title: Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans.
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.
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Yemao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Niu
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Qingyong
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Xuehai
authors.initials: X
authors.lastname: Hu
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Zhang
authors.affiliation: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan, China.
authors.forename: Jingbo
authors.initials: J
authors.lastname: Xia
keywords: Wilcoxon rank-sum test; association scan; metabolite; replication; upper tier metabolite pathway