Publications by authors named "Chengcai Chu"

147 Publications

Overexpression of the rice ORANGE gene OsOR negatively regulates carotenoid accumulation, leads to higher tiller numbers and decreases stress tolerance in Nipponbare rice.

Plant Sci 2021 Sep 7;310:110962. Epub 2021 Jun 7.

Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China; College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing, China. Electronic address:

The ORANGE (OR) gene has been reported to regulate chromoplast differentiation and enhance carotenoid biosynthesis in many dicotyledonous plants. However, the function of the OR gene in monocotyledons, especially rice, is poorly known. Here, the OR gene from rice, OsOR, was isolated and characterized by generating overexpressing and genome editing mutant lines. The OsOR-overexpressing plants exhibited pleiotropic phenotypes, such as alternating transverse green and white sectors on leaves at the early tillering stage, that were due to changes in thylakoid development and reduced carotenoid content. In addition, the number of tillers significantly increased in OsOR-overexpressing plants but decreased in osor mutant lines, a result similar to that previously reported for the carotenoid isomerase mutant mit3. The expression of the DWARF3 and DWARF53 genes that are involved in the strigolactone signalling pathway were similarly downregulated in OsOR-overexpressing plants but upregulated in osor mutants. Moreover, the OsOR-overexpressing plants exhibited greater sensitivity to salt and cold stress, and had lower total chlorophyll and higher MDA contents. All results suggest that the OsOR gene plays an important role not only in carotenoid accumulation but also in tiller number regulation and in responses to environmental stress in rice.
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http://dx.doi.org/10.1016/j.plantsci.2021.110962DOI Listing
September 2021

Synergistic interplay of ABA and BR signal in regulating plant growth and adaptation.

Nat Plants 2021 08 5;7(8):1108-1118. Epub 2021 Jul 5.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, and the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.

Complex antagonistic interactions between abscisic acid (ABA) and brassinosteroid (BR) signalling pathways have been widely documented. However, whether or how ABA interacts synergistically with BR in plants remains to be elucidated. Here, we report that low, but not high, concentration of ABA increases lamina joint inclination of rice seedling, which requires functional BR biosynthesis and signalling. Transcriptome analyses confirm that about 60% of low-concentration ABA early response genes can be regulated by BR in the same directions. ABA activates BR signal in a fast, limited and short-term manner and the BR-biosynthesis regulatory gene, OsGSR1, plays a key role during this process, whose expression is induced slightly by ABA through transcriptional factor ABI3. Moreover, the early short-term BR signal activation is also important for ABA-mediated salt stress tolerance. Intriguingly, the process and effect of short-term BR signal activation were covered by high concentration of ABA, implying adaptive mechanisms existed in plants to cope with varying degrees of stress.
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http://dx.doi.org/10.1038/s41477-021-00959-1DOI Listing
August 2021

Editorial Feature: Meet the PCP Editor-Chengcai Chu.

Authors:
Chengcai Chu

Plant Cell Physiol 2021 Jul 1. Epub 2021 Jul 1.

The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/pcp/pcab065DOI Listing
July 2021

Engineering of the cytosolic form of phosphoglucose isomerase into chloroplasts improves plant photosynthesis and biomass.

New Phytol 2021 07 2;231(1):315-325. Epub 2021 May 2.

State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

Starch is the most abundant carbohydrate synthesized in plant chloroplast as the product of photosynthetic carbon assimilation, serving a crucial role in the carbon budget as storage energy. Phosphoglucose isomerase (PGI) catalyzes the interconversion between glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P), which are important metabolic molecules in starch synthesis within chloroplasts and sucrose synthesis in cytosol. Here, we found that the specific activity of recombinantly purified PGI localized in cytosolic PGI (PGIc) was much higher than its plastidic isoenzyme counterpart (PGIp) originated from wheat, rice and Arabidopsis, with wheat PGIc having by far the highest activity. Crystal structures of wheat TaPGIc and TaPGIp proteins were solved and the functional units were homodimers. The active sites of PGIc and PGIp, constituted by the same amino acids, formed different binding pockets. Moreover, PGIc showed slightly lower affinity to the substrate F6P but with much faster turnover rates. Engineering of TaPGIc into chloroplasts of a pgip mutant of Arabidopsis thaliana (atpgip) resulted in starch overaccumulation, increased CO assimilation, up to 19% more plant biomass and 27% seed yield productivity. These results show that manipulating starch metabolic pathways in chloroplasts can improve plant biomass and yield productivity.
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http://dx.doi.org/10.1111/nph.17368DOI Listing
July 2021

Dual function of clock component OsLHY sets critical day length for photoperiodic flowering in rice.

Plant Biotechnol J 2021 08 5;19(8):1644-1657. Epub 2021 May 5.

State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China.

Circadian clock, an endogenous time-setting mechanism, allows plants to adapt to unstable photoperiod conditions and induces flowering with proper timing. In Arabidopsis, the central clock oscillator was formed by a series of interlocked transcriptional feedback loops, but little is known in rice so far. By MutMap technique, we identified the candidate gene OsLHY from a later flowering mutant lem1 and further confirmed it through genetic complementation, RNA interference knockdown, and CRISPR/Cas9-knockout. Global transcriptome profiling and expression analyses revealed that OsLHY might be a vital circadian rhythm component. Interestingly, oslhy flowered later under ≥12 h day length but headed earlier under ≤11 h day length. qRT-PCR results exhibited that OsLHY might function through OsGI-Hd1 pathway. Subsequent one-hybrid assays in yeast, DNA affinity purification qPCR, and electrophoretic mobility shift assays confirmed OsLHY could directly bind to the CBS element in OsGI promoter. Moreover, the critical day length (CDL) for function reversal of OsLHY in oslhy (11-12 h) was prolonged in the double mutant oslhy osgi (about 13.5 h), indicating that the CDL set by OsLHY was OsGI dependent. Additionally, the dual function of OsLHY entirely relied on Hd1, as the double mutant oslhy hd1 showed the same heading date with hd1 under about 11.5, 13.5, and 14 h day lengths. Together, OsLHY could fine-tune the CDL by directly regulating OsGI, and Hd1 acts as the final effector of CDL downstream of OsLHY. Our study illustrates a new regulatory mechanism between the circadian clock and photoperiodic flowering.
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http://dx.doi.org/10.1111/pbi.13580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8384598PMC
August 2021

A transceptor-channel complex couples nitrate sensing to calcium signaling in Arabidopsis.

Mol Plant 2021 05 16;14(5):774-786. Epub 2021 Feb 16.

College of Life Sciences, Capital Normal University, Beijing 100048, China. Electronic address:

Nitrate-induced Ca signaling is crucial for the primary nitrate response in plants. However, the molecular mechanism underlying the generation of the nitrate-specific calcium signature remains unknown. We report here that a cyclic nucleotide-gated channel (CNGC) protein, CNGC15, and the nitrate transceptor (NRT1.1) constitute a molecular switch that controls calcium influx depending on nitrate levels. The expression of CNGC15 is induced by nitrate, and its protein is localized at the plasma membrane after establishment of young seedlings. We found that disruption of CNGC15 results in the loss of the nitrate-induced Ca signature (primary nitrate response) and retards root growth, reminiscent of the phenotype observed in the nrt1.1 mutant. We further showed that CNGC15 is an active Ca-permeable channel that physically interacts with the NRT1.1 protein in the plasma membrane. Importantly, we discovered that CNGC15-NRT1.1 interaction silences the channel activity of the heterocomplex, which dissociates upon a rise in nitrate levels, leading to reactivation of the CNGC15 channel. The dynamic interactions between CNGC15 and NRT1.1 therefore control the channel activity and Ca influx in a nitrate-dependent manner. Our study reveals a new nutrient-sensing mechanism that utilizes a nutrient transceptor-channel complex assembly to couple nutrient status to a specific Ca signature.
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http://dx.doi.org/10.1016/j.molp.2021.02.005DOI Listing
May 2021

Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals.

New Phytol 2021 06 21;230(5):1731-1745. Epub 2021 Mar 21.

Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.
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http://dx.doi.org/10.1111/nph.17276DOI Listing
June 2021

A route to de novo domestication of wild allotetraploid rice.

Cell 2021 03 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

Epigenetic regulation of nitrogen and phosphorus responses in plants.

J Plant Physiol 2021 Mar-Apr;258-259:153363. Epub 2021 Jan 10.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Nitrogen (N) and phosphorus (P) are two of the most important nutrients for plant growth and crop yields. In the last decade, plenty of studies have revealed the genetic factors and their regulatory networks which are involved in N and/or P uptake and utilization in different model plant species, especially in Arabidopsis and rice. However, increasing evidences have shown that epigenetic regulation also plays a vital role in modulating plant responses to nutrient availability. In this review, we make a brief summary of epigenetic regulation including histone modifications, DNA methylation, and other chromatin structure alterations in tuning N and P responses. We also give an outlook for future research directions to comprehensively dissect the involvement of epigenetic regulation in modulating nutrient response in plants.
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http://dx.doi.org/10.1016/j.jplph.2021.153363DOI Listing
June 2021

Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling.

Plant Cell Physiol 2021 Sep;62(4):543-552

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.

Nitrogen is the most important macroelement required for the composition of key molecules, such as nucleic acids, proteins and other organic compounds. As sessile organisms, plants have evolved sophisticated mechanisms to acquire nitrogen for their normal growth and development. Besides the transcriptional and translational regulation of nitrogen uptake, assimilation, remobilization and signal transduction, posttranslational modifications (PTMs) are shown to participate in these processes in plants. In addition to alterations in protein abundance, PTMs may dramatically increase the complexity of the proteome without the concomitant changes in gene transcription and have emerged as an important type of protein regulation in terms of protein function, subcellular localization and protein activity and stability. Herein, we briefly summarize recent advances on the posttranslational regulation of nitrogen uptake, assimilation, remobilization and nitrogen signaling and discuss the underlying mechanisms of PTMs as well as the signal output of such PTMs. Understanding these regulation mechanisms will provide novel insights for improving the nitrogen use efficiency of plants.
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http://dx.doi.org/10.1093/pcp/pcab008DOI Listing
September 2021

Endoplasmic Reticulum-Localized PURINE PERMEASE1 Regulates Plant Height and Grain Weight by Modulating Cytokinin Distribution in Rice.

Front Plant Sci 2020 22;11:618560. Epub 2020 Dec 22.

Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, China.

Cytokinins (CKs) are a class of phytohormones playing essential roles in various biological processes. However, the mechanisms underlying CK transport as well as its function in plant growth and development are far from being fully elucidated. Here, we characterize the function of PURINE PERMEASE1 (OsPUP1) in rice ( L.). was predominantly expressed in the root, particularly in vascular cells, and CK treatment can induce its expression. Subcellular localization analysis showed that OsPUP1 was predominantly localized to the endoplasmic reticulum (ER). Overexpression of resulted in growth defect of various aerial tissues, including decreased leaf length, plant height, grain weight, panicle length, and grain number. Hormone profiling revealed that the CK content was decreased in the shoot of -overexpressing seedling, but increased in the root, compared with the wild type. The CK content in the panicle was also decreased. Quantitative reverse transcription-PCR (qRT-PCR) analysis using several CK type-A () as the marker genes suggested that the CK response in the shoot of -overexpressing seedling is decreased compared to the wild type when CKs are applied to the root. Genetic analysis revealed that BG3/OsPUP4, a putative plasma membrane-localized CK transporter, overcomes the function of OsPUP1. We hypothesize that OsPUP1 might be involved in importing CKs into ER to unload CKs from the vascular tissues by cell-to-cell transport.
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http://dx.doi.org/10.3389/fpls.2020.618560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783468PMC
December 2020

Genomic basis of geographical adaptation to soil nitrogen in rice.

Nature 2021 02 6;590(7847):600-605. Epub 2021 Jan 6.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT). A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.
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http://dx.doi.org/10.1038/s41586-020-03091-wDOI Listing
February 2021

Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus.

Mol Plant 2021 03 11;14(3):517-529. Epub 2020 Dec 11.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing, China. Electronic address:

The coordinated utilization of nitrogen (N) and phosphorus (P) is vital for plants to maintain nutrient balance and achieve optimal growth. Previously, we revealed a mechanism by which nitrate induces genes for phosphate utilization; this mechanism depends on NRT1.1B-facilitated degradation of cytoplasmic SPX4, which in turn promotes cytoplasmic-nuclear shuttling of PHR2, the central transcription factor of phosphate signaling, and triggers the nitrate-induced phosphate response (NIPR) and N-P coordinated utilization in rice. In this study, we unveiled a fine-tuning mechanism of NIPR in the nucleus regulated by Highly Induced by Nitrate Gene 1 (HINGE1, also known as RLI1), a MYB-transcription factor closely related to PHR2. RLI1/HINGE1, which is transcriptionally activated by PHR2 under nitrate induction, can directly activate the expression of phosphate starvation-induced genes. More importantly, RLI1/HINGE1 competes with PHR2 for binding to its repressor proteins in the nucleus (SPX proteins), and consequently releases PHR2 to further enhance phosphate response. Therefore, RLI1/HINGE1 amplifies the phosphate response in the nucleus downstream of the cytoplasmic SPX4-PHR2 cascade, thereby enabling fine-tuning of N-P balance when nitrate supply is sufficient.
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http://dx.doi.org/10.1016/j.molp.2020.12.005DOI Listing
March 2021

Natural variations of SLG1 confer high-temperature tolerance in indica rice.

Nat Commun 2020 10 28;11(1):5441. Epub 2020 Oct 28.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe.
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http://dx.doi.org/10.1038/s41467-020-19320-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595236PMC
October 2020

ζ-Carotene Isomerase Suppresses Tillering in Rice through the Coordinated Biosynthesis of Strigolactone and Abscisic Acid.

Mol Plant 2020 12 7;13(12):1784-1801. Epub 2020 Oct 7.

State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

Rice tillering is an important agronomic trait affecting grain yield. Here, we identified a high-tillering mutant tillering20 (t20), which could be restored to the wild type by treatment with the strigolactone (SL) analog rac-GR24. T20 encodes a chloroplast ζ-carotene isomerase (Z-ISO), which is involved in the biosynthesis of carotenoids and their metabolites, SL and abscisic acid (ABA). The t20 mutant has reduced SL and ABA, raising the question of how SL and ABA biosynthesis is coordinated, and whether they have overlapping functions in tillering. We discovered that rac-GR24 stimulated T20 expression and enhanced all-trans-β-carotene biosynthesis. Importantly, rac-GR24 also stimulated expression of Oryza sativa 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (OsNCED1) through induction of Oryza sativa HOMEOBOX12 (OsHOX12), promoting ABA biosynthesis in shoot base. On the other hand, ABA treatment significantly repressed SL biosynthesis and the ABA biosynthetic mutants displayed elevated SL biosynthesis. ABA treatment reduced the number of basal tillers in both t20 and wild-type plants. Furthermore, while ABA-deficient mutants aba1 and aba2 had the same number of basal tillers as wild type, they had more unproductive upper tillers at maturity. This work demonstrates complex interactions in the biosynthesis of carotenoid, SLs and ABA, and reveals a role for ABA in the regulation of rice tillering.
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http://dx.doi.org/10.1016/j.molp.2020.10.001DOI Listing
December 2020

Alterations in stomatal response to fluctuating light increase biomass and yield of rice under drought conditions.

Plant J 2020 12 4;104(5):1334-1347. Epub 2020 Nov 4.

National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200032, China.

The acceleration of stomatal closure upon high to low light transition could improve plant water use efficiency and drought tolerance. Herein, using genome-wide association study, we showed that the genetic variation in OsNHX1 was strongly associated with the changes in τ , the time constant of stomatal closure, in 206 rice accessions. OsNHX1 overexpression in rice resulted in a decrease in τ , and an increase in biomass, grain yield under drought. Conversely, OsNHX1 knockout by CRISPR/CAS9 shows opposite trends for these traits. We further found three haplotypes spanning the OsNHX1 promoter and CDS regions. Two among them, HapII and HapIII, were found to be associated with a high and low τ , respectively. A near-isogenic line (NIL, S464) was developed through replacing the genomic region harboring HapII (~10 kb) from MH63 (recipient) rice cultivar by the same sized genomic region containing Hap III from 02428 (donor). Compared with MH63, S464 shows a reduction by 35% in τ and an increase by 40% in the grain yield under drought. However, under normal conditions, S464 maintains closely similar grain yield as MH63. The global distribution of the two OsNHX1 haplotypes is associated with the local precipitation. Taken together, the natural variation in OsNHX1 could be utilized to manipulate the stomatal dynamics for an improved rice drought tolerance.
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http://dx.doi.org/10.1111/tpj.15004DOI Listing
December 2020

Rice NIN-LIKE PROTEIN 4 plays a pivotal role in nitrogen use efficiency.

Plant Biotechnol J 2021 03 17;19(3):448-461. Epub 2020 Sep 17.

School of Life Sciences and Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, China.

Nitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavour in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the rice NIN-like protein 4 (OsNLP4) significantly improves the rice NUE and yield. Field trials consistently showed that loss-of-OsNLP4 dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, the OsNLP4 overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signalling genes by directly binding to the nitrate-responsive cis-element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsis nlp7 mutant and enhance its biomass. Our results demonstrate that OsNLP4 plays a pivotal role in rice NUE and sheds light on crop NUE improvement.
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http://dx.doi.org/10.1111/pbi.13475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7955889PMC
March 2021

Gibberellin Metabolism and Signaling: Targets for Improving Agronomic Performance of Crops.

Plant Cell Physiol 2020 Dec;61(11):1902-1911

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.

Gibberellins (GAs) are a class of tetracyclic diterpenoid phytohormones that regulate many aspects of plant development, including seed germination, stem elongation, leaf expansion, pollen maturation, and the development of flowers, fruits and seeds. During the past decades, the primary objective of crop breeding programs has been to increase productivity or yields. 'Green Revolution' genes that can produce semidwarf, high-yielding crops were identified as GA synthesis or response genes, confirming the value of research on GAs in improving crop productivity. The manipulation of GA status either by genetic alteration or by exogenous application of GA or GA biosynthesis inhibitors is often used to optimize plant growth and yields. In this review, we summarize the roles of GAs in major aspects of crop growth and development and present the possible targets for the fine-tuning of GA metabolism and signaling as a promising strategy for crop improvement.
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http://dx.doi.org/10.1093/pcp/pcaa104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758032PMC
December 2020

Strigolactone Signaling: Repressor Proteins Are Transcription Factors.

Trends Plant Sci 2020 10 22;25(10):960-963. Epub 2020 Jul 22.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. Electronic address:

A recent landmark study by Wang et al. provides new insight into transcriptional regulation in strigolactone (SL) signaling. The finding that SUPPRESSOR OF MAX2 LIKE 6 (SMXL6) also functions as an autoregulated transcription factor (TF) causes a paradigm shift in the current view of transcriptional repressors in phytohormone signaling.
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http://dx.doi.org/10.1016/j.tplants.2020.07.002DOI Listing
October 2020

The OsGSK2 Kinase Integrates Brassinosteroid and Jasmonic Acid Signaling by Interacting with OsJAZ4.

Plant Cell 2020 09 25;32(9):2806-2822. Epub 2020 Jun 25.

State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.

The crosstalk between brassinosteroid (BR) and jasmonic acid (JA) signaling is crucial for plant growth and defense responses. However, the detailed interplay between BRs and JA remains obscure. Here, we found that the rice () Glycogen synthase kinase3 (GSK3)-like kinase OsGSK2, a conserved kinase serving as a key suppressor of BR signaling, enhanced antiviral defense and the JA response. We identified a member of the JASMONATE ZIM-domain (JAZ) family, OsJAZ4, as a OsGSK2 substrate and confirmed that OsGSK2 interacted with and phosphorylated OsJAZ4. We demonstrated that OsGSK2 disrupted the OsJAZ4-OsNINJA complex and OsJAZ4-OsJAZ11 dimerization by competitively binding to the ZIM domain, perhaps helping to facilitate the degradation of OsJAZ4 via the 26S proteasome pathway. We also showed that OsJAZ4 negatively modulated JA signaling and antiviral defense and that the BR pathway was involved in modulating the stability of OsJAZ4 protein in an -dependent manner. Collectively, these results suggest that OsGSK2 enhances plant antiviral defenses by activating JA signaling as it directly interacts with, phosphorylates, and destabilizes OsJAZ4. Thus, our findings provide a clear link between BR and JA signaling.
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http://dx.doi.org/10.1105/tpc.19.00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474301PMC
September 2020

S-Nitrosylation Control of ROS and RNS Homeostasis in Plants: The Switching Function of Catalase.

Mol Plant 2020 07 20;13(7):946-948. Epub 2020 May 20.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2020.05.013DOI Listing
July 2020

ARGONAUTE2 Enhances Grain Length and Salt Tolerance by Activating to Modulate Cytokinin Distribution in Rice.

Plant Cell 2020 07 14;32(7):2292-2306. Epub 2020 May 14.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Maintaining stable, high yields under fluctuating environmental conditions is a long-standing goal of crop improvement but is challenging due to internal trade-off mechanisms, which are poorly understood. Here, we identify ARGONAUTE2 (AGO2) as a candidate target for achieving this goal in rice (). Overexpressing led to a simultaneous increase in salt tolerance and grain length. These benefits were achieved via the activation of (), encoding a purine permease potentially involved in cytokinin transport. AGO2 can become enriched on the locus and alter its histone methylation level, thus promoting expression. Cytokinin levels decreased in shoots but increased in roots of -overexpressing plants. While knockout mutants were hypersensitive to salt stress, plants overexpressing showed strong salt tolerance and large grains. The knockout of significantly reduced grain length and salt tolerance in -overexpressing plants. Both genes were transcriptionally suppressed by salt treatment. Salt treatment markedly increased cytokinin levels in roots but decreased them in shoots, resulting in a hormone distribution pattern similar to that in -overexpressing plants. These findings highlight the critical roles of the spatial distribution of cytokinins in both stress responses and grain development. Therefore, optimizing cytokinin distribution represents a promising strategy for improving both grain yield and stress tolerance in rice.
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http://dx.doi.org/10.1105/tpc.19.00542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7346564PMC
July 2020

Towards understanding the hierarchical nitrogen signalling network in plants.

Curr Opin Plant Biol 2020 06 15;55:60-65. Epub 2020 Apr 15.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. Electronic address:

Nitrogen (N) is the most abundant mineral elements in plants, and the application of inorganic N fertilizer makes huge contribution to the crop production and global food security. However, low N use efficiency (NUE) and overapplication of N fertilizers causes ever-growing environmental problems. Understanding the molecular mechanisms of N sensing and signalling in plants will provide molecular basis for NUE improvement of crops. Forward genetics screening and functional analysis have characterized the NRT1.1-NLP centered N signalling pathway at the cellular level. With the incorporation of systems biology approaches, a preliminary N regulatory network has been delineated. Meanwhile, long-distance N signalling has also been unveiled at the whole plant level. This review highlights most recent understanding of the N signalling network in plants, and also discusses how to further integrate hierarchical regulation of N signalling in plants.
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http://dx.doi.org/10.1016/j.pbi.2020.03.006DOI Listing
June 2020

Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions.

Sci China Life Sci 2020 Nov 15;63(11):1688-1702. Epub 2020 Apr 15.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.
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http://dx.doi.org/10.1007/s11427-019-1682-6DOI Listing
November 2020

Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice.

J Exp Bot 2020 05;71(9):2723-2739

Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.

Due to its subtropical origins, rice (Oryza sativa) is sensitive to low-temperature stress. In this study, we identify LOC_Os04g24110, annotated to encode the UDP-glycosyltransferase enzyme UGT90A1, as a gene associated with the low-temperature seedling survivability (LTSS) quantitative trait locus qLTSS4-1. Differences between haplotypes in the control region of OsUGT90A1 correlate with chilling tolerance phenotypes, and reflect differential expression between tolerant and sensitive accessions rather than differences in protein sequences. Expression of OsUGT90A1 is initially enhanced by low temperature, and its overexpression helps to maintain membrane integrity during cold stress and promotes leaf growth during stress recovery, which are correlated with reduced levels of reactive oxygen species due to increased activities of antioxidant enzymes. In addition, overexpression of OsUGT90A1 in Arabidopsis improves freezing survival and tolerance to salt stress, again correlated with enhanced activities of antioxidant enzymes. Overexpression of OsUGT90A1 in rice decreases root lengths in 3-week-old seedlings while gene-knockout increases the length, indicating that its differential expression may affect phytohormone activities. We conclude that higher OsUGT90A1 expression in chilling-tolerant accessions helps to maintain cell membrane integrity as an abiotic stress-tolerance mechanism that prepares plants for the resumption of growth and development during subsequent stress recovery.
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http://dx.doi.org/10.1093/jxb/eraa025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210772PMC
May 2020

Nitrogen-Use Divergence Between Indica and Japonica Rice: Variation at Nitrate Assimilation.

Mol Plant 2020 01 2;13(1):6-7. Epub 2019 Dec 2.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2019.11.011DOI Listing
January 2020

GSK2 stabilizes OFP3 to suppress brassinosteroid responses in rice.

Plant J 2020 06 13;102(6):1187-1201. Epub 2020 Feb 13.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

Brassinosteroids (BRs) are a class of phytohormones that modulate several important agronomic traits in rice (Oryza sativa). GSK2 is one of the critical suppressors of BR signalling and targets transcription factors such as OsBZR1 and DLT to regulate BR responses. Here, we identified OFP3 (OVATE FAMILY PROTEIN 3) as an interactor of both GSK2 and DLT by yeast-two-hybrid screening and demonstrated that OFP3 plays a distinctly negative role in BR responses. While knockout of OFP3 promoted rice seedling growth, overexpression of OFP3 led to strong BR insensitivity, which resulted in reduced plant height, leaf angle, and grain size. Interestingly, both BR biosynthetic and signalling genes had decreased expression in the overexpression plants. OFP3 overexpression also enhanced the phenotypes of BR-deficient mutants, but largely suppressed those of BR-enhanced plants. Moreover, treatment with either BR or bikinin, a GSK3-like kinase inhibitor, induced OFP3 depletion, whereas GSK2 or brassinazole, a BR synthesis inhibitor, promoted OFP3 accumulation. Furthermore, OFP3 exhibited transcription repressor activity and was able to interact with itself as well as additional BR-related components, including OFP1, OSH1, OSH15, OsBZR1, and GF14c. Importantly, GSK2 can phosphorylate OFP3 and enhance these interactions. We propose that OFP3, as a suppressor of both BR synthesis and signalling but stabilized by GSK2, incorporates into a transcription factor complex to facilitate BR signalling control, which is critical for the proper development of various tissues.
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http://dx.doi.org/10.1111/tpj.14692DOI Listing
June 2020

Improvement of nutrient use efficiency in rice: current toolbox and future perspectives.

Theor Appl Genet 2020 May 9;133(5):1365-1384. Epub 2020 Jan 9.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.
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http://dx.doi.org/10.1007/s00122-019-03527-6DOI Listing
May 2020

NRT1.1s in plants: functions beyond nitrate transport.

J Exp Bot 2020 07;71(15):4373-4379

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.

Arabidopsis AtNRT1.1 (CHL1/AtNPF6.3) is the first nitrate transporter identified in plants and was initially found to play a role in nitrate uptake and transport. AtNRT1.1 also displays auxin transport activity and mediates nitrate-modulated root development, suggesting that it has transport capacity for multiple substrates. Subsequent work revealed that AtNRT1.1 can respond to environmental nitrate fluctuations by altering its nitrate transport activity, modulated by phosphorylation, leading to the critical finding that AtNRT1.1 acts as a transceptor for nitrate sensing. Recent studies have revealed how OsNRT1.1B, the functional homologue of AtNRT1.1 in rice, mediates nitrate signal transduction from the plasma membrane to the nucleus, and how OsNRT1.1B integrates the nitrate and phosphate signaling networks. OsNRT1.1B has also been shown to be involved in regulating the root microbiota to facilitate organic nitrogen mineralization in soil, thus mediating plant-microbe interactions. Furthermore, the divergent functions of OsNRT1.1A and OsNRT1.1B in regulating nitrogen use in rice suggest that the function of NRT1.1 is still far from fully understood. In this review, we focus on the most recent progress on the molecular mechanisms of NRT1.1s in plants, with the aim of providing an up-to-date view of the versatile functions of NRT1.1 in nitrogen utilization in plants.
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http://dx.doi.org/10.1093/jxb/erz554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382373PMC
July 2020

Vascular-specific expression of Gastrodia antifungal protein gene significantly enhanced cotton Verticillium wilt resistance.

Plant Biotechnol J 2020 07 4;18(7):1498-1500. Epub 2020 Jan 4.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1111/pbi.13308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292534PMC
July 2020
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