Abstract
Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.
Highlights
The leaves of plants are evaluated by studying the major photosynthetic organ
To investigate the genetic variation underlying leaf color in rice plants, we identified the sequence variations between each of the 10 accessions and the rice reference sequence (Nipponbare)
There is no direct evidence linking the functions of Phosphoadenosine 5’-Phosphosulfate Transporter1 (PAPST1) to leaf color, our results suggest that that gene plays a role in the regulation of the leaf-color pathway
Summary
The leaves of plants are evaluated by studying the major photosynthetic organ. The leaf color, size, and shape directly affect photosynthesis, crop yield, and grain quality. Previous studies of leaf color in rice focused on characterizing the correlation between fertilizer nitrogen and chlorophyll metabolism for photosynthesis. The leaf-color chart can indirectly estimate the nitrogen status of growing rice [1], and chlorophyll metabolism is very important to all plants in relation to photosynthesis [2]. The leaf color is an effective marker to identify hybridization in rice, because color phenotypes can be identified. Using various leaf-color mutants, genetic mechanisms have been analyzed to reveal the functions of color-related genes involved in chlorophyll biosynthesis [3], chloroplast structure and function [4], the regulation of chloroplast development, carotenoid biosynthesis, anthocyanins biosynthesis [5,6], programmed cell death, and photosynthesis [7]. Leaf color-mutant characters are normally controlled by recessive nuclear genes, with only a few cases of control by dominant or cytoplasmic genes [8]
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