High natural UVB radiation regulates grain pigmentation in black rice: insights from a genome-wide association study

Introduction Black rice gains recognition in functional food and nutraceutical for its secondary metabolite profiles, which exhibit antioxidant, anti-diabetic, anti-hyperlipidemic, and anti-cancer properties. Its unique purple-black color trait results from anthocyanin accumulation in the pericarp, a trait that varies across pigmented genotypes. While the genetic basis of grain pigmentation in black rice has been partially elucidated, the influence of environmental factors, particularly ultraviolet (UV) radiation, remains poorly understood. UVB radiation is thought to play a role in regulating anthocyanin regulation in various crops, suggesting a potential advantage for cultivating black rice in high UV regions. This research aimed to identify quantitative trait loci (QTL) linking grain pigmentations in response to UV exposure. Methods A genome-wide association study (GWAS) was performed on a diversity panel of 191 black rice accessions primarily sourced from the Asia-Pacific region. Results Utilizing 31,501 single-nucleotide polymorphisms (SNPs), GWAS revealed distinct associations for anthocyanin content under UV conditions versus under non-UV conditions. Notably, three putative candidate genes associated with anthocyanin biosynthesis under UV exposure were identified: OsBBX14 , known to activate OsC1 or OsB2 in anthocyanin biosynthesis pathway; OsMYB44 , a transcription factor that promotes UV-B tolerance; and OsbZIP71 , which improves abiotic stress tolerance by reducing reactive oxygen species (ROS) accumulation. Discussion These findings provide critical insights into the genetic associations regulating grain pigmentation under contrasting UV regimes and pinpoint potential candidate genes for further validation and molecular marker development. Ultimately, this research supports the development of black rice varieties with enhanced nutritional value and improved resilience to high-UV growing conditions.