Characterization and expression analysis of waxy alleles in barley accessions

Genetica

Volumn 141, Issue 4-6, 2013, Pages 227-238

  Ma, Jian ^a   Jiang, Qian Tao ^a   Zhao, Quan Zhi ^a   Zhao, Shan ^a   Lan, Xiu Jin ^a   Dai, Shou Fen ^a   Lu, Zhen Xiang ^b   Liu, Chunji ^c   Wei, Yu Ming ^a   Zheng, You Liang ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b LETHBRIDGE RESEARCH CENTRE   (Canada)

^c CSIRO   (Australia)

Author keywords

Amylose; Barley; GBSS I; Real time quantitative PCR; Waxy

Indexed keywords

AMYLOSE; GRANULE BOUND STARCH SYNTHASE I; GRANULE-BOUND STARCH SYNTHASE I; STARCH; STARCH SYNTHASE; WAX;

ALLELE; ARTICLE; CARBOHYDRATE METABOLISM; CHEMISTRY; GENE DELETION; GENE EXPRESSION; GENE ORDER; GENETIC POLYMORPHISM; GENETICS; HORDEUM; METABOLISM; NUCLEOTIDE MOTIF; PLANT GENE; PROMOTER REGION; ULTRASTRUCTURE;

ALLELES; AMYLOSE; CARBOHYDRATE METABOLISM; GENE EXPRESSION; GENE ORDER; GENES, PLANT; HORDEUM; NUCLEOTIDE MOTIFS; POLYMORPHISM, GENETIC; PROMOTER REGIONS, GENETIC; SEQUENCE DELETION; STARCH; STARCH SYNTHASE; WAXES;

HORDEUM;

EID: 84879715057     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-013-9721-x     Document Type: Article

References (48)

1. Bhatty R (1993) Nonmalting uses of barley, Barley: Chemistry and Technology. In: MacGregor AW and Bhatty RS (eds), Am. Assoc. Cereal Chem, St. Paul, MN, pp 355-417.
2. Bird AR, Brown IL, Topping DL (2000) Starches, resistant starches, the gut microflora and human health. Curr Issues Intestinal Microbiol 1: 25-37.
3. Boscari A, Clement M, Volkov V, Golldack D, Hybiak J, Miller AJ, Amtmann A, Fricke W (2009) Potassium channels in barley: cloning, functional characterization and expression analyses in relation to leaf growth and development. Plant, Cell Environ 32: 1761-1777.
4. Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) 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 14: 459-465.
5. Chen PY, Wang CK, Soong SC, To KY (2003) Complete sequence of the binary vector pBI121 and its application in cloning T-DNA insertion from transgenic plants. Mol Breed 11: 287-293.
6. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
7. Denyer K, Johnson P, Zeeman S, Smith AM (2001) The control of amylose synthesis. J Plant Physiol 158: 479-487.
8. Domon E, Fuijita M, Ishikawa N (2002a) The insertion/deletion polymorphisms in the waxy gene of barley genetic resources from East Asia. Theor Appl Genet 104: 132-138.
9. Domon E, Saito A, Takeda K (2002b) Comparison of the waxy locus sequence from a non-waxy strain and two waxy mutants of spontaneous and artificial origins in barley. Genes Genet Syst 77: 351-359.
10. Echt CS, Schwartz D (1981) Evidence for the inclusion of controlling elements within the structural gene at the waxy locus in maize. Genetics 99: 275-284.
11. Ezcurra I, Ellerström M, Wycliffe P, Stålberg K, Rask L (1999) Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression. Plant Mol Biol 40: 699-709.
12. Fukunaga K, Kawase M, Kato K (2002) Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype. Mol Genet Genomics 268: 214-222.
13. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300.
14. Hunt HV, Denyer K, Packman LC, Jones MK, Howe CJ (2010) Molecular basis of the waxy endosperm starch phenotype in broomcorn millet (Panicum miliaceum). Mol Biol Evol 27: 1478-1494.
15. James MG, Denyer K, Myers AM (2003) Starch synthesis in the cereal endosperm. Curr Opin Plant Biol 6: 215-222.
16. Jeng TL, Wang CS, Tseng TH, Wu MT, Sung JM (2009) Nucleotide polymorphisms in the waxy gene of NaN3-induced waxy rice mutants. J Cereal Sci 49: 112-116.
17. Jiang QT, Liu T, Ma J, Wei YM, Lu ZX, Lan XJ, Dai SF, Zheng YL (2012a) Characterization of barley Prp1 gene and its expression during seed development and under abiotic stress. Genetica 139: 1283-1292.
18. Jiang QT, Ma J, Zhao S, Zhao QZ, Lan XJ, Dai SF, Lu ZX, Zheng YL, Wei YM (2012b) Characterization of HMW-GSs and their gene inaction in tetraploid wheat. Genetica 140: 325-335.
19. Jobling S (2004) Improving starch for food and industrial applications. Curr Opin Plant Biol 7: 210-218.
20. Kluth A, Sprunck S, Becker D, Lörz H, Lütticke S (2002) 5′ deletion of a gbss1 promoter region from wheat leads to changes in tissue and developmental specificities. Plant Mol Biol 49: 665-678.
21. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
22. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30: 325-327.
23. Li J, Vasanthan T, Rossnagel B, Hoover R (2001) Starch from hull-less barley: i. Granule morphology, composition and amylopectin structure. Food Chem 74: 395-405.
24. Liu S, Bao Y (2009) Effects of copy number of an octopine synthase enhancer element and its distance from the TATA box on heterologous expression in transgenic tobacco. Acta Physiologiae Plantarum 31: 705-710.
25. Liu WX, Liu HL, Chai ZJ, Xu XP, Song YR, Qu LQ (2010) Evaluation of seed storage-protein gene 5′ untranslated regions in enhancing gene expression in transgenic rice seed. Theor Appl Genet 121: 1267-1274.
26. Ma J, Jiang QT, Wei YM, Andre L, Lu ZX, Chen GY, Liu YX, Zheng YL (2010) Molecular characterization and comparative analysis of two waxy alleles in barley. Genes Genom 32: 513-520.
27. Murray M, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4326.
28. Patron NJ, Smith AM, Fahy BF, Hylton CM, Naldrett MJ, Rossnagel BG, Denyer K (2002) 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 130: 190-198.
29. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45-e45.
30. Radchuk VV, Borisjuk L, Sreenivasulu N, Merx K, Mock HP, Rolletschek H, Wobus U, Weschke W (2009) Spatiotemporal profiling of starch biosynthesis and degradation in the developing barley grain. Plant Physiol 150: 190-204.
31. Regina A, Blazek J, Gilbert E, Flanagan BM, Gidley MJ, Cavanagh C, Ral J-P, Larroque O, Bird AR, Li Z, Morell MK (2012) Differential effects of genetically distinct mechanisms of elevating amylose on barley starch characteristics. Carbohydr Polym 89: 979-991.
32. Rogers H, Bate N, Combe J, Sullivan J, Sweetman J, Swan C, Lonsdale D, Twell D (2001) Functional analysis of cis-regulatory elements within the promoter of the tobacco late pollen gene g10. Plant Mol Biol 45: 577-585.
33. Rohde W, Becker D, Salamini F (1988) Structural analysis of the waxy locus from Hordeum vulgare. Nucleic Acids Res 16: 7185.
34. Rösti S, Rudi H, Rudi K, Opsahl-Sorteberg HG, Fahy B, Denyer K (2006) The gene encoding the cytosolic small subunit of ADP-glucose pyrophosphorylase in barley endosperm also encodes the major plastidial small subunit in the leaves. J Exp Bot 57: 3619-3626.
35. Rushton PJ, Reinstädler A, Lipka V, Lippok B, Somssich IE (2002) Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen-and wound-induced signaling. Plant Cell 14: 749-762.
36. Sattler SE, Singh J, Haas EJ, Guo L, Sarath G, Pedersen JF (2009) Two distinct waxy alleles impact the granule-bound starch synthase in sorghum. Mol Breeding 24: 349-359.
37. Soong R, Ruschoff J, Tabiti K (2000) Detection of colorectal micrometastasis by quantitative RT-PCR of cytokeratin 20 mRNA. Roche Diagnostics internal publication.
38. Swanston J, Ellis R, Stark J (1995) Effects on grain and malting quality of genes altering barley starch composition. J Cereal Sci 22: 265-273.
39. Swapna L, Khurana R, Vijaya Kumar S, Tyagi A, Rao K (2011) Pollen-specific expression of Oryza sativa indica pollen allergen gene (OSIPA) promoter in rice and Arabidopsis transgenic systems. Mol Biotechnol 48: 49-59.
40. Tang H, Watanabe K, Mitsunaga T (2002) Structure and functionality of large, medium and small granule starches in normal and waxy barley endosperms. Carbohydr Polym 49: 217-224.
41. Tester RF, Karkalas J, Qi X (2004) Starch-composition, fine structure and architecture. J Cereal Sci 39: 151-165.
42. van Hung P, Maeda T, Morita N (2006) Waxy and high-amylose wheat starches and flours-characteristics, functionality and application. Trends Food Sci Technol 17: 448-456.
43. Vandesompele J, De Preter K, Pattyn F, Poppe B, van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: research0034.
44. Weschke W, Panitz R, Gubatz S, Wang Q, Radchuk R, Weber H, Wobus U (2003) The role of invertases and hexose transporters in controlling sugar ratios in maternal and filial tissues of barley caryopses during early development. Plant J 33: 395-411.
45. Yanagisawa T, Kiribuchi-Otobe C, Yoshida H (2001) An alanine to threonine change in the Wx-D1 protein reduces GBSS I activity in waxy mutant wheat. Euphytica 121: 209-214.
46. Zeeman SC, Kossmann J, Smith AM (2010) Starch: its metabolism, evolution, and biotechnological modification in plants. Annu Rev Plant Biol 61: 209-234.
47. Zhu CM (2009) Research on genetic diversity of waxy germplasm resources and wx gene in Chinese barley. Chinese Academy of Agricultural Sciences Publishing, Beijing (in Chinese).
48. Zhu T, Jackson DS, Wehling RL, Geera B (2008) Comparison of amylose determination methods and the development of a dual wavelength Iodine binding technique 1. Cereal Chem 85: 51-58.