Open Access

ARTICLE

Integrative Genome-Wide Analysis of R2R3-MYB Transcription Factors in Oryza sativa subsp. japonica Reveals Candidate Regulators of Anthocyanin Biosynthesis

N. V. T. Jayaprada¹, Muhammad Hammad², S. Geekiyanage³, Muhammad Shafiq⁴, Heba I. Moamed^5,*, Haiam O. Elkatry⁶, Mohamed El Oirdi⁷, Ahmed Mahmoud Ismail⁸, Mohamed M. El-Mogy⁸, Abdelrahman R. Ahmed^6,*

1 Board of Study in Agriculture, Faculty of Graduate Studies, University of Ruhuna, Matara, Sri Lanka
2 Department of Horticulture, Faculty of Agriculture Sciences, University of the Punjab, Lahore, Pakistan
3 Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Mapalana, Kamburupitiya, Sri Lanka
4 Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
5 Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, Egypt
6 Food and Nutrition Science Department, Agricultural Science and Food, King Faisal University, Al Ahsa, Saudi Arabia
7 Department of Life Sciences, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
8 Department of Arid Land Agriculture, College of Agricultural and Food Sciences, King Faisal University, Al Ahsa, Saudi Arabia

* Corresponding Authors: Heba I. Moamed. Email: ; Abdelrahman R. Ahmed. Email:

(This article belongs to the Special Issue: Advances in Molecular Insights of Plant Secondary Metabolites: Biosynthesis, Regulation, and Applications)

Phyton-International Journal of Experimental Botany 2026, 95(4), 13 https://doi.org/10.32604/phyton.2026.078307

Received 29 December 2025; Accepted 19 March 2026; Issue published 28 April 2026

Abstract

Pigment biofortification in rice, particularly through enhanced anthocyanin accumulation, is increasingly recognized in Asia for its potential to improve nutritional quality and antioxidant capacity while addressing regional health challenges. However, the regulatory network underlying anthocyanin biosynthesis in rice remains incompletely characterized, especially regarding MYB transcription factors that may control pigment accumulation in diverse germplasm. In this study, a genome-wide analysis of MYB transcription factors in Oryza sativa subsp. japonica identified 109 OsMYB genes. Phylogenetic comparison with known anthocyanin regulators from Arabidopsis thaliana and Oryza rufipogon revealed conserved clades containing potential pigment-related regulators. Integrative analyses including gene structure, conserved motif identification, promoter cis-element profiling, and miRNA target prediction were conducted to explore their regulatory potential. Expression profiling during grain development in black and mixed rice identified 32 OsMYB genes as potential candidates associated with anthocyanin accumulation. Promoter analysis revealed enrichment of light-responsive, stress-responsive, and developmental regulatory elements, suggesting coordinated regulation by environmental and developmental signals. Predicted interactions with several Osa-miRNAs further indicate potential post-transcriptional control of these genes. Among the candidates, OsMYB65 showed strong differential expression in pigmented rice grains and possessed multiple regulatory elements associated with anthocyanin biosynthesis, highlighting it as a promising regulator. Overall, this integrative genome-wide analysis identifies a prioritized set of MYB transcription factors that may regulate anthocyanin biosynthesis in rice, providing valuable targets for functional validation and pigment-oriented crop improvement.

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Supplementary Material

Supplementary Material File

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