A computational systems biology study for understanding salt tolerance mechanism in rice.

Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving...

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Autores principales:	Juexin Wang, Liang Chen, Yan Wang, Jingfen Zhang, Yanchun Liang, Dong Xu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ef6d30950add4e158e0745d4c6292818
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spelling	oai:doaj.org-article:ef6d30950add4e158e0745d4c62928182021-11-18T07:42:40ZA computational systems biology study for understanding salt tolerance mechanism in rice.1932-620310.1371/journal.pone.0064929https://doaj.org/article/ef6d30950add4e158e0745d4c62928182013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23762267/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving grain yield. In this study, a gene regulatory network of rice salt tolerance is constructed using a systems biology approach with a number of novel computational methods. We developed an improved volcano plot method in conjunction with a new machine-learning method for gene selection based on gene expression data and applied the method to choose genes related to salt tolerance in rice. The results were then assessed by quantitative trait loci (QTL), co-expression and regulatory binding motif analysis. The selected genes were constructed into a number of network modules based on predicted protein interactions including modules of phosphorylation activity, ubiquity activity, and several proteinase activities such as peroxidase, aspartic proteinase, glucosyltransferase, and flavonol synthase. All of these discovered modules are related to the salt tolerance mechanism of signal transduction, ion pump, abscisic acid mediation, reactive oxygen species scavenging and ion sequestration. We also predicted the three-dimensional structures of some crucial proteins related to the salt tolerance QTL for understanding the roles of these proteins in the network. Our computational study sheds some new light on the mechanism of salt tolerance and provides a systems biology pipeline for studying plant traits in general.Juexin WangLiang ChenYan WangJingfen ZhangYanchun LiangDong XuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 6, p e64929 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Juexin Wang Liang Chen Yan Wang Jingfen Zhang Yanchun Liang Dong Xu A computational systems biology study for understanding salt tolerance mechanism in rice.
description	Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving grain yield. In this study, a gene regulatory network of rice salt tolerance is constructed using a systems biology approach with a number of novel computational methods. We developed an improved volcano plot method in conjunction with a new machine-learning method for gene selection based on gene expression data and applied the method to choose genes related to salt tolerance in rice. The results were then assessed by quantitative trait loci (QTL), co-expression and regulatory binding motif analysis. The selected genes were constructed into a number of network modules based on predicted protein interactions including modules of phosphorylation activity, ubiquity activity, and several proteinase activities such as peroxidase, aspartic proteinase, glucosyltransferase, and flavonol synthase. All of these discovered modules are related to the salt tolerance mechanism of signal transduction, ion pump, abscisic acid mediation, reactive oxygen species scavenging and ion sequestration. We also predicted the three-dimensional structures of some crucial proteins related to the salt tolerance QTL for understanding the roles of these proteins in the network. Our computational study sheds some new light on the mechanism of salt tolerance and provides a systems biology pipeline for studying plant traits in general.
format	article
author	Juexin Wang Liang Chen Yan Wang Jingfen Zhang Yanchun Liang Dong Xu
author_facet	Juexin Wang Liang Chen Yan Wang Jingfen Zhang Yanchun Liang Dong Xu
author_sort	Juexin Wang
title	A computational systems biology study for understanding salt tolerance mechanism in rice.
title_short	A computational systems biology study for understanding salt tolerance mechanism in rice.
title_full	A computational systems biology study for understanding salt tolerance mechanism in rice.
title_fullStr	A computational systems biology study for understanding salt tolerance mechanism in rice.
title_full_unstemmed	A computational systems biology study for understanding salt tolerance mechanism in rice.
title_sort	computational systems biology study for understanding salt tolerance mechanism in rice.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/ef6d30950add4e158e0745d4c6292818
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A computational systems biology study for understanding salt tolerance mechanism in rice.

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