Natural variation and underlying genetic loci of gamma-oryzanol in Asian cultivated rice seeds

gamma-oryzanol is the most studied component in rice (Oryza sativa L.) bran oil. It is not only associated with physiological processes of rice growth and development but also grain quality that is related to human health. Previous studies focused mainly on gamma-oryzanol composition and content in various rice cultivars, while its biosynthetic and regulatory pathways remain unknown. Here we present the quantitative identification of gamma-oryzanol in rice seeds across 179 Asian cultivated accessions using ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF/MS), which revealed a significant natural variation in gamma-oryzanol content among these tested rice accessions. In addition, we present, for the first time, the genome-wide association study (GWAS) on rice seed gamma-oryzanol, which identified 187 GWAS signal hot spots and 13 candidate genes that are associated with variable gamma-oryzanol content and provided the top 10 rice haplotypes with high gamma-oryzanol content for breeding. Collectively, our study provides valuable germplasms for breeding rice cultivars rich in gamma-oryzanol and genetic resources for elucidating genetic and biochemical bases of variable gamma-oryzanol in rice.