Publications by authors named "Qian Qian"

353 Publications

A β-Ketoacyl carrier protein reductase confers heat tolerance via the regulation of fatty acid biosynthesis and stress signaling in rice.

New Phytol 2021 Jul 14. Epub 2021 Jul 14.

College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.

Heat stress is a major environmental threat affecting crop growth and productivity. However, the molecular mechanisms associated with plant response to heat stress are poorly understood. Here, we identified a heat stress-sensitive mutant, hts1, in rice. HTS1 encodes a thylakoid membrane-localized β-ketoacyl carrier protein reductase (KAR) involved in de novo fatty acid biosynthesis. Phylogenetic and bioinformatic analysis showed that HTS1 likely originated from streptophyte algae and is evolutionarily conserved in land plants. Thermostable HTS1 is predominantly expressed in green tissues and strongly induced by heat stress but is less responsive to salinity, cold and drought treatments. An amino acid substitution at A254T in HTS1 causes a significant decrease in KAR enzymatic activity and, consequently, impairs fatty acid synthesis and lipid metabolism in the hts1 mutant, especially under heat stress. Compared to the wild-type, hts1 exhibited heat-induced higher H O accumulation, a larger Ca influx to mesophyll cells and more damage to membranes and chloroplasts. Also, disrupted heat stress signaling in the hts1 mutant depresses the transcriptional activation of HsfA2s and the downstream target genes. We propose that HTS1 is critical for underpinning membrane stability, chloroplast integrity, and stress signaling for heat tolerance in rice.
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http://dx.doi.org/10.1111/nph.17619DOI Listing
July 2021

Decoding of Motor Coordination Imagery Involving the Lower Limbs by the EEG-Based Brain Network.

Comput Intell Neurosci 2021 23;2021:5565824. Epub 2021 Jun 23.

Brain Cognition and Brain-computer Intelligence Integration Group, Kunming University of Science and Technology, Kunming 650500, China.

Compared with the efficacy of traditional physical therapy, a new therapy utilizing motor imagery can induce brain plasticity and allows partial recovery of motor ability in patients with hemiplegia after stroke. Here, we proposed an updated paradigm utilizing motor coordination imagery involving the lower limbs (normal gait imagery and hemiplegic gait imagery after stroke) and decoded such imagery via an electroencephalogram- (EEG-) based brain network. Thirty subjects were recruited to collect EEGs during motor coordination imagery involving the lower limbs. Time-domain analysis, power spectrum analysis, time-frequency analysis, brain network analysis, and statistical analysis were used to explore the neural mechanisms of motor coordination imagery involving the lower limbs. Then, EEG-based brain network features were extracted, and a support vector machine was used for decoding. The results showed that the two employed motor coordination imageries mainly activated sensorimotor areas; the frequency band power was mainly concentrated within theta and alpha bands, and brain functional connections mainly occurred in the right forehead. The combination of the network attributes of the EEG-based brain network and the spatial features of the adjacency matrix had good separability for the two kinds of gait imagery ( < 0.05), and the average classification accuracy of the combination feature was 92.96% ± 7.54%. Taken together, our findings suggest that brain network features can be used to identify normal gait imagery and hemiplegic gait imagery after stroke.
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http://dx.doi.org/10.1155/2021/5565824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245246PMC
June 2021

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan.

Sci China Life Sci 2021 Jun 28. Epub 2021 Jun 28.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two "golden quality" rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the "golden quality" rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.
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http://dx.doi.org/10.1007/s11427-020-1940-9DOI Listing
June 2021

Sequencing and analysis of the complete mitochondrial genome of the lesser bandicoot rat () from China and its phylogenetic analysis.

Mitochondrial DNA B Resour 2021 Jun 21;6(7):2063-2065. Epub 2021 Jun 21.

College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China.

The complete mitogenome sequence of the lesser bandicoot rat ( Gray and Hardwicke, 1833) was determined using long PCR. The genome was 16,327 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (34.2%), C (24.9%), T (28.5%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the genetic background. The two species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
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http://dx.doi.org/10.1080/23802359.2021.1942273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8218843PMC
June 2021

A Novel miR167a-OsARF6-OsAUX3 Module Regulates Grain Length and Weight in Rice.

Mol Plant 2021 Jun 26. Epub 2021 Jun 26.

State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China. Electronic address:

Grain size is one of the most import factors of controlling rice yield, as it is associated with grain weight (GW). To date, several rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Herein, a quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB), and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter, and loss-of-function of OsAUX3 led to increased GL and GW. RNA-sequencing, gene expression quantification, dual-luciferase reporter assay, chromatin immunoprecipitation-quantitative polymerase chain reaction, and yeast one-hybrid assay demonstrated that OsARF6 is an upstream transcription factor of OsAUX3. OsARF6 directly binds to the auxin response elements of the OsAUX3 promoter, covering a single nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, thereby controlling GL by altering longitudinal expansion and auxin distribution/content in glume cells. miR167a was also confirmed to positively regulate GL and GW by directing OsARF6 mRNA silencing. Therefore, the miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, representing a potential target for improving rice yield.
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http://dx.doi.org/10.1016/j.molp.2021.06.023DOI Listing
June 2021

Primary root and root hair development regulation by OsAUX4 and its participation in the phosphate starvation response.

J Integr Plant Biol 2021 Jun 10. Epub 2021 Jun 10.

State Key Laboratory of Plant Physiology and Biochemistry, College of ZZ Sciences, Zhejiang University, Hangzhou, 310058, China.

Among the five members of AUX1/LAX genes coding for auxin carriers in rice, only OsAUX1 and OsAUX3 have been reported. To understand the function of the other AUX1/LAX genes, two independent alleles of osaux4 mutants, osaux4-1, and osaux4-2, were constructed using the CRISPR/Cas9 editing system. Homozygous osaux4-1 or osaux4-2 exhibited shorter primary root (PR) and longer root hair (RH) compared to the wild-type Dongjin (WT/DJ), and lost response to IAA treatment. OsAUX4 is intensively expressed in roots and localized on the plasma membrane, suggesting that OsAUX4 might function in the regulation of root development. The decreased meristem cell division activity and the downregulated expression of cell cycle genes in root apices of osaux4 mutants supported the hypothesis that OsAUX4 positively regulates PR elongation. OsAUX4 is expressed in RH, and osaux4 mutants showing longer RH compared to WT/DJ implies that OsAUX4 negatively regulates RH development. Furthermore, osaux4 mutants are insensitive to phosphate starvation (-Pi) and OsAUX4 effects on the -Pi response is associated with altered expression levels of Pi starvation regulated genes, and auxin distribution/contents. This study revealed that OsAUX4 not only regulates PR and RH development but also plays a regulatory role in crosstalk between auxin and -Pi signaling. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1111/jipb.13142DOI Listing
June 2021

CD151 drives cancer progression depending on integrin α3β1 through EGFR signaling in non-small cell lung cancer.

J Exp Clin Cancer Res 2021 Jun 9;40(1):192. Epub 2021 Jun 9.

Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.

Background: Tetraspanins CD151, a transmembrane 4 superfamily protein, has been identified participating in the initiation of a variety of cancers. However, the precise function of CD151 in non-small cell lung cancer (NSCLC) remains unclear. Here, we addressed the pro-tumoral role of CD151 in NSCLC by targeting EGFR/ErbB2 which favors tumor proliferation, migration and invasion.

Methods: First, the mRNA expression levels of CD151 in NSCLC tissues and cell lines were measured by RT-PCR. Meanwhile, CD151 and its associated proteins were analyzed by western blotting. The expression levels of CD151 in NSCLC samples and its paired adjacent lung tissues were then verified by Immunohistochemistry. The protein interactions are evaluated by co-immunoprecipitation. Flow cytometry was applied to cell cycle analysis. CCK-8, EdU Incorporation, and clonogenic assays were used to analyze cell viability. Wound healing, transwell migration, and matrigel invasion assays were utilized to assess the motility of tumor cells. To investigate the role of CD151 in vivo, lung carcinoma xenograft mouse model was applied.

Results: High CD151 expression was identified in NSCLC tissues and cell lines, and its high expression was significantly associated with poor prognosis of NSCLC patients. Further, knockdown of CD151 in vitro inhibited tumor proliferation, migration, and invasion. Besides, inoculation of nude mice with CD151-overexpressing tumor cells exhibited substantial tumor proliferation compared to that in control mice which inoculated with vector-transfected tumor cells. Noteworthy, we found that overexpression of CD151 conferred cell migration and invasion by interacting with integrins. We next sought to demonstrate that CD151 regulated downstream signaling pathways via activation of EGFR/ErbB2 in NSCLC cells. Therefore, we infer that CD151 probably affects the sensitivity of NSCLC in response to anti-cancer drugs.

Conclusions: Based on these results, we demonstrated a new mechanism of CD151-mediated tumor progression by targeting EGFR/ErbB2 signaling pathway, by which CD151 promotes NSCLC proliferation, migration, and invasion, which may considered as a potential target of NSCLC treatment.
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http://dx.doi.org/10.1186/s13046-021-01998-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8191020PMC
June 2021

, a new executor gene that confers durable and broad-spectrum resistance to bacterial blight disease in rice.

Plant Commun 2021 May 9;2(3):100143. Epub 2021 Jan 9.

College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.

Bacterial blight (BB) is a globally devastating rice disease caused by pv. (). The use of disease resistance () genes in rice breeding is an effective and economical strategy for the control of this disease. Nevertheless, a majority of genes lack durable resistance for long-term use under global warming conditions. Here, we report the isolation of a novel executor gene, , that confers extremely durable, broad-spectrum, and heat-tolerant resistance to . The expression of was induced by incompatible strains that secreted the transcription activator-like effector (TALE) AvrXa7 or PthXo3, which recognized effector binding elements (EBEs) in the promoter. Furthermore, induction was faster and stronger under high temperatures. Overexpression of or co-transformation of with triggered a hypersensitive response in plants. Constitutive expression of activated a defense response in the absence of but inhibited the growth of transgenic rice plants. In addition, analysis of over 3000 rice varieties showed that the locus was found primarily in the and subgroups. A variation consisting of an 11-bp insertion and a base substitution (G to T) was found in in the tested varieties, resulting in a loss of BB resistance. Through a decade of effort, we have identified an important BB resistance gene and characterized its distinctive interaction with strains; these findings will greatly facilitate research on the molecular mechanism of -mediated resistance and promote the use of this valuable gene in breeding.
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http://dx.doi.org/10.1016/j.xplc.2021.100143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8132130PMC
May 2021

Rice Ferredoxins localize to chloroplasts/plastids and may function in different tissues.

Plant Signal Behav 2021 Sep 14;16(9):1926813. Epub 2021 May 14.

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.

Ferredoxins (Fds) play a unique and important role in photosynthetic electron transport. Recently, we characterized the function of Fd1 in rice ( L.), showing that Fd1 is the primary photosynthetic electron transport protein and that Fd1 participates in carbon assimilation. However, the subcellular localization and specific functions of other Fds in rice are not yet fully understood. Here, our subcellular localization analysis of the seven Fds in rice showed that they are located in the chloroplasts of photosynthetic tissues and the plastids of non-photosynthetic tissues. Moreover, qRT-PCR indicated that transcript levels were highest in photosynthetic tissues, while transcript levels were highest in non-photosynthetic tissues. Collectively, our results suggest that rice Fds are located in chloroplasts/plastids, but may function in different tissues, and Fd4 may be a non-photosynthetic type Fd.
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http://dx.doi.org/10.1080/15592324.2021.1926813DOI Listing
September 2021

Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought tolerance in rice.

Mol Plant 2021 May 4. Epub 2021 May 4.

State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China. Electronic address:

Drought is the leading environmental threat affecting crop productivity, and plants have evolved a series of mechanisms to adapt to drought stress. The FT-interacting proteins (FTIPs) and phosphatidylethanolamine-binding proteins (PEBPs) play key roles in developmental processes, whereas their roles in the regulation of stress response are still largely unknown. Here, we report that OsFTIP1 negatively regulates drought response in rice. We showed that OsFTIP1 interacts with rice MOTHER OF FT AND TFL1 (OsMFT1), a PEBP that promotes rice tolerance to drought treatment. Further studies discovered that OsMFT1 interacts with two key drought-related transcription factors, OsbZIP66 and OsMYB26, regulating their binding capacity on drought-related genes and thereby enhancing drought tolerance in rice. Interestingly, we found that OsFTIP1 impedes the nucleocytoplasmic translocation of OsMFT1, implying that dynamic modulation of drought-responsive genes by the OsMFT1-OsMYB26 and OsMFT1-OsbZIP66 complexes is integral to OsFTIP1-modulated nuclear accumulation of OsMFT1. Our findings also suggest that OsMFT1 might act as a hitherto unknown nucleocytoplasmic trafficking signal that regulates drought tolerance in rice in response to environmental signals.
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http://dx.doi.org/10.1016/j.molp.2021.05.001DOI Listing
May 2021

NF-YCs modulate histone variant H2A.Z deposition to regulate photomorphogenic growth in Arabidopsis.

J Integr Plant Biol 2021 Jun 3;63(6):1120-1132. Epub 2021 Jun 3.

Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China.

In plants, light signals trigger a photomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2A.Z, which functions in transcriptional regulation, is deposited in chromatin by the SWI2/SNF2-RELATED 1 complex (SWR1c). However, the role of H2A.Z in photomorphogenesis and its deposition mechanism remain unclear. Here, we show that in Arabidopsis thaliana, H2A.Z deposition at its target loci is induced by light irradiation via NUCLEAR FACTOR-Y, subunit C (NF-YC) proteins, thereby inhibiting photomorphogenic growth. NF-YCs physically interact with ACTIN-RELATED PROTEIN6 (ARP6), a key component of the SWR1c that is essential for depositing H2A.Z, in a light-dependent manner. NF-YCs and ARP6 function together as negative regulators of hypocotyl growth by depositing H2A.Z at their target genes during photomorphogenesis. Our findings reveal an important role for the histone variant H2A.Z in photomorphogenic growth and provide insights into a novel transcription regulatory node that mediates H2A.Z deposition to control plant growth in response to changing light conditions.
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http://dx.doi.org/10.1111/jipb.13109DOI Listing
June 2021

The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice.

Mol Plant 2021 Apr 27. Epub 2021 Apr 27.

State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China. Electronic address:

Regulation of seed size is a key strategy for improving crop yield and is also a basic biological question. However, the molecular mechanisms by which plants determine their seed size remain elusive. Here, we report that the GW2-WG1-OsbZIP47 regulatory module controls grain width and weight in rice. WG1, which encodes a glutaredoxin protein, promotes grain growth by increasing cell proliferation. Interestingly, WG1 interacts with the transcription factor OsbZIP47 and represses its transcriptional activity by associating with the transcriptional co-repressor ASP1, indicating that WG1 may act as an adaptor protein to recruit the transcriptional co-repressor. In contrary, OsbZIP47 restricts grain growth by decreasing cell proliferation. Further studies reveal that the E3 ubiquitin ligase GW2 ubiquitinates WG1 and targets it for degradation. Genetic analyses confirm that GW2, WG1, and OsbZIP47 function in a common pathway to control grain growth. Taken together, our findings reveal a genetic and molecular framework for the control of grain size and weight by the GW2-WG1-OsbZIP47 regulatory module, providing new targets for improving seed size and weight in crops.
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http://dx.doi.org/10.1016/j.molp.2021.04.011DOI Listing
April 2021

The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice.

Mol Plant 2021 Jun 27;14(6):1012-1023. Epub 2021 Apr 27.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China. Electronic address:

The genetic improvement of nitrogen use efficiency (NUE) of crops is vital for grain productivity and sustainable agriculture. However, the regulatory mechanism of NUE remains largely elusive. Here, we report that the rice Grain number, plant height, and heading date7 (Ghd7) gene genetically acts upstream of ABC1 REPRESSOR1 (ARE1), a negative regulator of NUE, to positively regulate nitrogen utilization. As a transcriptional repressor, Ghd7 directly binds to two Evening Element-like motifs in the promoter and intron 1 of ARE1, likely in a cooperative manner, to repress its expression. Ghd7 and ARE1 display diurnal expression patterns in an inverse oscillation manner, mirroring a regulatory scheme based on these two loci. Analysis of a panel of 2656 rice varieties suggests that the elite alleles of Ghd7 and ARE1 have undergone diversifying selection during breeding. Moreover, the allelic distribution of Ghd7 and ARE1 is associated with the soil nitrogen deposition rate in East Asia and South Asia. Remarkably, the combination of the Ghd7 and ARE1 elite alleles substantially improves NUE and yield performance under nitrogen-limiting conditions. Collectively, these results define a Ghd7-ARE1-based regulatory mechanism of nitrogen utilization, providing useful targets for genetic improvement of rice NUE.
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http://dx.doi.org/10.1016/j.molp.2021.04.012DOI Listing
June 2021

[Human factors engineering of brain-computer interface and its applications: Human-centered brain-computer interface design and evaluation methodology].

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2021 Apr;38(2):210-223

School of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650500, P.R.China.

Brain-computer interface (BCI) is a revolutionizing human-computer Interaction, which is developing towards the direction of intelligent brain-computer interaction and brain-computer intelligent integration. However, the practical application of BCI is facing great challenges. The maturity of BCI technology has not yet reached the needs of users. The traditional design method of BCI needs to be improved. It is necessary to pay attention to BCI human factors engineering, which plays an important role in narrowing the gap between research and practical application, but it has not attracted enough attention and has not been specifically discussed in depth. Aiming at BCI human factors engineering, this article expounds the design requirements (from users), design ideas, objectives and methods, as well as evaluation indexes of BCI with the human-centred-design. BCI human factors engineering is expected to make BCI system design under different use conditions more in line with human characteristics, abilities and needs, improve the user satisfaction of BCI system, enhance the user experience of BCI system, improve the intelligence of BCI, and make BCI move towards practical application.
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http://dx.doi.org/10.7507/1001-5515.202101093DOI Listing
April 2021

OsMORF9 is necessary for chloroplast development and seedling survival in rice.

Plant Sci 2021 Jun 7;307:110907. Epub 2021 Apr 7.

State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. Electronic address:

Chloroplasts are closely associated with the growth and development of higher plants. Accumulating evidence has revealed that the multiple organellar RNA editing factors (MORF) family of proteins influences plastidic and mitochondrial development through post-transcriptional regulation. However, the role of MORFs in regulating the development of chloroplasts in rice is still unclear. The OsMORF9 gene belongs to a small family of 7 genes in rice and is highly expressed in young leaves. We used the CRISPR/Cas9 system to mutate OsMORF9. The resulting knockout lines osmorf9-1 and osmorf9-2 exhibited an albino seedling lethal phenotype. Besides, the expression of many plastid-encoded genes involved in photosynthesis, the biogenesis of plastidic ribosomes and the editing and splicing of specific plastidic RNA molecules were severely affected in these two OsMORF9 mutants. Furthermore, yeast two-hybrid analysis revealed that OsMORF9 could interact with OsSLA4 and DUA1 which are members of the pentatricopeptide repeat (PPR) family of proteins. Analysis of subcellular localization of OsMORF9 also suggested that it might function in chloroplasts. The findings from the present study demonstrated the critical role of OsMORF9 in the biogenesis of chloroplast ribosomes, chloroplast development and seedling survival. This therefore provides new insights on the function of MORF proteins in rice.
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http://dx.doi.org/10.1016/j.plantsci.2021.110907DOI Listing
June 2021

The gibberellin signaling negative regulator RGA-LIKE3 promotes seed storage protein accumulation.

Plant Physiol 2021 Apr;185(4):1697-1707

Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China.

Seed storage protein (SSP) acts as one of the main components of seed storage reserves, of which accumulation is tightly mediated by a sophisticated regulatory network. However, whether and how gibberellin (GA) signaling is involved in this important biological event is not fully understood. Here, we show that SSP content in Arabidopsis (Arabidopsis thaliana) is significantly reduced by GA and increased in the GA biosynthesis triple mutant ga3ox1/3/4. Further investigation shows that the DELLA protein RGA-LIKE3 (RGL3), a negative regulator of GA signaling, is important for SSP accumulation. In rgl3 and 35S:RGL3-HA, the expression of SSP genes is down- and upregulated, respectively, compared with that in the wild-type. RGL3 interacts with ABSCISIC ACID INSENSITIVE3 (ABI3), a critical transcription factor for seed developmental processes governing SSP accumulation, both in vivo and in vitro, thus greatly promoting the transcriptional activating ability of ABI3 on SSP genes. In addition, genetic evidence shows that RGL3 and ABI3 regulate SSP accumulation in an interdependent manner. Therefore, we reveal a function of RGL3, a little studied DELLA member, as a coactivator of ABI3 to promote SSP biosynthesis during seed maturation stage. This finding advances the understanding of mechanisms in GA-mediated seed storage reserve accumulation.
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http://dx.doi.org/10.1093/plphys/kiaa114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133674PMC
April 2021

The mutation disrupts tryptophan metabolism and induces cell death.

Plant Signal Behav 2021 Jun 26;16(6):1905336. Epub 2021 Mar 26.

State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P. R. China.

Tryptophan metabolism pathways are important components of the plant immune system; for example, serotonin is derived from tryptophan, and plays a vital role in rice () innate immunity. Recently, we isolated a rice mutant, (), which exhibits lesions. RNA-seq analysis revealed that KEGG pathways related to amino acid metabolism were significantly enriched in the transcripts differentially expressed in this mutant. Furthermore, measurements of free amino acid contents revealed the accumulated tryptophan of mutant. In addition, the transcript levels of genes related to tryptophan biosynthesis were significantly enhanced in the mutant. These results revealed that plays a critical role in tryptophan metabolism. Based on these findings, it is revealed that loss of function may disrupt tryptophan metabolism, thereby inducing cell death and forming lesions in rice.
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http://dx.doi.org/10.1080/15592324.2021.1905336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143217PMC
June 2021

The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice.

Plant Cell 2021 May;33(4):1212-1228

State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

Panicle size and grain number are important agronomic traits and influence grain yield in rice (Oryza sativa), but the molecular and genetic mechanisms underlying panicle size and grain number control remain largely unknown in crops. Here we report that LARGE2 encodes a HECT-domain E3 ubiquitin ligase OsUPL2 and regulates panicle size and grain number in rice. The loss of function large2 mutants produce large panicles with increased grain number, wide grains and leaves, and thick culms. LARGE2 regulates panicle size and grain number by repressing meristematic activity. LARGE2 is highly expressed in young panicles and grains. Biochemical analyses show that LARGE2 physically associates with ABERRANT PANICLE ORGANIZATION1 (APO1) and APO2, two positive regulators of panicle size and grain number, and modulates their stabilities. Genetic analyses support that LARGE2 functions with APO1 and APO2 in a common pathway to regulate panicle size and grain number. These findings reveal a novel genetic and molecular mechanism of the LARGE2-APO1/APO2 module-mediated control of panicle size and grain number in rice, suggesting that this module is a promising target for improving panicle size and grain number in crops.
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http://dx.doi.org/10.1093/plcell/koab041DOI Listing
May 2021

A novel Arabidopsis gene RGAT1 is required for GA-mediated tapetum and pollen development.

New Phytol 2021 07 30;231(1):137-151. Epub 2021 Mar 30.

Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, 510650, China.

The phytohormone gibberellin (GA) is critical for anther development. RGA, a member of the DELLA family of proteins that are central GA signalling repressors, is a key regulator of male fertility in plants. However, the downstream genes in GA-RGA-mediated anther development remain to be characterised. We identified RGA Target 1 (RGAT1), a novel Arabidopsis gene, that functions as an important RGA-regulated target in pollen development. RGAT1 is predominantly expressed in the tapetum and microspores during anther stages 8-11, and can be directly activated by RGA and suppressed by GA in inflorescence apices. Both loss of function and gain of function of RGAT1 led to abnormal tapetum development, resulting in abortive pollen and short siliques. In RGAT1-knockdown and overexpression lines, pollen abortion occurred at stage 10. Loss of RGAT1 function induced the premature degeneration of tapetal cells with defective ER-derived tapetosomes, while RGAT1 overexpression delayed tapetum degeneration. TUNEL assay confirmed that RGAT1 participates in timely tapetal programmed cell death. Moreover, reducing RGAT1 expression partially rescued the tapetal developmental defects in GA-deficient ga1-3 mutant. Our findings revealed that RGAT1 is a direct target of RGA and plays an essential role in GA-mediated tapetum and pollen development.
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http://dx.doi.org/10.1111/nph.17314DOI Listing
July 2021

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress.

BMC Plant Biol 2021 Feb 9;21(1):85. Epub 2021 Feb 9.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Background: Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.

Result: Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.

Conclusions: The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.
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http://dx.doi.org/10.1186/s12870-021-02857-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874481PMC
February 2021

A route to de novo domestication of wild allotetraploid rice.

Cell 2021 Mar 3;184(5):1156-1170.e14. Epub 2021 Feb 3.

State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China. Electronic address:

Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.
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http://dx.doi.org/10.1016/j.cell.2021.01.013DOI Listing
March 2021

Reduction of essential amino acid levels and sex-specific alterations in serum amino acid concentration profiles in children with autism spectrum disorder.

Psychiatry Res 2021 03 24;297:113675. Epub 2020 Dec 24.

Child Developmental & Behavioral Center, The Third Affiliated Hospital of Sun Yat-sen University, 2693 Kaichuang Avenue, Huangpu District, Guangzhou 510630, China. Electronic address:

Background: Existing evidence has shown that metabolic disturbances may be involved in the pathological process of autism spectrum disorder(ASD). This study aimed to investigate the alterations of serum amino acid concentration profiles in Chinese Han children with ASD.

Methods: Serum amino acid levels were measured using tandem mass spectrometry in 60 children with ASD and 30 typically developing (TD) controls. The Chinese Wechsler Young Children Scale of Intelligence (C-WYCSI) was used to evaluate the ASD subjects' intelligence quotient (IQ).

Results: The serum levels of essential amino acids and some non-essential amino acids (glutamine, glycine, alanine, citrulline, cysteine, serine, tyrosine, and proline) in the ASD group were significantly lower than those in controls. The serum glutamate/glutamine (Glu/Gln) ratio was elevated in the ASD PIQ≥70 group, while serum levels of alanine, cysteine, phenylalanine, methionine and proline were significantly higher in male children with ASD than that in the female group.

Conclusion: The study revealed that children with ASD exhibit alterations in the serum levels of certain amino acids, and the divergence can be sex-related or associated with different cognitive function, which might provide clues for further etiological research of ASD.
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http://dx.doi.org/10.1016/j.psychres.2020.113675DOI Listing
March 2021

Efficient deletion of multiple circle RNA loci by CRISPR-Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice.

Plant Biotechnol J 2021 06 28;19(6):1240-1252. Epub 2021 Jan 28.

Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

CRISPR-Cas9 is an emerging genome editing tool for reverse genetics in plants. However, its application for functional study of non-coding RNAs in plants is still at its infancy. Despite being a major class of non-coding RNAs, the biological roles of circle RNAs (circRNAs) remain largely unknown in plants. Previous plant circRNA studies have focused on identification and annotation of putative circRNAs, with their functions largely uninvestigated by genetic approaches. Here, we applied a multiplexed CRISPR-Cas9 strategy to efficiently acquire individual null mutants for four circRNAs in rice. We showed each of these rice circRNA loci (Os02circ25329, Os06circ02797, Os03circ00204 and Os05circ02465) can be deleted at 10% or higher efficiency in both protoplasts and stable transgenic T0 lines. Such high efficiency deletion enabled the generation of circRNA null allele plants without the CRISPR-Cas9 transgene in the T1 generation. Characterization of the mutants reveals these circRNAs' participation in salt stress response during seed germination and in particular the Os05circ02465 null mutant showed high salt tolerance. Notably, the seedlings of the Os06circ02797 mutant showed rapid growth phenotype after seed germination with the seedlings containing higher chlorophyll A/B content. Further molecular and computational analyses suggested a circRNA-miRNA-mRNA regulatory network where Os06circ02797 functions to bind and sequester OsMIR408, an important and conserved microRNA in plants. This study not only presents genetic evidence for the first time in plants that certain circRNAs may serve as sponges to negatively regulate miRNAs, a phenomenon previously demonstrated in mammalian cells, but also provides important insights for improving agronomic traits through gene editing of circRNA loci in crops.
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http://dx.doi.org/10.1111/pbi.13544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196656PMC
June 2021

The complete chloroplast genome of (Asteraceae), a rare subnival plant in Qinghai-Tibetan Plateau.

Mitochondrial DNA B Resour 2020 Oct 21;5(3):3581-3582. Epub 2020 Oct 21.

Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.

Maxim. is a subnival plant of Asteraceae with abundant medicinal and ecological value. Until now, few studies have been conducted on , especially in phylogenetic relationships and species identification. The cp genome had a typical quadripartite structure with a conserved genome arrangement. It was 152,500 bp in size, consisting of a large single copy (LSC) region of 83,553 bp and a small single copy (SSC) region of 18,545 bp, separated by a pair of inverted repeats (IRs) of 25,201 bp. It contained 113 unique genes, including 80 protein-coding genes (PCGs), 29 tRNA and four rRNA genes. The overall GC content was 37.67%. Moreover, a phylogenetic analysis, based on 48 complete cp genomes using Maximum Likelihood (ML) method, indicated that was relatively closed to and was well-clustered within genus .
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http://dx.doi.org/10.1080/23802359.2020.1829130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7594724PMC
October 2020

[An in vitro study on metabolic interaction between main active components of Salviae Miltiorrhizae Radix et Rhizoma and tacrolimus].

Zhongguo Zhong Yao Za Zhi 2020 Nov;45(21):5289-5295

Longhua Hospital, Shanghai University of Traditional Chinese Medicine Shanghai 200032, China.

The purpose of this study was to investigate the inhibitory effects of the main active components of Salviae Miltiorrhizae Radix et Rhizoma on the metabolism of tacrolimus mediated by CYP3 A4/5 enzyme, so as to predict the potential drug-drug interaction(DDI) in clinical use. First, the reversible inhibitory activities of five active components of Salviae Miltiorrhizae Radix et Rhizoma(tanshinone Ⅰ, tanshinone Ⅱ_A, cryptotanshinone, salvianolic acid B, dihydrotanshinone Ⅰ) on the metabolism of tacrolimus was investigated by using human liver microsomes(HLM) and recombinant human CYP3 A4/5 enzyme in vitro, then the dose-dependent inhibition of CYP3 A4/5 activity was calculated in HLM. Finally, the time-dependent inhibition(TDI) activities of five active components were studied in HLM through the robust single point inhibition test. In addition, a simple and rapid liquid chromatography tandem mass spectrometry method(HPLC-MS/MS) for the determination of tacrolimus was established in this study. The results showed that dihydrotanshinone Ⅰ had a strong inhibitory effect on the metabolism of tacrolimus in both HLM and rCYP3 A4/5 enzyme systems, and the inhibitory potential IC_(50) in HLM was 6.0 μmol·L~(-1), while the other four active components of Salviae Miltiorrhizae Radix et Rhizoma exhibited relatively weak inhibition on CYP3 A4/5 activity with inhibition rate less than 30% at 10 μmol·L~(-1). Furthermore, the TDI activity of five active components of Salviae Miltiorrhizae Radix et Rhizoma at 50 μmol·L~(-1) was 5.5%-15.9%. The above results suggested that clinical DDI between tacrolimus and Salviae Miltiorrhizae Radix et Rhizoma may occur when the active components of Salviae Miltiorrhizae Radix et Rhizoma achieved a relative high concentration in human. In conclusion, this study provided a data reference for the research on drug interaction of tacrolimus and Salviae Miltiorrhizae Radix et Rhizoma as well as rational drug use in clinical practice.
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http://dx.doi.org/10.19540/j.cnki.cjcmm.20200715.201DOI Listing
November 2020

[Active components and mechanism of Taohong Siwu Decoction in treatment of primary dysmenorrhea based on network pharmacology and molecular docking technology].

Zhongguo Zhong Yao Za Zhi 2020 Nov;45(22):5373-5382

Key Laboratory of Ministry of Education for the Standardization of Traditional Chinese Medicine, School of Pharmacy,Chengdu University of Traditional Chinese Medicine Chengdu 611137, China.

This paper aimed to investigate the active components and mechanism of Taohong Siwu Decoction in the treatment of primary dysmenorrhea(PD) based on network pharmacology and molecular docking technology. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) was used to search the chemical compositions and targets of six herbs in Taohong Siwu Decoction. The targets for PD treatment were selected through the databases of DrugBank, OMIM, TTD and CTD, and gene annotation of the targets was conducted with UniProt database. Cytoscape 3.7.2 was then used to construct the drug-compound-target network. The protein-protein interaction(PPI) network was constructed based on STRING, and the core targets of Taohong Siwu Decoction in the treatment of PD were selected according to the topological parameters. David database was used for GO enrichment analysis and KOBAS 3.0 was used for KEGG enrichment analysis. The molecular docking technology was used to connect the components with higher medium values in the network with core targets. The results showed that the network contained 36 compounds such as quercetin, kaempferol, luteolin, myricanone and ferulic acid, and 99 targets such as PTGS2, PTGS2, PGR and PPARG. Totally 102 GO terms were obtained by GO functional enrichment analysis(P<0.01), and 228 signal pathways were obtained by KEGG pathway enrichment(P<0.05), mainly involving inflammatory factors, hormone regulation, central analgesia, amino acid metabolism and spasmolysis. The results of molecular docking showed that the main active components can spontaneously bind to the targets. This study preliminarily revealed the mechanism of Taohong Siwu Decoction for treatment of primary dysmenorrheal through multi-components, multi-targets and multi-pathways, providing theoretical references for further researches on mechanism of Taohong Siwu Decoction.
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http://dx.doi.org/10.19540/j.cnki.cjcmm.20200723.401DOI Listing
November 2020

Community structure of bacterioplankton and its relationship with environmental factors in the upper reaches of the Heihe River in Qinghai Plateau.

Environ Microbiol 2021 02 5;23(2):1210-1221. Epub 2021 Jan 5.

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.

Planktonic microorganisms play a key role in the biogeochemical processes of the aquatic system, and they may be affected by many factors. High-throughput sequencing technology was used in this study to investigate and study the bacterioplankton community of water bodies in the upper reaches of the Heihe River Basin in Qinghai Plateau. Results showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the predominant phyla in this river section, while the main genera are Thiomonas, Acidibacillus, Acidocella, Rhodanobacter, Acidithiobacter and Gallionella, which are autochthonous in the acid-mine drainage. Additionally, total nitrogen, total phosphorus, permanganate index and pH are significantly correlated with the bacterioplankton abundance and are the main limiting factors for the spatial distribution of the bacterioplankton. PICRUSt inferred that the mainstream microbial assemblages had a higher abundance of KOs belong to metabolism of terpenoids and polyketides, while the tributary had higher abundance of KOs belong to the immune system. The relationship between bacterioplankton community composition and environmental factors in the Heihe River basin was discussed for the first time in this study, which provides a theoretical basis for the healthy, orderly development of the water environment in the Heihe River Basin.
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http://dx.doi.org/10.1111/1462-2920.15358DOI Listing
February 2021

The rice LRR-like1 protein YELLOW AND PREMATURE DWARF 1 is involved in leaf senescence induced by high light.

J Exp Bot 2021 02;72(5):1589-1605

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.

Senescence in plants is induced by endogenous physiological changes and exogenous stresses. In this study, we isolated two alleles of a novel rice (Oryza sativa) mutant, yellow and premature dwarf 1 (ypd1). The ypd1 mutants exhibited a yellow and dwarf phenotype from germination, and premature senescence starting at tillering. Moreover, the ypd1 mutants were sensitive to high light, which accelerated cell death and senescence. Consistent with their yellow phenotype, the ypd1 mutants had abnormal chloroplasts and lower levels of photosynthetic pigments. TUNEL assays together with histochemical staining demonstrated that ypd1 mutants showed cell death and that they accumulated reactive oxygen species. The ypd1 mutants also showed increased expression of genes associated with senescence. Map-based cloning revealed a G→A substitution in exon 6 (ypd1-1) and exon 13 (ypd1-2) of LOC_Os06g13050 that affected splicing and caused premature termination of the encoded protein. YPD1 was found to be preferentially expressed in the leaf and it encodes a LRR-like1 protein. Complementation, overexpression, and targeted deletion confirmed that the mutations in YPD1 caused the ypd1 phenotype. YPD1 was localized on the chloroplast membrane. Our results thus demonstrate that the novel rice LRR-like1 protein YPD1 affects chloroplast development and leaf senescence.
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http://dx.doi.org/10.1093/jxb/eraa532DOI Listing
February 2021

Disruption of EARLY LESION LEAF 1, encoding a cytochrome P450 monooxygenase, induces ROS accumulation and cell death in rice.

Plant J 2021 02 20;105(4):942-956. Epub 2020 Dec 20.

State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, P. R. China.

Lesion-mimic mutants (LMMs) provide a valuable tool to reveal the molecular mechanisms determining programmed cell death (PCD) in plants. Despite intensive research, the mechanisms behind PCD and the formation of lesions in various LMMs still remain to be elucidated. Here, we identified a rice (Oryza sativa) LMM, early lesion leaf 1 (ell1), cloned the causal gene by map-based cloning, and verified this by complementation. ELL1 encodes a cytochrome P450 monooxygenase, and the ELL1 protein was located in the endoplasmic reticulum. The ell1 mutant exhibited decreased chlorophyll contents, serious chloroplast degradation, upregulated expression of chloroplast degradation-related genes, and attenuated photosynthetic protein activity, indicating that ELL1 is involved in chloroplast development. RNA sequencing analysis showed that genes related to oxygen binding were differentially expressed in ell1 and wild-type plants; histochemistry and paraffin sectioning results indicated that hydrogen peroxide (H O ) and callose accumulated in the ell1 leaves, and the cell structure around the lesions was severely damaged, which indicated that reactive oxygen species (ROS) accumulated and cell death occurred in the mutant. TUNEL staining and comet experiments revealed that severe DNA degradation and abnormal PCD occurred in the ell1 mutants, which implied that excessive ROS accumulation may induce DNA damage and ROS-mediated cell death in the mutant. Additionally, lesion initiation in the ell1 mutant was light dependent and temperature sensitive. Our findings revealed that ELL1 affects chloroplast development or function, and that loss of ELL1 function induces ROS accumulation and lesion formation in rice.
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http://dx.doi.org/10.1111/tpj.15079DOI Listing
February 2021