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

Jianyong Wang,Chenhao Zhang,Yangsheng Li

doi:10.3390/genes13030410

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.

Highlights

Introduction published maps and institutional affilFlavonoids, synthesized by the phenylpropanoid pathway, one of the largest families of polyphenolic secondary metabolites in the world, are extensively distributed in all different organs and tissues depending on the plant developmental and environmental conditions [1]
BLASTP searches were performed in the rice database by using the deduced protein homologues of the 13 flavonoid biosynthesis-related genes as a query sequence, including chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase (FNS), flavanone 2-hydroxylase (F2H), flavonoid 30 -hydroxylase (F30 H), F30 50 H, dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR) from various plant species downloaded from the National Center for Biotechnology Information (NCBI) database (Tables S1–S5)
We found gene clusters with a relative high density were observed among the distinct gene family members on Chrs 4, 6, 7, 8, 9 and 10, which might provide the chance for these genes to form macromolecular complexes in physical position or space during the rice flavonoid biosynthesis process

Summary

Introduction

Flavonoids, synthesized by the phenylpropanoid pathway, one of the largest families of polyphenolic secondary metabolites in the world, are extensively distributed in all different organs and tissues depending on the plant developmental and environmental conditions [1]. Most flavonoids contain the common diphenylpropane (C6-C3-C6) carbon framework with two aromatic rings (A-ring and B-ring) interconnected by a three-carbon heterocyclic pyran ring (C-ring chain) [2,3]. Based on the degree of heterocyclic C-ring oxidation, the position of hydroxyl and methyl groups on the A- and B-rings and the degree of modifications (including glycosylation, acylation and polymerization ), flavonoids can be categorized into six classes: flavones, flavanones, flavonols, flavanols, anthocyanins and isoflavones [3,4]. An enormous amount of research during the last few decades has revealed that flavonoids, as the most bioactive plant secondary metabolites, might iations.

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