In this study, we analyzed the Rc and Rd genes that are responsible for the coloration of rice pericarps from six upland rice varieties. We also examined the association of pericarp coloration to the single nucleotide polymorphism in 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), a key gene involved in abscisic acid (ABA) biosynthesis. Our findings demonstrated that all the upland rice varieties analyzed have a Rd gene which encodes a complete dihydroflavonol-4-reductase without early translational termination codon irrespective of their pericarp colors. However, the upland rice varieties with white pericarps were found to have a defective Rc gene with a 14-base deletion at exon 7 which could disrupt the function of a positive regulator of proanthocyanidin biosynthesis. In addition, the NCED2 genes from the upland rice varieties with white pericarps in this study have a C-allele while the NCED2 genes from Pandasan Red, Tomou and Taragang varieties that bear red pericarps were found to have a T-allele which was reported to be associated with a higher ABA level in upland rice. A better understanding of the gene sequences of upland rice varieties with red pericarp may provide important information for rice breeding programs.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Price includes VAT for USA
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
This is the net price. Taxes to be calculated in checkout.
Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL (2015) SNP-seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res 43:D1023–D1027
An JP, Yao JF, Xu RR, You CX, Wang XF, Hao YJ (2018) Apple bZIP transcription factor MdbZIP44 regulates abscisic acid-promoted anthocyanin accumulation. Plant Cell Environ 41:2678–2692
Chen M, San Miguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435–443
Cullings KW (1992) Design and testing of a plant-specific PCR primer for ecological and evolutionary studies. Mol Ecol 1:233–240
Doyle JJ, Dickson EE (1987) Preservation of plant samples for DNA restriction endonuclease analysis. Taxon 36:715–722
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Finkelstein R (2013) Abscisic acid synthesis and response. Arabidopsis Book 2013:1–36
Finocchiaro F, Ferrari B, Gianinetti A, Dall’Asta C, Galaverna G, Scazzina F, Pellegrini N (2007) Characterization of antioxidant compounds of red and white rice and changes in total antioxidant capacity during processing. Mol Nutr Food Res 51:1006–1019
Furukawa T, Maekawa M, Oki T, Suda I, Iida S, Shimada H, Takamure I, Kadowaki K (2006) The Rc and Rd genes are involved in proanthocyanidinsynthesis in rice pericarp. Plant J 49:91–102
Green R, Rogers EJ (2013) Transformation of chemically competent E. coli. Methods Enzymol 529:329–336
Gu XY, Foley ME, Horvath DP, Anderson JV, Feng J, Zhang L, Mowry CR, Ye H, Suttle JC, Kadowaki K, Chen Z (2011) Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice. Genetics 189:1515–1524
Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol Biol 59:155–171
Huang Y, Guo Y, Liu Y, Zhang F, Wang Z, Wang H, Wang F, Li D, Mao D, Luan S, Liang M, Chen L (2018) 9-cis-epoxycarotenoid dioxygenase 3 regulates plant growth and enhances multi-abiotic stress tolerance in rice. Front Plant Sci 9:1–18
Hwang SG, Lee CY, Tseng CS (2018) Heterologous expression of rice 9-cis-epoxycarotenoid dioxygenase 4 (OsNCED4) in Arabidopsis confers sugar oversensitivity and drought tolerance. Bot Stud 59:1–12
Ithal N, Reddy AR (2004) Rice flavonoid pathway genes, OsDfr and OsAns, are induced by dehydration, high salt and ABA, and contain stress responsive promoter elements that interact with the transcription activator, OsC1-MYB. Plant Sci 166:1505–1513
Jaakola L (2013) New insights into the regulation of anthocyanin biosynthesis in fruits. Trends Plant Sci 18:477–483
Jia HF, Chai YM, Li CL, Lu D, Luo JJ, Qin L, Shen YY (2011) Abscisic acid plays an important role in the regulation of strawberry fruit ripening. Plant Physiol 157:188–199
Karppinen K, Tegelberg P, Häggman H, Jaakola L (2018) Abscisic acid regulates anthocyanin biosynthesis and gene expression associated with cell wall modification in ripening bilberry (Vaccinium myrtillus L.) fruits. Front Plant Sci 9:1–17
Kornerup A, Wanscher JH (1967) Methuen Handbook of Color, 2nd edn. Methuen, London
Li G, Zhao J, Qin B, Yin Y, An W, Mu Z, Cao Z (2019) ABA mediates development-dependent anthocyanin biosynthesis and fruit coloration in Lycium plants. BMC Plant Biol 19:1–13
Ling WH, Cheng QX, Ma J, Wang T (2001) Red and black rice decrease atherosclerotic plaque formation and increase antioxidant status in rabbits. J Nutr 131:1421–1426
Lyu J, Zhang S, Dong Y, He W, Zhang J, Deng X, Zhang Y, Li X, Li B, Huang W, Wan W, Yu Y, Li Q, Li Liu X, Wang B, Tao D, Zhang G, Wang J, Xu X, Hu F, Wang W (2013) Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nat Commun 4:1–9
Mansueto L, Fuentes RR, Borja FN, Detras J, Abrio-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovye V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N (2017) Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res 45:D1075–D1081
Nakai K, Inagaki Y, Nagata H, Miyazaki C, Iida S (1998) Molecular characterization of the gene for dihydroflavonol 4-reductase of japonica rice varieties. Plant Biotech 15:221–225
Reddy VS, Dash S, Reddy AR (1995) Anthocyanin pathway in rice (Oryza sativa L.): identification of a mutant showing dominant inhibition of anthocyanins in leaf and accumulation of proanthocyanidins in pericarp. Theor Appl Genet 91:301–312
Shirley B (1998) Flavonoids in seeds and grains: physiological function, agronomic importance and the genetics of biosynthesis. Seed Sci Res 8:415–422
Sweeney MT, Thomson MJ, Pfeil BE, McCouch S (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Xie DY, Dixon RA (2005) Proanthocyanidin biosynthesis–still more questions than answers? Phytochemistry 66:2127–2144
Xie X, Li S, Zhang R, Zhao J, Chen Y, Zhao Q, Yao Y, You C, Zhang X, Hao Y (2012) The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant Cell Environ 35:1884–1897
The project was supported by Ministry of Education, Malaysia under the Fundamental Research Grant Scheme (Project No. FRGS/1/2016/STG05/UPM/02/18). Teh CY was supported by the UPM post-doctoral scheme. Mohd Kasim NA was supported by FRGS/1/2016/STG05/UPM/02/18 and Graduate Research Fund (GRF) from UPM. Amer Hamzah M was supported by FRGS/1/2016/STG05/UPM/02/18 and MyBrainSc from the Ministry of Education, Malaysia. We acknowledge Gene Bank and Seed Centre, Malaysian Agricultural Research and Development Institute (MARDI), Kepala Batas, Malaysia for providing the rice seeds; and Rice SNP-Seek Database for providing access to the research data.
Conflict of interest
The authors declared no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
About this article
Cite this article
Amer Hamzah, M., Mohd Kasim, N.A., Shamsuddin, A. et al. Nucleotide variations of 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) and pericarp coloration genes (Rc and Rd) from upland rice varieties. 3 Biotech 10, 105 (2020). https://doi.org/10.1007/s13205-020-2092-y
- Abscisic acid
- Proanthocyanidin biosynthesis
- Rice pericarp colors
- Single nucleotide polymorphism