Metabolite Quantitative Trait Loci Mapping for Fragrance and Fatty Acid Composition in Rice (Oryza Sativa L.)

Fragrance is a premium trait of grain quality in the traditional, Jasmine-style rice (Oryza sativa L.) variety Phka Rumduol (PRD). Rice fragrance is a combination of various volatile compounds with characteristic odours and flavours that can be traced back to fatty acids. Given the complexity of fragrance phenotype, the use of a robust phenotyping platform in identifying metabolite quantitative trait loci (mQTL) is essential to providing the most suitable set of genetic markers associated with desirable fragrance metabolites and their fatty acid origins in PRD-derived rice breeding lines.

Using combined untargeted metabolomics via GC×GC-TOF-MS, targeted fatty acid analysis with GC-MS, mQTL for individual volatile compounds and fatty acids were identified in a SNP-genotyped F₆ recombinant-inbred rice population developed from a cross between PRD and Thmar Krem (TMK; non-fragrant). This study confirmed the genetic link between 2-acetyl-1-pyrroline and its derivatives with SNPs on chromosomes 8, 3, 4, and 1 and revealed novel mQTLs on chromosomes 2 and 6. MQTLs identified for saturated aldehydes, alcohols, ketones and alkylfurans co-localised on chromosomes 1, 3, and 6 were mainly contributed by PRD, whereas sulfur-containing compounds were contributed by TMK and associated with mQTLs on chromosomes 5 and 6. Oleic and linoleic acid composition were associated with a common QTL on chromosome 7.

Our results demonstrate the ability of untargeted metabolomics to reveal the uniqueness of the fragrance profile of individual rice breeding lines in a mapping population which would allow for improved precision in marker-assisted selection. The various mQTLs verified in this study reaffirm the need for more in-depth metabolite-based selection incorporated in rice breeding. The information from this research is valuable for rice breeding and food quality improvement programs.