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Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq.
BMC Plant Biol. 2019 Jun 11; 19(1):250.BP

Abstract

BACKGROUND

Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants.

RESULTS

In this study, a mutant displaying extremely low Cd accumulation (lcd1) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5. This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant.

CONCLUSIONS

An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding.

Authors+Show Affiliations

Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China. happycaozhen520@163.com.Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China.Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China.Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China.Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China.Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou 310006, PR, No.28 Shuidaosuo Rd., Fuyang, 311400, Zhejiang, China. cmingxue@126.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31185911

Citation

Cao, Zhen Zhen, et al. "Gene Identification and Transcriptome Analysis of Low Cadmium Accumulation Rice Mutant (lcd1) in Response to Cadmium Stress Using MutMap and RNA-seq." BMC Plant Biology, vol. 19, no. 1, 2019, p. 250.
Cao ZZ, Lin XY, Yang YJ, et al. Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq. BMC Plant Biol. 2019;19(1):250.
Cao, Z. Z., Lin, X. Y., Yang, Y. J., Guan, M. Y., Xu, P., & Chen, M. X. (2019). Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq. BMC Plant Biology, 19(1), 250. https://doi.org/10.1186/s12870-019-1867-y
Cao ZZ, et al. Gene Identification and Transcriptome Analysis of Low Cadmium Accumulation Rice Mutant (lcd1) in Response to Cadmium Stress Using MutMap and RNA-seq. BMC Plant Biol. 2019 Jun 11;19(1):250. PubMed PMID: 31185911.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq. AU - Cao,Zhen Zhen, AU - Lin,Xiao Yan, AU - Yang,Yong Jie, AU - Guan,Mei Yan, AU - Xu,Ping, AU - Chen,Ming Xue, Y1 - 2019/06/11/ PY - 2019/03/13/received PY - 2019/06/03/accepted PY - 2019/6/13/entrez PY - 2019/6/13/pubmed PY - 2019/7/17/medline KW - Cadmium KW - MutMap KW - RNA-seq KW - Rice (Oryza sativa L.) KW - SNP KW - Transcriptome analysis SP - 250 EP - 250 JF - BMC plant biology JO - BMC Plant Biol VL - 19 IS - 1 N2 - BACKGROUND: Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants. RESULTS: In this study, a mutant displaying extremely low Cd accumulation (lcd1) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5. This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant. CONCLUSIONS: An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/31185911/Gene_identification_and_transcriptome_analysis_of_low_cadmium_accumulation_rice_mutant__lcd1__in_response_to_cadmium_stress_using_MutMap_and_RNA_seq_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-1867-y DB - PRIME DP - Unbound Medicine ER -