DM, Anderson OD. Transcriptional profiling of wheat caryopsis development using cDNA microarrays. Plant Mol Biol 2006, 63:651-668.
56. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.
57. Neff MM, Neff JD, Chory J, Pepper AE. dCAPS, a simple technique for the genetic analysis of single nucleotide polym.orphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 1998, 14:387-392. 10.1046/j.1365-313X.1998.00124.x, 9628033.
58. Chrastil J. Improved colorimetric determination of amylose in starches or flours. Carbohydr Res 1987, 159:154-158.
59. Vansteelandt J, Delcour JA. Physical behaviour of durum wheat starch (Triticum durum) during industrial pasta processing. J Agric Food Chem 1988, 46:2499-2503.