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Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans
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 Phen...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661230/ https://www.ncbi.nlm.nih.gov/pubmed/26640468 http://dx.doi.org/10.3389/fpls.2015.01027 |
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author | Lu, Yaping Liu, Yemao Niu, Xiaohui Yang, Qingyong Hu, Xuehai Zhang, Hong-Yu Xia, Jingbo |
author_facet | Lu, Yaping Liu, Yemao Niu, Xiaohui Yang, Qingyong Hu, Xuehai Zhang, Hong-Yu Xia, Jingbo |
author_sort | Lu, Yaping |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4661230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-46612302015-12-04 Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans Lu, Yaping Liu, Yemao Niu, Xiaohui Yang, Qingyong Hu, Xuehai Zhang, Hong-Yu Xia, Jingbo Front Plant Sci Genetics 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. Frontiers Media S.A. 2015-11-27 /pmc/articles/PMC4661230/ /pubmed/26640468 http://dx.doi.org/10.3389/fpls.2015.01027 Text en Copyright © 2015 Lu, Liu, Niu, Yang, Hu, Zhang and Xia. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Lu, Yaping Liu, Yemao Niu, Xiaohui Yang, Qingyong Hu, Xuehai Zhang, Hong-Yu Xia, Jingbo Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title | Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title_full | Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title_fullStr | Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title_full_unstemmed | Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title_short | Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans |
title_sort | systems genetic validation of the snp-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661230/ https://www.ncbi.nlm.nih.gov/pubmed/26640468 http://dx.doi.org/10.3389/fpls.2015.01027 |
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