Genomics and Applied Biology 2024, Vol.15, No.4, 200-211 http://bioscipublisher.com/index.php/gab 200 Feature Review Open Access Comprehensive Genomic Identification and Characterization of R2R3-MYB Genes in Colored Rice (Oryza sativaL.): A Phylogenetic and Expression Analysis Mengmeng Yin 1,2,4, Fan Luo 1,2,4, Xiaoli Zhou 1,2,4, Changhe Wei 5, Qian Zhu 1,2,3, Hui Zhang 2,3, Dong Sun Lee 1,2,3 , Lijuan Chen 1,2,3 1 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 3 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 College of Agricultural Science, Xichang University, Xichang, 615013, Sichuan, China 5 Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, 615013, Sichuan, China Co-corresponding authors: dongeast@naver.com; chenlijuan@hotmail.com Genomics and Applied Biology, 2024, Vol.15, No.4 doi: 10.5376/gab.2024.15.0022 Received: 27 Jun., 2024 Accepted: 04 Aug., 2024 Published: 17Aug., 2024 Copyright © 2024 Yin et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Yin M.M., Luo F., Zhou X.L., Wei C.H., Zhu Q., Zhang H., Lee D.S., and Chen L.J., 2024, Comprehensive genomic identification and characterization of R2R3-MYB genes in colored rice (Oryza sativa L.): a phylogenetic and expression analysis, Genomics and Applied Biology, 15(4): 200-211 (doi: 10.5376/gab.2024.15.0022) Abstract This review provides a comprehensive identification and characterization of the R2R3-MYB gene family in colored rice (Oryza sativa L.), offering significant insights into their evolutionary relationships, structural features, and expression profiles. Notable findings include the distinctive structural characteristics of R2R3-MYB genes, such as the high prevalence of non-synonymous substitutions in the DNA-binding domains, particularly in the α-helix regions. This suggests adaptive selection and functional diversification. The phylogenetic analysis revealed the existence of distinct clades that correspond to different evolutionary lineages. Of particular interest is a key clade that is closely related to the ancestral species, wild rice (O. rufipogon and O. nivara), which indicates the conservation of evolutionary lineages. The expression patterns of R2R3-MYBgenes were found to be specific to different tissues and developmentally regulated, with specialized roles in photosynthesis-related processes and root development. Furthermore, the study underscores the functional roles of R2R3-MYB genes in anthocyanin biosynthesis. Genes such as OsC1 and OsKala3 play pivotal roles in modulating the expression of anthocyanin biosynthetic pathway genes, thereby contributing to the distinctive purple pigmentation and associated health benefits of purple rice. Furthermore, the case study of OsMYB30 and OsMYB60 illustrates their pivotal roles in plant defense mechanisms and leaf morphology, respectively. The insights gained from this review have significant implications for the breeding and genetic engineering of colored rice, emphasizing the potential for improving agronomic traits and enhancing crop performance through targeted manipulation of R2R3-MYBgenes. Keywords Colored rice; R2R3-MYBgenes; Phylogenetic analysis; Gene expression analysis; Anthocyanin biosynthesis 1 Introduction R2R3-MYB transcription factors (TFs) are a prominent family of regulatory proteins in plants, characterized by the presence of two MYB domains at the N-terminus. These TFs play crucial roles in various plant processes, including cell cycle regulation, secondary metabolism, and responses to biotic and abiotic stresses. Specifically, R2R3-MYB genes are integral to the regulation of anthocyanin biosynthesis, a pathway responsible for the production of pigments that contribute to the coloration of plant tissues (Feng et al., 2018). The functional diversity of R2R3-MYB genes is attributed to their ability to interact with other proteins, such as basic helix-loop-helix (bHLH) proteins, to form transcriptional complexes that modulate gene expression (Sakamoto et al., 2001; Feng et al., 2018). Anthocyanins are a class of flavonoid pigments that impart red, purple, and blue colors to various plant tissues, including flowers, fruits, and leaves. These pigments serve a dual role in the plant kingdom, acting as both attractants for pollinators and seed dispersers, and as a means of protection against environmental stresses, including UV radiation, pathogen attack, and oxidative stress (Zhu et al., 2017; Dwiningsih and Alkahtani, 2022). The biosynthesis of anthocyanins is a complex process involving a network of structural and regulatory genes. R2R3-MYB transcription factors play a pivotal role as key regulators of this pathway. In rice, anthocyanin
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