Genomics and Applied Biology 2024, Vol.15, No.4, 200-211 http://bioscipublisher.com/index.php/gab 201 accumulation is influenced by both genetic and environmental factors (Mackon et al., 2021). The presence of specific alleles can lead to tissue-specific pigmentation patterns (Zhu et al., 2017). Purple rice is distinguished by its high anthocyanin content, which gives the grains and other plant parts their characteristic purple color (Xia et al., 2021). The pigmentation is not only aesthetically appealing but also associated with numerous health benefits due to the antioxidant properties of anthocyanins (Lachagari et al., 2019; Dwiningsih and Alkahtani, 2022). Genomic studies have been conducted on purple rice varieties, including the landrace Purpleputtu, to elucidate the genetic basis of anthocyanin biosynthesis and its regulation (Lachagari et al., 2019). These studies have revealed significant allelic variations and unique genetic features that contribute to the purple coloration, thus making purple rice an excellent model for studying the molecular mechanisms underlying anthocyanin biosynthesis (Lachagari et al., 2019). Moreover, the creation of biofortified rice varieties with elevated anthocyanin levels, exemplified by the "Purple Endosperm Rice" underscores the potential of genetic engineering to enhance the nutritional profile of staple crops (Zhu et al., 2017). The objective of this review is to conduct a comprehensive genomic identification and characterization of R2R3-MYB genes in colored rice. This will entail a comprehensive phylogenetic analysis to elucidate the evolutionary relationships among these genes and an expression analysis to ascertain their roles in anthocyanin biosynthesis and other biological processes. By integrating bioinformatics and experimental approaches, this reviwe aims to provide insights into the functional diversity and regulatory mechanisms of R2R3-MYB genes in colored rice, thereby contributing to a more comprehensive understanding of plant secondary metabolism and stress responses. 2 Genome-Wide Identification of R2R3-MYBGenes in Colored Rice 2.1 Data resources and genome databases The identification of R2R3-MYB genes in rice is dependent upon the utilization of comprehensive genomic data from a multitude of sources. Whole genome sequencing and comparative genomic analysis have been instrumental in elucidating the genetic intricacies and allelic variations that are exclusive to purple rice landraces, such as Purpleputtu (Lachagari et al., 2019). Furthermore, databases such as the SNP-Seek database, which contains a comprehensive set of single nucleotide polymorphism (SNP) data from a diverse range of rice lines, serve as a valuable resource for identifying genetic variations (Lachagari et al., 2019). The utilization of these databases enables a comprehensive comparison of the colored rice genome with other rice cultivars, thereby facilitating the identification of specific genes involved in anthocyanin biosynthesis and other related pathways (Yan et al., 2020). 2.2 Bioinformatics tools and methodologies The use of bioinformatics tools and methodologies is a crucial aspect of genome-wide identification of R2R3-MYBgenes. Multiple sequence alignment tools are employed to compare gene sequences across diverse rice cultivars, thereby elucidating deletions, insertions, and other variations that may impact gene function (Lachagari et al., 2019). Phylogenetic analysis tools facilitate comprehension of the evolutionary relationships between identified genes and their homologs in other species, thereby providing insights into their functional roles (Lachagari et al., 2019). Furthermore, cDNA microarray approaches are utilized to monitor gene expression profiles under diverse stress conditions, facilitating the identification of R2R3-MYB genes that are differentially expressed (Dai et al., 2007; Dai et al., 2012). These methodologies collectively facilitate a comprehensive analysis of the R2R3-MYBgene family in colored rice. 2.3 Criteria for gene identification The identification of R2R3-MYB genes in colored rice is based on several criteria. Firstly, genes must exhibit sequence homology to known R2R3-MYBgenes in other plant species, particularly in their DNA-binding domains (Jia et al., 2004; Li et al., 2020). Secondly, the presence of characteristic motifs and domains, such as the R2 and R3 repeats, is essential for confirming the identity of these TFs (Jia et al., 2004; Hua et al., 2020). Moreover, genes must demonstrate differential expression patterns in response to specific stimuli or conditions, such as phosphate starvation or abiotic stress, which indicate their regulatory roles (Dai et al., 2007; Dai et al., 2012).
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