Transcriptome Analysis Reveals the Roles of Stem Nodes in Cadmium Transport to Rice Grain

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Feb 8

PMID 32028884

Citations 14

Authors

Ailing Liu

Zhibo Zhou

Yake Yi

Guanghui Chen

Affiliations

Soon will be listed here.

Abstract

Background: Node is the central organ of transferring nutrients and ions in plants. Cadmium (Cd) induced crop pollution threatens the food safety. Breeding of low Cd accumulation cultivar is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 (low Cd accumulation cultivar) and Yuzhenxiang (high Cd accumulation cultivar). RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs.

Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node I had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4535 DEGs and 70 miRNAs between the two cultivars. Most genesrelated to the "transporter activity", such as OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1, play roles in blocking the upward transport of Cd. Among the genes related to "response to stimulus", we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) in Xiangwanxian No. 12 played a potent role in lowering Cd accumulation via down regulating the expression of candidate genes, such as bZIP, ERF, MYB, SnRK1 and HSPs.

Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in Cd stress response.

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References

Chen N . Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2008; Chapter 4:Unit 4.10. DOI: 10.1002/0471250953.bi0410s05. View

Chen C, Lv X, Li J, Yi H, Gong J . Arabidopsis NRT1.5 is another essential component in the regulation of nitrate reallocation and stress tolerance. Plant Physiol. 2012; 159(4):1582-90. PMC: 3425198. DOI: 10.1104/pp.112.199257. View

Huang Y, Shen C, Chen J, He C, Zhou Q, Tan X . Comparative Transcriptome Analysis of Two Ipomoea aquatica Forsk. Cultivars Targeted To Explore Possible Mechanism of Genotype-Dependent Accumulation of Cadmium. J Agric Food Chem. 2016; 64(25):5241-50. DOI: 10.1021/acs.jafc.6b01267. View

Chen Y, Zhi J, Zhang H, Li J, Zhao Q, Xu J . Transcriptome analysis of Phytolacca americana L. in response to cadmium stress. PLoS One. 2017; 12(9):e0184681. PMC: 5595333. DOI: 10.1371/journal.pone.0184681. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Wang C, Mo Z, Wang H, Wang Z, Cao Z . The transportation, time-dependent distribution of heavy metals in paddy crops. Chemosphere. 2003; 50(6):717-23. DOI: 10.1016/s0045-6535(02)00211-4. View

Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T . Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2010; 27(3):431-2. PMC: 3031041. DOI: 10.1093/bioinformatics/btq675. View

Sharma D, Tiwari M, Lakhwani D, Tripathi R, Trivedi P . Differential expression of microRNAs by arsenate and arsenite stress in natural accessions of rice. Metallomics. 2014; 7(1):174-87. DOI: 10.1039/c4mt00264d. View

Yamaji N, Ma J . The node, a hub for mineral nutrient distribution in graminaceous plants. Trends Plant Sci. 2014; 19(9):556-63. DOI: 10.1016/j.tplants.2014.05.007. View

10.

Guan M, Fan S, Fang X, Jin C . Modification of nitrate uptake pathway in plants affects the cadmium uptake by roots. Plant Signal Behav. 2015; 10(3):e990794. PMC: 4622925. DOI: 10.4161/15592324.2014.990794. View

11.

Steudle E . THE COHESION-TENSION MECHANISM AND THE ACQUISITION OF WATER BY PLANT ROOTS. Annu Rev Plant Physiol Plant Mol Biol. 2001; 52:847-875. DOI: 10.1146/annurev.arplant.52.1.847. View

12.

Denman R . Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques. 1993; 15(6):1090-5. View

13.

Connorton J, Jones E, Rodriguez-Ramiro I, Fairweather-Tait S, Uauy C, Balk J . Wheat Vacuolar Iron Transporter TaVIT2 Transports Fe and Mn and Is Effective for Biofortification. Plant Physiol. 2017; 174(4):2434-2444. PMC: 5543970. DOI: 10.1104/pp.17.00672. View

14.

Wan X, Steudle E, Hartung W . Gating of water channels (aquaporins) in cortical cells of young corn roots by mechanical stimuli (pressure pulses): effects of ABA and of HgCl2. J Exp Bot. 2004; 55(396):411-22. DOI: 10.1093/jxb/erh051. View

15.

Ueno D, Yamaji N, Kono I, Huang C, Ando T, Yano M . Gene limiting cadmium accumulation in rice. Proc Natl Acad Sci U S A. 2010; 107(38):16500-5. PMC: 2944702. DOI: 10.1073/pnas.1005396107. View

16.

Wang M, Chen A, Wong M, Qiu R, Cheng H, Ye Z . Cadmium accumulation in and tolerance of rice (Oryza sativa L.) varieties with different rates of radial oxygen loss. Environ Pollut. 2011; 159(6):1730-6. DOI: 10.1016/j.envpol.2011.02.025. View

17.

Gu C, Liu L, Song A, Liu Z, Zhang Y, Huang S . Iris lactea var. chinensis (Fisch.) cysteine-rich gene llCDT1 enhances cadmium tolerance in yeast cells and Arabidopsis thaliana. Ecotoxicol Environ Saf. 2018; 157:67-72. DOI: 10.1016/j.ecoenv.2018.03.059. View

18.

Tang L, Mao B, Li Y, Lv Q, Zhang L, Chen C . Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Sci Rep. 2017; 7(1):14438. PMC: 5663754. DOI: 10.1038/s41598-017-14832-9. View

19.

Li J, Fu Y, Pike S, Bao J, Tian W, Zhang Y . The Arabidopsis nitrate transporter NRT1.8 functions in nitrate removal from the xylem sap and mediates cadmium tolerance. Plant Cell. 2010; 22(5):1633-46. PMC: 2899866. DOI: 10.1105/tpc.110.075242. View

20.

Fahlgren N, Carrington J . miRNA Target Prediction in Plants. Methods Mol Biol. 2009; 592:51-7. DOI: 10.1007/978-1-60327-005-2_4. View