Transcriptome analysis of grain-filling caryopses reveals the potential formation mechanism of the rice sugary mutant

Gene

Volumn 546, Issue 2, 2014, Pages 318-326

  Li, Feng peng ^a   Yoon, Min Young ^a   Li, Gang ^a   Ra, Won Hee ^a   Park, Jae Wan ^a   Kwon, Soon Jae ^b   Kwon, Soon Wook ^c   Ahn, Il Pyung ^d   Park, Yong Jin ^a  

^a Kongju National University   (South Korea)

^b Atomic Energy Research Institute   (South Korea)

^c Pusan National University   (South Korea)

^d National Institute of Animal Science   (South Korea)

Author keywords

ADP glucose pyrophosphorylase; Rice; Starch synthesis related genes; Sugary mutant; Transcriptome

Indexed keywords

GLUCOSE; PHYTOHORMONE; GLUCOSE 1 PHOSPHATE ADENYLYLTRANSFERASE; STARCH; SUGAR; TRANSCRIPTOME;

ARTICLE; GENE EXPRESSION; GRAIN FILLING; METABOLIC REGULATION; NONHUMAN; PHYSICAL CHEMISTRY; PLANT GENE; PLANT PATHOGEN INTERACTION; PRIORITY JOURNAL; PROTEIN CONTENT; RICE; RNA SEQUENCE; SEED DEVELOPMENT; SIGNAL TRANSDUCTION; SINDONGJIN GENE; SUGARY GENE; TRANSCRIPTOMICS; BIOSYNTHESIS; CARYOPSIS; FLOWERING; FRUIT; GENE; GRAIN; METABOLISM; MUTANT; PHENOTYPE; PLANT SEED; REAL TIME POLYMERASE CHAIN REACTION; SYNTHESIS;

ADP-GLUCOSE PYROPHOSPHORYLASE; RICE; STARCH-SYNTHESIS RELATED GENES; SUGARY MUTANT; TRANSCRIPTOME;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE; MUTATION; ORYZA SATIVA; PLANT PROTEINS; REAL-TIME POLYMERASE CHAIN REACTION; STARCH; SUCROSE; TRANSCRIPTOME;

EID: 84903517949     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.05.059     Document Type: Article

References (78)

1. A.o.O.A.C. (AOAC), 18th ed., AOAC Intl., Gaithersburg, MD, USA, (2005).
2. Akihiro T., Mizuno K., Fujimura T. Plant Cell Physiol. Plant. 2005, 46:937-946.
3. Anisimov S.V. Curr. Pharm. Biotechnol. 2008, 9.
4. Ball S.G., Morell M.K. Annu. Rev. Plant Biol. 2003, 54:207-233.
5. Bhave M.R., Lawrence S., Barton C., Hannah L.C. Plant Cell 1990, 2:581-588. (Online).
6. Boyer C.D., Shannon J.C. Plant Breed. 1983, 1:139-161.
7. Cheong Y.H., Chang H.S., Gupta R., Wang X., Zhu T., Luan S. Plant Physiol. 2002, 129:661-677.
8. Cho Y.H., Lee S.Y., Kim S.M., Yu J.M., Lee J.R., Hong H.C., Kim J.B., Ma K.H., Kwon T.R., Kang H.K., Lee G.A., Gwag J.G., Kim T.S., Park Y.J. J. Crop. Sci. Biotechnol. 2008, 11:181-186.
9. Cloonan N., Forrest A., Kolle G., Gardiner B., Faulkner G.J., Brown M.K., Taylor D.F., Steptoe A.L., Wani S., Bethel G., Alan J.R., Andrew C.P., Stephen J.B., Clarence C.L., Swati S.R., Heather E.P., Jonathan M.M., Kevin J.M., Sean M.G. Nat. Methods 2008, 5:613-619.
10. Colleoni C., Dauville'e D., Mouille G. Plant Physiol. 1999, 120:993-1003.
11. Conesa A., Götz S., García-Gómez J.M., Terol J., Talón M., Robles M. Bioinformatics 2005, 21:3674-3676.
12. Dung L.V., Mikami I., Amano E., Sano Y. Breed. Sci. 2000, 50:215-219.
13. Eveland A.L., Satoh-Nagasawa N., Goldshmidt A., Meyer S., Beatty M., Sakai H., Ware D., Jackson D. Plant Physiol. 2010, 154:1024-1039.
14. Filichkin S.A., Priest H.D., Givan S.A., Shen R.K., Bryant D.W., Fox S.E., Wong W.K., Mockler T.C. Genome Res. 2010, 20:45-58.
15. Gao Y., Xu H., Shen Y.Y., Wang J.B. Plant Mol. Biol. 2013, 81:363-378.
16. Garber M., Grabherr M.G., Guttman M., Trapnell C. Nat Methods 2011, 8:469-477.
17. Greene T.W., Hannah L.C. Plant Cell 1998, 10:1295-1306.
18. Han X.Z., Hamaker B.R. J. Cereal Sci. 2001, 34:279-284.
19. Hannah L.C., Shaw J.R., Giroux M.J., Reyss A., Prioul J.L., Bae J.M., Lee J.Y. Plant Physiol. 2001, 127:173-183.
20. Haugen T.H., Ishaque A., Preiss J. J. Biol. Chem. 1976, 251:7880-7885.
21. Hirose T., Ohdan T., Nakamurac Y., Teraoa T. Physiol. Plant. 2006, 128:425-435.
22. Hoshikawa K. Proc. Crop Sci. Soc. Jpn. 1968, 37:207-216.
23. Isshiki M., Nakajima M., Satoh H., Shimamoto K. Plant J. 2000, 23:451-460.
24. Isshiki M., Matsuda Y., Takasaki A., Wong H.L., Satoh H., Shimamoto K. Plant Biotechnol. 2008, 25:483-487.
25. James M., Denyer K., Myres A. Curr. Opin. Plant Biol. 2003, 6:215-222.
26. Johnson P., Patron N., Bottrill A., Dinges J., Fahy B., Parker M., Waite D., Denyer K. Plant Physiol. 2003, 131:684-696.
27. Kang H.G., Park S.H., Matsuoka M., An G.H. Plant J. 2005, 42:901-911.
28. Kawasaki T., Mizuno K., Shimada H., Satoh H., Kishimoto N., Okumura S., Ichikawa N., Baba T. Plant Physiol. 1996, 110:89-96.
29. Koh H.J., Heu M.H. Korean J. Crop Sci. 1994, 39:1-6.
30. Lan L.F., Chen W., Lai Y., Suo J.F., Kong Z.S., Li C., Lu Y., Zhang Y.J., Zhao X.Y., Zhang X.S., Zhang Y.S., Han B., Cheng J., Xue Y.B. Plant Mol. Biol. 2004, 54:471-487.
31. Lee S.K., Hwang S.K., Han M., Eom J.S., Kang H.G., Han Y., Choi S.B., Cho M.H., Bhoo S.H., An G., Hahn T.R., Okita T.W., Jeon J.S. Plant Mol. Biol. 2007, 65:531-546.
32. Lee D.J., Kim S., Ha Y.M., Kim J. Planta 2007, 227:577-587.
33. Li P., Ponnala L., Gandotra N., Wang L., Si Y., Tausta S.L., Kebrom T.H., Provart N., Patel R., Myers C.R., Reidel E.J., Turgeon R., Liu P., Sun Q., Nelson T., Brutnell T.P. Nat. Genet. 2010, 42:1060-1067.
34. Li B., Ruotti V., Stewart R.M., Thomson J.A., Dewey C.N. Bioinformatics 2010, 26:493-500.
35. Li F.P., Lee Y.S., Kwon S.W., Li G., Park Y.J. Genet. Mol. Res. 2014 Apr 14, 13(AOP). (Epub ahead of print).
36. Liu X.L., Guo T.L., Wan X.Y., Wang H.Y., Zhu M.Z., Li A.L., Su N., Shen Y.Y., Mao B.G., Zhai H.Q., Mao L., Wan J.M. BMC Genomics 2010, 11(730):1-15.
37. Lu F.H., Park Y.J. J. Cereal Sci. 2012, 56:1-7.
38. Lu F.H., Park Y.J. Genet. Res. 2012, 94:179-189.
39. Lu T.T., Lu G.J., Fan D.L., Zhu C.R., Li W., Zhao Q., Feng Q., Zhao Y., Guo Y.L., Li W.J., Huang X.H., Han B. Genome Res. 2010, 20:1238-1249.
40. Lu F.H., Yoon M.Y., Cho Y.I., Chung J.W., Kim K.T., Cho M.C., Cheong S.R., Park Y.J. Sci. Hortic. 2011, 129(1):38-45.
41. Luo M., Taylor J.M., Spriggs A., Zhang H., Wu X. PLoS Genet. 2011, 7:e1002125.
42. Ma T.L., Wu W.H., Wang Y. BMC Plant Biol. 2012, 12:161.
43. Marioni J.C., Mason C.E., Mane S.M., Stephens M., Gilad Y. Genome Res. 2008, 18:1509-1517.
44. Morell M.K., Myers A.M. Curr. Opin. Plant Biol. 2005, 8:204-210.
45. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Nat. Methods 2008, 5:621-628.
46. Nagalakshmi U., Wang Z., Waern K., Shou C., Raha D., Gerstein M., Snyder M. Science 2008, 320:1344-1349.
47. Nakamura Y., Kubo A., Shimamune T., Matsuda T., Harada K., Satoh H. Plant J. 1997, 12:143-153.
48. Nishi A., Nakamura Y., Tanaka N., Satoh H. Plant Physiol. 2001, 127:459-472.
49. Ohdan T., Francisco P.B., Sawada T., Hirose T., Terao T., Satoh H., Nakamura Y. J. Exp. Bot. 2005, 56:3229-3244.
50. Okita T.W., Nakata P.A., Anderson J.M., Sowokinos J., Morell M., Preiss J. Plant Physiol. 1990, 93:785-790.
51. Omura T., Satoh H. Biology of Rice 1984, 293-313.
52. Ozsolak F., Ting D.T., Wittner B.S., Brannigan B.W., Paul S., Bardeesy N., Ramaswamy S., Milos P., Haber D.A. Nat. Methods 2010, 7:619-621.
53. Perez C.M., Juliano B.O. Starch-Starke 1978, 30:424-426.
54. Ryoo N., Yu C., Park C.S., Baik M.Y., Park I., Cho M.H., Bhoo S., An G., Hahn T.R., Jeon J.S. Plant Cell Rep. 2007, 26:1083-1095.
55. Sakai H., Lee S.S., Tanaka T., Numa H., Kim J., Kawahara Y., Wakimoto H., Yang C.C., Iwamoto M., Abe T., Yamada Y., Muto A., Inokuchi H., Ikemura T., Matsumoto T., Sasaki T., Itoh T. Plant Cell Physiol. 2013, 54:e6.
56. Sasaki T., Burr B. Curr. Opin. Plant Biol. 2000, 3:138-142.
57. Satheeshkumar P., Saravanan K. Plant Arch. 2012, 12:639-644.
58. Satoh H., Omura T. Jpn. J. Breed. 1981, 31:316-326.
59. Sekhon R.S., Briskine R., Hirsch C.N., Myers C.L., Springer N.M. PLoS ONE 2013, 8:e61005.
60. Severin A., Woody J., Bolon Y.T., Joseph B., Diers B., Farmer A., Muehlbauer G., Nelson R., Grant D., Specht J., Graham M., Cannon S., May G., Vance C., Shoemaker R. BMC Plant Biol. 2010, 10:160.
61. Smith-White B.J., Preiss J. J. Mol. Evol. 1992, 34:449-464.
62. Sultan M., Schulz M.H., Richard H., Magen A., Klingenhoff A., Scherf M., Seifert M., Borodina T., Soldatov A., Parkhomchuk D., Schmidt D., O'Keeffe S., Haas S., Vingron M., Lehrach H., Yaspo M.-L. Science 2008, 321:956-960.
63. Tetlow I.J., Wait R., Lu Z.X., Akkasaeng R., Bowsher C.G., Esposito S., Kosar-Hashemi B., Morell M.K., Emes M.J. Plant Cell 2004, 16:694-708. (Online).
64. Trapnell C., Williams B., Pertea G., Mortazavi A., Kwan G., van Baren M., Salzberg S., Wold B., Pachter L. Nat. Biotechnol. 2010, 28:511-515.
65. Van Camp W. Curr. Opin. Biotechnol. 2005, 16:147-153.
66. Villand P., Olsen O., Kleczkowski L.A. Plant Mol. Biol. 1993, 23:1279-1284.
67. Wang J., Wang W., Li R., Li Y., Tian G., Goodman L., Fan W., Zhang J., Li J., Zhang J., Guo Y., Feng B., Li H., Lu Y., Fang X., Liang H., Du Z., Li D., Zhao Y., Hu Y., Yang Z., Zheng H., Hellmann I., Inouye M., Pool J., Yi X., Zhao J., Duan J., Zhou Y., Qin J. Nature 2008, 456:60-65.
68. Wang Z., Gerstein M., Snyder M. Nat. Rev. Genet. 2009, 10:57-63.
69. Wilhelm B.T., Marguerat S., Watt S., Schubert F., Wood V., Goodhead I., Penkett C.J., Rogers J., Bahler J. Nature 2008, 453:1239-1243.
70. Wong K.S., Kubo A., Jane J.L., Harada K., Satoh H., Nakamura Y. J. Cereal Sci. 2003, 37:139-149.
71. Xiang D.Q., Venglat P., Tibiche C., Yang H., Risseeuw E., Cao Y., Babic V., Cloutier M., Keller W., Wang E., Selvaraj G., Datla R. Plant Physiol. 2011, 156:346-356.
72. Xie C., Mao X.Z., Huang J.J., Ding Y., Wu J.M., Dong S., Kong L., Gao G., Li C.Y., Wei L.P. Nucleic Acids Res. 2011, 39:316-322.
73. Xu H., Gao Y., Wang J.B. PLoS ONE 2012, 7:e30646.
74. Yoon M.R., Koh H.J., Lee S.C., Kang M.Y. J. Korean Soc. Appl. Biol. Chem. 2009, 52:509-515.
75. Zhai R., Feng Y., Wang H., Zhan X., Shen X., Wu W., Zhang Y., Chen D., Dai G., Yang Z., Cao L., Cheng S. BMC Genomics 2013, 2164:14-19.
76. Zhang X., Colleoni C., Ratushna V., Sirghie-Colleoni M., James M., Myers A. Plant Mol. Biol. 2004, 54:865-879.
77. Zhang G., Guo G., Hu X., Zhang Y., Li Q., Li R., Zhuang R., Lu Z., He Z., Fang X., Chen L., Tian W., Tao Y., Kristiansen K., Zhang X., Li S., Yang H., Wang J., Wang J. Genome Res. 2010, 20:646-654.
78. Zhao W.G., Chung J.W., Kwon S.W., Lee J.H., Ma K.H., Park Y.J. Euphytica 2013, 191:9-21.