Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Abstract

Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants

“…In addition, the correlation coefficient between OsCHI6 and OsCHI7 was 0.95 at the transcriptional level (Figures 5A and S7A). These investigations were similar to our previous study mining the publicly available rice databases [34]. In T. aestivum, there was a clear transcriptional divergence between three types of CHIs, even within the same types.…”

“…Functional diversification after gene expansion could occur at the transcriptional level. To date, 12 differentially expressed CHIs in G. max [ 25 ], 5 tissue-specific CHIs in A. thaliana [ 15 ], 33 CHIs in cotton [ 32 ], 7 CHIs in rice [ 33 , 34 ], 30 CHIs in six Citrus species [ 35 ], 31 CHIs in liverwort and Selaginella species [ 18 ], 56 CHIs in fern species [ 26 ], and 11 CHIs in D. cambodiana [ 36 ], have been reported. These observations showed that CHIs usually have tissue-specific expression in various tissues, and often respond to various environmental stressors.…”

“…With the sequencing of plant genomes and transcriptomes, more and more plant CHI family genes have been discovered from many species, including primitive seedless plants and higher seed plants. To date, 12 CHIs in Glycine max [ 25 ], 5 CHIs in Arabidopsis thaliana [ 15 ], 33 CHIs in cotton [ 32 ], 7 CHIs in Oryza sativa [ 33 , 34 ], 30 CHIs in six Citrus species [ 35 ], 31 CHIs in liverwort and Selaginella species [ 18 ], 56 CHIs in fern species [ 26 ], and 11 CHIs in Dracaena cambodiana [ 36 ], have been identified based on their corresponding genomic or transcriptomic data. Acquisition of CHI enzymatic activity in plants during evolution is an intriguing topic, because both type III and type IV CHIs are devoid of bona fide CHI catalytic activity.…”

Functional identification of ANR genes in apple (Malus halliana) that reduce saline–alkali stress tolerance

“…ANR is a key enzyme in the anthocyanin metabolic pathway and plays an important role in abiotic stress (Han et al 2012). Previous studies on flavonoid synthesis in rice showed that ANR responds to abiotic stress, six hormones and salt treatment (Wang et al 2022c). Poudel et al (2020) revealed that temperature had a significant effect on the biosynthesis of proanthocyanidin (PA) in grapes by increasing expression of anthocyanin reductase (ANR).…”

“…Previous studies on flavonoid synthesis in rice showed that ANR responds to abiotic stress, six hormones and salt treatment (Wang et al . 2022c). Poudel et al .…”