Phenome-wide Association Study Based On Metabolite Pathway In Rice

Rice, as one of the most vital food crops, offers food resource to nearly half of the population around the globe. It is of great importance to comprehend the genetic and biochemical basis of metabolic traits, so as to produce excellent varieties with both strong stress resistance and high nutritional quality.A systematic genetics strategy, Metabolite-pathway-based Phenome-wide Association Scan(M-PheWAS) is proposed in this research. First, M-PheWAS involved correlation analysis on phenotypes and genotypes. Second, by combining M-PheWAS with pathway-based analysis, we identified genetic loci related to metabolites with enrichment effects, and we also identified catalytic proteases with relevant biochemical reactions.Consequently, we obtained 105 significant SNPs and 52 catalytic proteases through metabolite pathway enrichment analysis. Meanwhile, we found and confirmed a genetic regulatory pathway that two SNPs, sf0315305925 and sf0315308337, control a target gene LOC_Os03g60509. Through chalcone isomerase(EC: 5.5.1.6), a encoding protease, the loci ultimately control the biochemical synthesis of Naringenin.The results showed that M-PheWAS is a practical strategy. Furthermore, additional theoretical foundation is provided from the analysis on genetic regulatory pathways of 4, 5, 7- Naringenin biochemical synthesis process.