AUTHOR=Lu Yaping , Liu Yemao , Niu Xiaohui , Yang Qingyong , Hu Xuehai , Zhang Hong-Yu , Xia Jingbo TITLE=Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans JOURNAL=Frontiers in Plant Science VOLUME=6 YEAR=2015 URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2015.01027 DOI=10.3389/fpls.2015.01027 ISSN=1664-462X ABSTRACT=

In the post-GWAS (Genome-Wide Association Scan) era, the interpretation of GWAS results is crucial to screen for highly relevant phenotype-genotype association pairs. Based on the single genotype-phenotype association test and a pathway enrichment analysis, we propose a Metabolite-pathway-based Phenome-Wide Association Scan (M-PheWAS) to analyze the key metabolite-SNP pairs in rice and determine the regulatory relationship by assessing similarities in the changes of enzymes and downstream products in a pathway. Two SNPs, sf0315305925 and sf0315308337, were selected using this approach, and their molecular function and regulatory relationship with Enzyme EC:5.5.1.6 and with flavonoids, a significant downstream regulatory metabolite product, were demonstrated. Moreover, a total of 105 crucial SNPs were screened using M-PheWAS, which may be important for metabolite associations.