Article3 Biotech2018
Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants.
Article in 3 Biotech, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
- Identification and Functional Characterization of Anthocyanidin 3-O-Glucosyltransferases OsA3GT1 and OsA3GT2 in Black Rice.Rice (New York, N.Y.) · 2026Article
- Advances and Future Prospects of Pigment Deposition in Pigmented Rice.Plants (Basel, Switzerland) · 2025Review
- Breeding Rice to Increase Anthocyanin Yield Per Area through Small, Black Grain Size and Three Grains per Spikelet.Plants (Basel, Switzerland) · 2024Article
- Transcriptomic-based analysis to identify candidate genes for blue color rose breeding.Plant molecular biology · 2023Article
- Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association.Plants (Basel, Switzerland) · 2023Article
- Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice (Frontiers in plant science · 2023Article
- Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Biomolecules · 2022Article
- Recent Insights into Anthocyanin Pigmentation, Synthesis, Trafficking, and Regulatory Mechanisms in Rice (Biomolecules · 2021Review
- The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain.Frontiers in genetics · 2020Review
- Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics.Scientific reports · 2019Article
- Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress.Genes · 2019Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
- Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Frontiers in plant science · 2019Article
- Seed coats as an alternative molecular factory: thinking outside the box.Plant reproduction · 2018Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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