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Nucleotide variations of 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) and pericarp coloration genes (Rc and Rd) from upland rice varieties

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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.

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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.

Author information

CLH and CYT designed the experiments; MAH, NAMK, AS, NM. NIMR conducted the experiments and analyzed the data; CLH wrote the article with the contributions of all authors; all authors approved the manuscript.

Correspondence to Chai-Ling Ho.

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The authors declared no conflict of interest.

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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

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  • Abscisic acid
  • Proanthocyanidin biosynthesis
  • Rice pericarp colors
  • Single nucleotide polymorphism