scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2020 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Expression Patterns ◽  
Critical Role ◽  
Rice Grain ◽  
Rice Cultivars ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

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 4,535 DEGs and 70 miRNAs between the two cultivars. Most genes related 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.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Expression Patterns ◽  
Critical Role ◽  
Rice Grain ◽  
Rice Cultivars ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

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 4,535 DEGs and 70 miRNAs between the two cultivars. Most genes related 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.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation 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 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. 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 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. 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 stress response, which contribute to the response to Cd stress in rice.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation 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 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. 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 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes (OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1) related to the “transporter activity” play roles in blocking the upward transport of Cd in the low Cd-accumulative cultivar. 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) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP, ERF, MYB, SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. 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 stress response, which contribute to the response to Cd stress in rice.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V. bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V. bonariensis was analyzed as well as an overall analysis of transcriptome. Results In this study, the tolerance of V. bonariensis to Cd stress was investigated in four aspects: germination, development, physiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237, 866 transcripts and 191, 370 unigenes were constructed in the transcriptome data of V. bonariensis roots. The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis, but also for the improvement molecular breeding and phytoremediation.

scholarly journals Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events

Blood ◽  
2011 ◽  
Vol 118 (7) ◽  
pp. 1903-1911 ◽  
Author(s):  
Luca Cecchetti ◽  
Neal D. Tolley ◽  
Noemi Michetti ◽  
Loredana Bury ◽  
Andrew S. Weyrich ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Matrix Metalloproteinases ◽  
Mrna Expression ◽  
Vascular Remodeling ◽  
Differentially Express ◽  
Expression Patterns ◽  
Critical Role ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing

Abstract Megakaryocytes transfer a diverse and functional transcriptome to platelets during the final stages of thrombopoiesis. In platelets, these transcripts reflect the expression of their corresponding proteins and, in some cases, serve as a template for translation. It is not known, however, if megakaryocytes differentially sort mRNAs into platelets. Given their critical role in vascular remodeling and inflammation, we determined whether megakaryocytes selectively dispense transcripts for matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) into platelets. Next-generation sequencing (RNA-Seq) revealed that megakaryocytes express mRNA for 10 of the 24 human MMP family members. mRNA for all of these MMPs are present in platelets with the exception of MMP-2, 14, and 15. Megakaryocytes and platelets also express mRNA for TIMPs 1-3, but not TIMP-4. mRNA expression patterns predicted the presence and, in most cases, the abundance of each corresponding protein. Nonetheless, exceptions were observed: MMP-2 protein is present in platelets but not its transcript. In contrast, quiescent platelets express TIMP-2 mRNA but only traces of TIMP-2 protein. In response to activating signals, however, platelets synthesize significant amounts of TIMP-2 protein. These results demonstrate that megakaryocytes differentially express mRNAs for MMPs and TIMPs and selectively transfer a subset of these into platelets. Among the platelet messages, TIMP-2 serves as a template for signal-dependent translation.

scholarly journals Aspects of cultivar variation in physiological traits related to Cd distribution in rice plants with a short-term stress

2020 ◽  
Author(s):  
Wan-Ting Chiao ◽  
Bo-Ching Chen ◽  
Chien-Hui Syu ◽  
Kai-Wei Juang
Keyword(s):  
Shoot Growth ◽  
Rice Grain ◽  
Rice Cultivars ◽  
Cd Accumulation ◽  
Physiological Regulation ◽  
Rice Plants ◽  
Cd Contamination ◽  
Cultivar Variation ◽  
Cd Distribution ◽  
Cd Translocation

Abstract Background Genotypic variations are seen in cadmium (Cd) tolerance and accumulation in rice plants. Cultivars that show low Cd translocation from the root into shoot can be selected to reduce Cd contamination in rice grains. This study aims to clarify the physiological regulation related to Cd absorption by rice plants for screening out the cultivars, which have relatively low Cd accumulation in grains. Eight Taiwan mega cultivars of paddy rice: japonica (TY3, TK9, TNG71, and KH145 cultivars), indica (TCS10 and TCS17 cultivars), and glutinous (TKW1 and TKW3 cultivars), which are qualified with the criteria for rice grain quality by the Council of Agriculture, Taiwan, were used for illustration. An experiment in hydroponics was conducted for the rice seedlings with a treatment of 50 μM CdCl 2 for 7 days. Results and discussion After the Cd treatment, the reductions in shoot growth were more significant than those in root growth; however, Cd absorbed in the rice plant was sequestered much more in the root. The malondialdehyde (MDA) was preferentially accumulated in rice root but the hydrogen peroxide (H 2 O 2 ) was increased more significantly in the shoot; the antioxidative enzymes, superoxide dismutase (SOD) and ascorbate peroxidase (APX), were pronounced more in rice shoot. Conclusions The rice cultivars preferentially accumulated Cd in the root rather than the shoot with the Cd treatment, which resulted in significant enhancements of MDA and growth reductions in the root. However, H 2 O 2 accumulation was toward the shoot to retard shoot growth suddenly and then the root could keep a gradual growth. Also, the rice cultivars, which preferentially accumulate Cd in the root, would have the regulation tendency of SOD toward the shoot. Due to that SOD is responsible for H 2 O 2 production, H 2 O 2 accumulation would be thus toward the shoot. Moreover, the cultivars, which have a less regulation tendency of APX toward the shoot, would present higher translocation of Cd into the shoot.

Different tolerance of photosynthetic apparatus to Cd stress in two rice cultivars with the same leaf Cd accumulation

2019 ◽  
Vol 41 (12) ◽  
Author(s):  
Yang-Er Chen ◽  
Hao-Tian Mao ◽  
Nan Wu ◽  
Ahsin Khan ◽  
Atta Mohi Ud Din ◽  
...  
Keyword(s):  
Photosynthetic Apparatus ◽  
Rice Cultivars ◽  
Cd Stress ◽  
Cd Accumulation

scholarly journals Aspects of cultivar variation in physiological traits related to Cd distribution in rice plants with a short-term stress

2020 ◽  
Author(s):  
Wan-Ting Chiao ◽  
Bo-Ching Chen ◽  
Chien-Hui Syu ◽  
Kai-Wei Juang
Keyword(s):  
Shoot Growth ◽  
Rice Grain ◽  
Rice Cultivars ◽  
Cd Accumulation ◽  
Physiological Regulation ◽  
Rice Plants ◽  
Cd Contamination ◽  
Cultivar Variation ◽  
Cd Distribution ◽  
Cd Translocation

Abstract Background Genotypic variations are seen in Cd tolerance and accumulation in rice plants. Cultivars that show low Cd translocation from the root into shoot can be selected to reduce Cd contamination in rice grains. This study aims to clarify the physiological regulation related to cadmium (Cd) absorption by rice plants for screening out the cultivars, which have relatively low Cd accumulation in grains. Eight Taiwan mega cultivars of paddy rice: japonica (TY3, TK9, TNG71, and KH145 cultivars), indica (TCS10 and TCS17 cultivars), and glutinous (TKW1 and TKW3 cultivars), which are qualified with the criteria for rice grain quality by the Council of Agriculture, Taiwan, were used for illustration. An experiment in hydroponics was conducted for the rice seedlings with a treatment of 50 µM CdCl2 for 7 days. Results and discussion After the Cd treatment, the reductions in shoot growth were more significant than those in root growth; however, Cd absorbed in the rice plant was sequestered much more in the root. The malondialdehyde (MDA) was preferentially accumulated in rice root but the hydrogen peroxide (H2O2) was increased more significantly in the shoot; the antioxidative enzymes, superoxide dismutase (SOD) and ascorbate peroxidase (APX), were pronounced more in rice shoot. Conclusions The rice cultivars preferentially accumulated Cd in the root rather than the shoot with the Cd treatment, which resulted in significant enhancements of MDA and growth reductions in the root. However, H2O2 accumulation was toward the shoot to retard shoot growth suddenly and then the root could keep a gradual growth. Also, the rice cultivars, which preferentially accumulate Cd in the root, would have the regulation tendency of SOD toward the shoot. Due to that SOD is responsible for H2O2 production, H2O2 accumulation would be thus toward the shoot. Also, the cultivars, which have a less regulation tendency of APX toward the shoot, would present higher translocation of Cd into the shoot.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

2019 ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background: Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V.bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V.bonariensis was analyzed as well as overall analysis of transcriptome. Results: In this study, the tolerance of V.bonariensis to Cd stress was investigated in four aspects: germination, development, pysiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237,866 transcripts and 191,370 unigenes were constructed in the transcriptome data of V.bonariensis roots . The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis , but also for the improvement molecular breeding and phytoremediation.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

2019 ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background: Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V.bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V.bonariensis was analyzed as well as overall analysis of transcriptome. Results: In this study, the tolerance of V.bonariensis to Cd stress was investigated in four aspects: germination, development, pysiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237,866 transcripts and 191,370 unigenes were constructed in the transcriptome data of V.bonariensis roots . The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis , but also for the improvement molecular breeding and phytoremediation.

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