Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

Abstract

Anthocyanins are involved in many diverse functions in rice, but their benefits have yet to be clearly demonstrated. Our objective in this study was to identify anthocyanin-related genes in black rice plants. We identified anthocyanin-related genes in black rice plants using a combination of whole-genome resequencing, RNA-sequencing (RNA-seq), microarray experiments, and reverse-transcriptase polymerase chain reaction (RT-PCR). Using multi-layer screening from 30 rice accessions, we identified 172,922 single-nucleotide polymorphisms (SNPs) and 1276 differentially expressed genes that appear to be related to anthocyanin biosynthesis. We identified 18 putative genes from 172,922 SNPs using intensive selective sweeps. The 18 candidate genes identified from SNPs were not significantly correlated with the RNA-seq expression pattern or other well-known anthocyanin biosynthesis/metabolism genes. We also identified nine putative genes from 1276 differentially expressed genes using RNA-seq transcriptome analysis. In addition, we identified four phylogenetic groups from these nine candidate genes and 51 pathway-network genes. Finally, we verified nine anthocyanin-related genes using a newly designed microarray and semi-quantitative RT-PCR. We suggest that these nine identified genes appear to be related to the regulation of anthocyanin biosynthesis and/or metabolism.Electronic supplementary materialThe online version of this article (10.1007/s13205-018-1140-3) contains supplementary material, which is available to authorized users.

The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain

“…Differential transcriptomic analyses between pigmented and non-pigmented rice grains identified regulators and downstream targets of flavonoid pathway genes (Oh et al, 2018). The high anthocyanin content of black rice was associated with enhanced transcription of genes encoding anthocyanidin synthase, while high proanthocyanin content, characteristic of red rice, was accompanied by a notable abundance of transcript for a gene encoding leucoanthocyanidin reductase .…”

“…The application of 'omics-based platforms have begun to reveal the genetic and biochemical basis of the grain pigment parameters a * , b * , L * , hue, and chroma. While transcriptomic and metabolomic analyses have identified certain important structural and regulatory genes influencing core components of flavonoid synthesis Oh et al, 2018), what is still lacking is a comprehensive understanding of the molecular machinery underlying key metabolic processes such as the polymerization and transport of tannins. A more integrated approach, focusing on identifying linkages between regulatory networks is needed (Figure 2).…”

Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform

“…The reference-based transcriptome was performed on a total of four rice samples with two biological replicates each from both black rice as well as white rice [36]. The raw data generated were checked for the quality using FastQC and preprocessed, which include removing the adapter sequences and the low-quality bases (<q30).…”

Whole genome sequencing and comparative genomic analysis reveal novel allelic variations unique to a purple colored rice landrace (Oryza sativa ssp. indica cv. Purpleputtu)

“…Anthocyanins, the end products of anthocyanin pathway, are ubiquitous pigments known to be present in flowering plants. Naturally occurring rice landraces that accumulate anthocyanins, proanthocyanins and anthocyanin derivatives have been widely described (Reddy et al , 1995; Oh et al , 2018). Historically, colored rices have been deemed specialty rices by various ancient Asian cultures.…”

“…It is an indica landrace cultivated in small restricted areas in farmer fields in southern India, often used as border lines to demarcate test plots in experimental fields, primarily serving as a pollen barrier due to its height (Rangaswamy et al , 1988). The genetic control of pericarp colour in PP has been described and molecular biological basis of the control of the underlying anthocyanin pathway has been elucidated (Reddy et al , 1994; Reddy et al , 1995; Reddy et al , 2007; Oh et al , 2018). Earlier studies on color in japonica rices revealed the contours of the genetic circuitry that govern color pathway (Furukawa et al , 2007).…”