ArticleThe plant genome2022
Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole-genome resequencing.
Article in The plant genome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Targeted anthocyanin biofortification in black rice: a review of spatial metabolic control, growth-defence trade-offs and genotype-environment-management design.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- The Science of Colour in Rice: A Review on Health Benefits, Genetic Regulation, and Anthocyanin Stability.Rice (New York, N.Y.) · 2026Review
- Analysis of Genetic Variation of Rice Straw Characteristics and Its Influence on Biomass.Plant direct · 2026Article
- Genome-wide association study (GWAS) and transcription analysis of candidate genes for rice grain eating and cooking quality (ECQ) traits.BMC genomics · 2025Article
- Advances and Future Prospects of Pigment Deposition in Pigmented Rice.Plants (Basel, Switzerland) · 2025Review
- Genome-wide association study of metabolic traits in the giant duckweed Spirodela polyrhiza.Plant biology (Stuttgart, Germany) · 2025Article
- New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study.BMC plant biology · 2024Article
- Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole-genome resequencing.The plant genome · 2022Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Anthocyanin pigment as a phenolic secondary metabolite is accumulated in areal organs of some rice cultivars. Despite several research attempts, the majority of genomic regions and candidate genes for purple-colored stem (Ps) resulting from anthocyanin pigmentation of rice leaf sheath have not been identified. A genome-wide association study (GWAS) and whole-genome resequencing (WGR) analysis was applied for genetic dissection of anthocyanin pigmentation of rice stem. Using GWAS, the genomic regions (on chromosomes 2, 4, and 6) tagged to eight single-nucleotide polymorphisms (SNPs) were identified to be significantly associated with purple stem, and in the vicinity of GWAS signals, 19 genes were highlighted as putative candidate genes. To narrow down the genomic regions more highly associated to the trait, a WGR study on recombinant inbred lines (RIL) with opposite phenotypes was conducted. After defining the DNA variation between reference genome, maternal parent and the two sister lines, a narrow genomic region on the short arm of chromosome 6 (4.7-6.2 Mbp interval) was identified to be highly associated with anthocyanin pigmentation of rice stem. In the interval, a few candidate genes with probable role in anthocyanin biosynthesis and accumulation were identified, which included five structural genes involved in the known pathways [one chalcone isomerase (CHI), two glycosyl transferases, and two UDP-flavonoid-3-O-glucosyl (UFGT) transferases] and two transcription factors [one basic helix-loop-helix (bHLH)- and one myeloblastosis (MYB)-coding genes]. The identified candidate genes can be used in breeding programs of rice or other Gramineae species for anthocyanin accumulation in areal organs.
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