Thesis
Resolving the Genetics of Grain Pigmentation Traits in Rice
Southern Cross University
Doctor of Philosophy (PhD), Southern Cross University
2025
DOI:
https://doi.org/10.25918/thesis.552
Appears in Recent Southern Cross PhD Theses
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Abstract
Black rice holds significant cultural value across Asia. Its unique purple-black colour is due to anthocyanin accumulation in the pericarp, a trait that varies significantly across genotypes and environments. Black rice has recently gained recognition as a functional food for its antioxidant, anti-diabetic and anti-cancer properties. While some genetic factors involved in grain pigmentation have been identified, the influence of environmental factors, such as ultraviolet (UV) radiation, on trait expression remains poorly understood. The aim of this thesis was to explore variation in UV-dependent grain pigmentation through quantitative genetics and functional genomics approaches.
Firstly, a diversity panel of 191 black rice japonica accessions was characterised for variations in agronomic, grain morphology and vegetative colour traits under UV and non-UV conditions. Population structure analysis revealed two major subpopulations corresponding to geographic origins: maritime Southeast Asia (SEA) and mainland SEA. Genome-wide association study (GWAS) identified known agronomic genes across both conditions and uncovered novel UV-associated loci linked to flowering, grain width and lemma colour.
Secondly, the panel was evaluated for variation in grain anthocyanin accumulation and composition and GWAS revealed distinct associations for contrasting UV treatments. Notably, three transcription factors were located in peak regions associated with anthocyanin content under UV exposure: OsBBX14, activator of OsC1 or OsB2 in anthocyanin biosynthesis; OsMYB44, implicated in UV-B tolerance; and OsbZIP71, with roles in abiotic stress tolerance.
Thirdly, a transcriptomic study was conducted on two genotypes with differential anthocyanin accumulation under contrasting UV conditions. Analysis of differentially expressed genes (DEG) and Weighted Gene Co-expression Network Analysis (WGCNA) suggested several candidate genes with known roles in anthocyanin biosynthesis and UV-B tolerance to be implicated in UV-dependent anthocyanin accumulation.
Collectively, the findings provide critical insights into the genotype-by-environment interactions of grain pigmentation and pinpoint potential candidate genes for molecular marker development to support the breeding of black rice varieties with enhanced nutritional value and improved UV resilience.
Details
- Title
- Resolving the Genetics of Grain Pigmentation Traits in Rice
- Creators
- Truong Duc Nguyen
- Contributors
- Tobias Kretzschmar (Supervisor) - Southern Cross UniversitySzabolcs Lehoczki-Krsjak (Supervisor) - Southern Cross UniversityBen Liu (Supervisor) - Southern Cross University
- Awarding Institution
- Southern Cross University; Doctor of Philosophy (PhD)
- Theses
- Doctor of Philosophy (PhD), Southern Cross University
- Publisher
- Southern Cross University
- Number of pages
- 186
- Identifiers
- 991013350873502368
- Copyright
- © Truong Duc Nguyen 2025
- Academic Unit
- Faculty of Science and Engineering
- Resource Type
- Thesis