High natural UVB radiation regulates grain pigmentation in black rice: insights from a genome-wide association study
Abstract
IntroductionBlack 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.MethodsA genome-wide association study (GWAS) was performed on a diversity panel of 191 black rice accessions primarily sourced from the Asia-Pacific region.ResultsUtilizing 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.DiscussionThese 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.
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BibTeX
@article{nguyen2026high,
title = {{High natural UVB radiation regulates grain pigmentation in black rice: insights from a genome-wide association study}},
author = {Truong Duc Nguyen and Manisha Thapa and Erwin Tandayu and Lei Liu and Szabolcs Lehoczki-Krsjak and Tobias Kretzschmar},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1943027},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1943027},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - High natural UVB radiation regulates grain pigmentation in black rice: insights from a genome-wide association study
AU - Truong Duc Nguyen
AU - Manisha Thapa
AU - Erwin Tandayu
AU - Lei Liu
AU - Szabolcs Lehoczki-Krsjak
AU - Tobias Kretzschmar
PY - 2026
DA - 2026/10/30
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1943027
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1943027
AB - IntroductionBlack 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.MethodsA genome-wide association study (GWAS) was performed on a diversity panel of 191 black rice accessions primarily sourced from the Asia-Pacific region.ResultsUtilizing 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.DiscussionThese 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.
SN - 1664-462X
ER -