A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root

Yingmei Huang, Huiqiong Chen, John Reinfelder, Xiaoyu Liang, Chongjun Sun, Chuanping Liu, Fangbai Li, Jicai Yi

Research output: Contribution to journalArticle

Abstract

Cadmium (Cd) and arsenic (As) are nonessential and toxic elements in rice that often occur together in contaminated paddy field soils. To understand whether rice has a common molecular response mechanism against Cd and As toxicity, 30-day seedlings (Oryza sativa L. indica) were exposed separately to Cd and As 3+ in hydroponic cultures for up to 7 days. Root transcriptomic analysis of plants exposed to Cd and As for 3 days revealed that a total of 2224 genes in rice roots responded to Cd stress, while 1503 genes responded to As stress. Of these, 841 genes responded to both stressors. The genes in common to Cd and As stress were associated with redox control, stress response, transcriptional regulation, transmembrane transport, signal transduction, as well as biosynthesis and metabolism of macromolecules and sulfur compounds. In plants exposed to Cd and As separately or in combination for 3 and 7 days, qRT-PCR verification revealed that the glutathione metabolism associated gene Os09g0367700 was significantly up-regulated with respect to unexposed controls and had a positive synergistic effect under combined Cd and As stress. In addition, the redox control related genes Os06g0216000, Os07g0638300 and Os01g0294500, the glutathione metabolism related gene Os01g0530900, the cell wall biogenesis related genes Os05g0247800, Os11g0592000 and Os03g0416200, the expression regulation related genes Os07g0597200 and Os02g0168200, and the transmembrane transport related genes Os04g0524500, also varied significantly with respect to an unexposed control and displayed synergistic effects after 7 days of simultaneous exposure to Cd and As. Our identification of a novel set of genes in rice which responded to both Cd and As 3+ stress may be of value in mitigating the toxicity of co-contaminated soils. These results also provide a deeper understanding of the molecular mechanisms involved in response to multi-metal/loids stress, and may be used in the genetic improvement of rice varieties.

Original languageEnglish (US)
Pages (from-to)445-460
Number of pages16
JournalScience of the Total Environment
Volume666
DOIs
StatePublished - May 20 2019

Fingerprint

Arsenic
RNA
Cadmium
arsenic
cadmium
rice
Genes
gene
Metabolism
metabolism
Glutathione
Toxicity
analysis
toxicity
Soils
Sulfur Compounds
Signal transduction
Sulfur compounds
Poisons
hydroponics

All Science Journal Classification (ASJC) codes

  • Pollution
  • Waste Management and Disposal
  • Environmental Engineering
  • Environmental Chemistry

Keywords

  • Arsenic
  • Cadmium
  • Common response gene
  • RNA-seq
  • Synergistic effect

Cite this

Huang, Yingmei ; Chen, Huiqiong ; Reinfelder, John ; Liang, Xiaoyu ; Sun, Chongjun ; Liu, Chuanping ; Li, Fangbai ; Yi, Jicai. / A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root. In: Science of the Total Environment. 2019 ; Vol. 666. pp. 445-460.
@article{49a545aa243241d0a526e7bf97b9533d,
title = "A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root",
abstract = "Cadmium (Cd) and arsenic (As) are nonessential and toxic elements in rice that often occur together in contaminated paddy field soils. To understand whether rice has a common molecular response mechanism against Cd and As toxicity, 30-day seedlings (Oryza sativa L. indica) were exposed separately to Cd and As 3+ in hydroponic cultures for up to 7 days. Root transcriptomic analysis of plants exposed to Cd and As for 3 days revealed that a total of 2224 genes in rice roots responded to Cd stress, while 1503 genes responded to As stress. Of these, 841 genes responded to both stressors. The genes in common to Cd and As stress were associated with redox control, stress response, transcriptional regulation, transmembrane transport, signal transduction, as well as biosynthesis and metabolism of macromolecules and sulfur compounds. In plants exposed to Cd and As separately or in combination for 3 and 7 days, qRT-PCR verification revealed that the glutathione metabolism associated gene Os09g0367700 was significantly up-regulated with respect to unexposed controls and had a positive synergistic effect under combined Cd and As stress. In addition, the redox control related genes Os06g0216000, Os07g0638300 and Os01g0294500, the glutathione metabolism related gene Os01g0530900, the cell wall biogenesis related genes Os05g0247800, Os11g0592000 and Os03g0416200, the expression regulation related genes Os07g0597200 and Os02g0168200, and the transmembrane transport related genes Os04g0524500, also varied significantly with respect to an unexposed control and displayed synergistic effects after 7 days of simultaneous exposure to Cd and As. Our identification of a novel set of genes in rice which responded to both Cd and As 3+ stress may be of value in mitigating the toxicity of co-contaminated soils. These results also provide a deeper understanding of the molecular mechanisms involved in response to multi-metal/loids stress, and may be used in the genetic improvement of rice varieties.",
keywords = "Arsenic, Cadmium, Common response gene, RNA-seq, Synergistic effect",
author = "Yingmei Huang and Huiqiong Chen and John Reinfelder and Xiaoyu Liang and Chongjun Sun and Chuanping Liu and Fangbai Li and Jicai Yi",
year = "2019",
month = "5",
day = "20",
doi = "https://doi.org/10.1016/j.scitotenv.2019.02.281",
language = "English (US)",
volume = "666",
pages = "445--460",
journal = "Science of the Total Environment",
issn = "0048-9697",
publisher = "Elsevier",

}

A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root. / Huang, Yingmei; Chen, Huiqiong; Reinfelder, John; Liang, Xiaoyu; Sun, Chongjun; Liu, Chuanping; Li, Fangbai; Yi, Jicai.

In: Science of the Total Environment, Vol. 666, 20.05.2019, p. 445-460.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A transcriptomic (RNA-seq) analysis of genes responsive to both cadmium and arsenic stress in rice root

AU - Huang, Yingmei

AU - Chen, Huiqiong

AU - Reinfelder, John

AU - Liang, Xiaoyu

AU - Sun, Chongjun

AU - Liu, Chuanping

AU - Li, Fangbai

AU - Yi, Jicai

PY - 2019/5/20

Y1 - 2019/5/20

N2 - Cadmium (Cd) and arsenic (As) are nonessential and toxic elements in rice that often occur together in contaminated paddy field soils. To understand whether rice has a common molecular response mechanism against Cd and As toxicity, 30-day seedlings (Oryza sativa L. indica) were exposed separately to Cd and As 3+ in hydroponic cultures for up to 7 days. Root transcriptomic analysis of plants exposed to Cd and As for 3 days revealed that a total of 2224 genes in rice roots responded to Cd stress, while 1503 genes responded to As stress. Of these, 841 genes responded to both stressors. The genes in common to Cd and As stress were associated with redox control, stress response, transcriptional regulation, transmembrane transport, signal transduction, as well as biosynthesis and metabolism of macromolecules and sulfur compounds. In plants exposed to Cd and As separately or in combination for 3 and 7 days, qRT-PCR verification revealed that the glutathione metabolism associated gene Os09g0367700 was significantly up-regulated with respect to unexposed controls and had a positive synergistic effect under combined Cd and As stress. In addition, the redox control related genes Os06g0216000, Os07g0638300 and Os01g0294500, the glutathione metabolism related gene Os01g0530900, the cell wall biogenesis related genes Os05g0247800, Os11g0592000 and Os03g0416200, the expression regulation related genes Os07g0597200 and Os02g0168200, and the transmembrane transport related genes Os04g0524500, also varied significantly with respect to an unexposed control and displayed synergistic effects after 7 days of simultaneous exposure to Cd and As. Our identification of a novel set of genes in rice which responded to both Cd and As 3+ stress may be of value in mitigating the toxicity of co-contaminated soils. These results also provide a deeper understanding of the molecular mechanisms involved in response to multi-metal/loids stress, and may be used in the genetic improvement of rice varieties.

AB - Cadmium (Cd) and arsenic (As) are nonessential and toxic elements in rice that often occur together in contaminated paddy field soils. To understand whether rice has a common molecular response mechanism against Cd and As toxicity, 30-day seedlings (Oryza sativa L. indica) were exposed separately to Cd and As 3+ in hydroponic cultures for up to 7 days. Root transcriptomic analysis of plants exposed to Cd and As for 3 days revealed that a total of 2224 genes in rice roots responded to Cd stress, while 1503 genes responded to As stress. Of these, 841 genes responded to both stressors. The genes in common to Cd and As stress were associated with redox control, stress response, transcriptional regulation, transmembrane transport, signal transduction, as well as biosynthesis and metabolism of macromolecules and sulfur compounds. In plants exposed to Cd and As separately or in combination for 3 and 7 days, qRT-PCR verification revealed that the glutathione metabolism associated gene Os09g0367700 was significantly up-regulated with respect to unexposed controls and had a positive synergistic effect under combined Cd and As stress. In addition, the redox control related genes Os06g0216000, Os07g0638300 and Os01g0294500, the glutathione metabolism related gene Os01g0530900, the cell wall biogenesis related genes Os05g0247800, Os11g0592000 and Os03g0416200, the expression regulation related genes Os07g0597200 and Os02g0168200, and the transmembrane transport related genes Os04g0524500, also varied significantly with respect to an unexposed control and displayed synergistic effects after 7 days of simultaneous exposure to Cd and As. Our identification of a novel set of genes in rice which responded to both Cd and As 3+ stress may be of value in mitigating the toxicity of co-contaminated soils. These results also provide a deeper understanding of the molecular mechanisms involved in response to multi-metal/loids stress, and may be used in the genetic improvement of rice varieties.

KW - Arsenic

KW - Cadmium

KW - Common response gene

KW - RNA-seq

KW - Synergistic effect

UR - http://www.scopus.com/inward/record.url?scp=85061794835&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85061794835&partnerID=8YFLogxK

U2 - https://doi.org/10.1016/j.scitotenv.2019.02.281

DO - https://doi.org/10.1016/j.scitotenv.2019.02.281

M3 - Article

C2 - 30802660

VL - 666

SP - 445

EP - 460

JO - Science of the Total Environment

JF - Science of the Total Environment

SN - 0048-9697

ER -