Identification of key genes and modules in response to Cadmium stress in different rice varieties and stem nodes by weighted gene co-expression network analysis.

Scientific Reports
Qi WangYongcai Lai

Abstract

Soil cadmium (Cd) pollution threatens food safety. This study aimed to identify genes related to Cd accumulation in rice. Low- (Shennong 315, short for S315) and high- (Shendao 47, short for S47) Cd-accumulative rice cultivars were incubated with CdCl2·2.5H2O. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify the modules and genes associated with Cd-accumulative traits of rice. After Cd stress treatment, the Cd content in various tissues of S315 was significantly higher than that of S47. In the stem nodes, the Cd distribution results of the two varieties indicated that the unelongated nodes near the root (short for node A) had a stronger ability to block Cd transfer upwards than the panicle node (short for node B). Cd stress induced huge changes in gene expression profiles. After analyzing the differentially expressed genes (DEGs) in significantly correlated WGCNA modules, we found that genes related to heavy metal transportation had higher expression levels in node A than that in node B, such as Copper transporter 6 (OS04G0415600), Zinc transporter 10 (OS06G0566300), and some heavy-metal associated proteins (OS11G0147500, OS03G0861400, and OS10G0506100). In the comparison results betwe...Continue Reading

References

Jun 1, 2002·Current Opinion in Chemical Biology·Sergi Puig, Dennis J Thiele
Jan 1, 1997·Environmental Pollution·P DasG R Rout
May 8, 2004·Trends in Plant Science·Wangxia WangArie Altman
Aug 19, 2007·Molecular Biology Reports·Beata BékésiováIldikó Matusíková
Dec 14, 2007·Nucleic Acids Research·Minoru KanehisaYoshihiro Yamanishi
Aug 5, 2008·Plant Physiology and Biochemistry : PPB·Jan SelsMiguel F C De Bolle
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jul 28, 2009·Functional & Integrative Genomics·Vinoth Babu V Rajan, Patrick D'Silva
Feb 1, 2012·Journal of Experimental Botany·Noriko YamaguchiYasuko Terada
Nov 15, 2013·Journal of Experimental Botany·Fanying KongQingwei Meng
Jun 24, 2014·Trends in Plant Science·Naoki Yamaji, Jian Feng Ma
Jul 16, 2014·Plant Cell Reports·Patrik MészárosIldikó Matušíková
Aug 26, 2014·Journal of Experimental Botany·Akimasa SasakiJian Feng Ma
Dec 18, 2015·The Plant Pathology Journal·Chang-Jin Park, Young-Su Seo
Mar 22, 2016·Environmental Science and Pollution Research International·Muhammad RizwanYong Sik Ok
Apr 12, 2016·Ecotoxicology and Environmental Safety·Muhammad RizwanYong Sik Ok
Jan 18, 2017·Journal of Pineal Research·Shu-Yu CaiJie Zhou
May 6, 2017·Frontiers in Plant Science·Saurabh PandeyMalireddy K Reddy
May 13, 2017·Environmental Science and Pollution Research International·Hongwen Dai, Zhongyi Yang
Jul 3, 2018·Environmental Science and Pollution Research International·Yanhua LiDeyu Feng
May 23, 2019·Plant, Cell & Environment·Jin-Song LuoZhenhua Zhang

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Methods Mentioned

BETA
transgenic
RNA-seq
electrophoresis
PCR

Software Mentioned

R package
WGCNA
GraphPad Prism
hisat2
Cufflinks
pheatmap

Related Concepts