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Comparative transcriptomics provide new insights into the mechanisms by which foliar silicon alleviates the effects of cadmium exposure in rice

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Journal of Environmental Sciences 2022年第5期34卷 294-307页

作者： Chongjun Sun Xiaoyu Liang Xiaomei Gong Huamei Chen Xiulian Liu Shuchang Zhang Fangbai Li Junliang Zhao Jicai Yi College of Life Sciences South China Agricultural UniversityGuangzhou 510642China Guangdong Institute of Eco-environmental Science and Technology Guangzhou 510650China rice Research Institute and Guangdong Key Laboratory of New Technology in rice Breeding Guangdong Academy of Agricultural SciencesGuangzhou 510640China

Silicon(Si)has been shown to alleviate Cd stress in rice.Here,we investigated the beneficial effects of foliar Si in an indica rice Huanghuazhan(HHZ).Our results showed that foliar Si in-creases the dry weight and decreases Cd translocation in Cd-exposed rice at the grain-filling stage only,implying that the filling stage is critical for foliar Si to reduce Cd accumulation.We also investigated the transcriptomics in flag leaves(FLs),spikelets(SPs),and node Is(NIs)of Cd-exposed HHZ after foliar Si application at the filling stage.Importantly,the gene expression profiles associated with the Si-mediated alleviation of Cd stress were tissue spe-cific,while shared pathways were mediated by Si in Cd-exposed rice tissues.Furthermore,after the Si treatment of Cd-exposed rice,the ATP-binding cassette(ABC)-transporters were mostly upregulated in FL and SP,while the bivalent cation transporters were mostly down-regulated in FL and NI,possibly helping to reduce Cd accumulation.The genes associated with essential nutrient transporters,carbohydrate and secondary metabolite biosynthesis,and cytochrome oxidase activity were mostly upregulated in Cd-exposed FL and SP,which may help to alleviate oxidative stress and improve plant growth under Cd exposure.Inter-estingly,genes responsible for signal transduction were negatively regulated in FL,but pos-itively regulated in SP,by foliar Si.Our results provide transcriptomic evidence that foliar Si plays an active role in alleviating the effects of Cd exposure in rice.In particular,foliar Si may alter the expression pattern of genes associated with transport,biosynthesis and metabolism,and oxidation reduction.

关键词： rice Transcriptomics Foliar silicon Cadmium exposure

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Genomic decoding of breeding history to guide breeding-by-design in rice

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National Science Review 2023年第5期10卷 124-137页

作者： Zhuo Chen Qingyun Bu Guifu Liu Maoqing Wang Hongru Wang Huazhao Liu Xiufeng Li Hong Li Jun Fang Yan Liang Zhenfeng Teng Sai Kang Hong Yu Zhukuan Cheng Yongbiao Xue Chengzhi Liang Jiuyou Tang Jiayang Li Chengcai Chu State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of Sciences Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture and Rural Affairs Beidahuang Kenfeng Seed Co.Ltd Institute of Botany Chinese Academy of Sciences Guangdong Laboratory for Lingnan Modern Agriculture and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of AgricultureSouth China Agricultural University University of Chinese Academy of Sciences State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Hainan Yazhou Bay Seed Laboratory

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design(BbD),but remains not well established.Here,we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China(NEC).We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study(GWAS)-detected quantitative trait loci(QTLs),or introgressions from indica sub-species with chronological changes in allele frequencies.Then we summarized a rice breeding trend/principle in NEC,and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in practice.Our study provides a paradigm for decoding the breeding history of a specific crop to guide BbD,which may have implications in different crop breeding.

关键词： rice breeding-by-design breeding history genome-wide association study genomic decoding

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Generation of low-cadmium rice germplasms via knockout of OsLCD using CRISPR/Cas9

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Journal of Environmental Sciences 2023年第4期126卷 138-152页

作者： Huamei Chen Rong Ye Ying Liang Shuchang Zhang Xiulian Liu Chongjun Sun Fangbai Li Jicai Yi College of Life Sciences South China Agricultural UniversityGuangzhou 510642China Institute of Eco-environmental and Soil Sciences Guangdong Academy of SciencesGuangzhou 510650China

The OsLCD gene,which has been implicated in cadmium (Cd) accumulation in rice,might be a useful target for CRISPR/Cas9 editing.However,the effects of Os LCD gene editing on Cd accumulation,plant growth,and yield traits remain unknown.Here,we used CRISPR/Cas9to generate oslcd single mutants from indica and japonica rice cultivars.We also generated osnramp5 single mutants and oslcd osnramp5 double mutants in the indica background.When grown in Cd-contaminated paddy soils,all oslcd single mutants accumulated less Cd than the wild types (WTs).Consistent with this,oslcd single mutants grown in Cd-contaminated hydroponic culture accumulated significantly less Cd in the shoots as compared to WTs.This decrease in accumulation probably resulted from the reduction of Cd translocation under Cd stress.Oxidative damage also decreased,and plant growth increased in all oslcd single mutant seedlings as compared to WTs in the presence of Cd.Plant growth and most yield traits,as well essential element concentrations in rice seedling shoots,brown rice,and rice straw,were similar between oslcd single mutants and WTs.In the presence of Cd,Cd concentrations in the brown rice and shoots of oslcd osnramp5 double mutants were significantly decreased compared with WTs as well as osnramp single mutants.Our results suggested that OsL CD knockout may reduce Cd accumulation alone or in combination with other knockout mutations in a variety of rice genotypes;unlike Os Nramp5 mutations,Os LCD knockout did not reduce essential element contents.Therefore,Os LCD knockout might be used to generate low-Cd rice germplasms.

关键词： Cadmium rice OsLCD Crispr/Cas9 editing

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The divergence of brassinosteroid sensitivity between rice subspecies involves natural variation conferring altered internal auto-binding of OsBSK2

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Journal of Integrative Plant Biology 2022年第8期64卷 1614-1630页

作者： Wenchao Yin Lulu Li Zhikun Yu Fan Zhang Dapu Liu Hongkai Wu Mei Niu Wenjing Meng Xiaoxing Zhang Nana Dong Yanzhao Yang Jihong Liu Yongqiang Liu Guoxia Zhang Jianlong Xu Shimei Wang Chengcai Chu Qian Qian Hongning Tong National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China rice Research Institute of Anhui Academy of Agricultural Sciences Hefei 230001China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biologythe Innovative Academy for Seed DesignChinese Academy of SciencesBeijing 100101China

Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains elusive.Brassinosteroids(BRs)are a class of steroid phytohormones that modulate many important agronomic traits in rice.Here,using different physiological assays,we revealed that japonica rice exhibits an overall lower BR sensitivity than indica.Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms.Among these,we demonstrate that the C38/T variant in BR Signaling Kinase2(OsBSK2),causing the amino acid change P13L,plays a central role in mediating differential BR signaling in japonica and indica rice.OsBSK2in indica plays a greater role in BR signaling than OsB SK2in japonica by affecting the auto-binding and protein accumulation of OsBSK2.Finally,we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice,including grain shape,tiller number,cold adaptation,and nitrogen-use efficiency.Our study suggests that the natural variation in OsB SK2 plays a key role in the divergence of BR signaling,which underlies multiple divergent traits between japonica and indica.

关键词： brassinosteroid divergence grain shape natural variation rice

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Autophagy targets Hd1 for vacuolar degradation to regulate rice flowering

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Molecular Plant 2022年第7期15卷 1137-1156页

作者： Zhi Hu Zhipan Yang Yi Zhang Aihong Zhang Qingtao Lu Ying Fang Congming Lu Key Laboratory of Photobiology Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Crop Biology College of Life ScienceShandong Agricultural UniversityTaianShandong 271018China

Flowering time(heading date)is a critical agronomic trait that determines the yield and regional adaptability of crops.Heading date 1(Hd1)is a central regulator of photoperiodic flowering in rice(Oryza sativa).However,how the homeostasis of Hd1 protein is achieved is poorly understood.Here,we report that the nuclear autophagy pathway mediates Hd1 degradation in the dark to regulate flowering.Loss of autophagy function results in an accumulation of Hd1 and delays flowering under both short-day and long-day conditions.In the dark,nucleus-localized Hd1 is recognized as a substrate for autophagy and is subjected to vacuolar degradation via the autophagy protein OsATG8.The Hd1-0sATG8 interaction is required for autophagic degradation of Hd1 in the dark.Our study reveals a new mechanism by which Hd1 protein homeostasis is regulated by autophagy to control rice flowering.Our study also indicates that the regulation of flowering by autophagic degradation of Hd1 orthologs may have arisen over the course of mesangiosperm evolution,which would have increased their flexibility and adaptability to the environment by modulating flowering time.

关键词： autophagy heading date rice Hd1 homeostasis

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Hd1,Ghd7,and DTH8 synergistically determine the rice heading date and yield-related agronomic traits

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Journal of Genetics and Genomics 2022年第5期49卷 437-447页

作者： Kangli Sun Minghui Huang Wubei Zong Dongdong Xiao Chen Lei Yanqiu Luo Yingang Song Shengting Li Yu Hao Wanni Luo Bingqun Xu Xiaotong Guo Guangliang Wei Letian Chen Yao-Guang Liu Jingxin Guo State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life SciencesSouth China Agricultural UniversitySCAUGuangzhouGuangdong 510642China Guangdong Laboratory for Lingnan Modern Agriculture GuangzhouGuangdong 510642China

Heading date determines the seasonal and regional adaptation of rice(Oryza sativa L.)varieties and is mainly controlled by photoperiod sensitivity(PS).The core heading date genes Hd1,Ghd7,DTH8,and PRR37 act synergistically in regulating the PS.In this study,we systematically analyze the heading date,PS,and agronomic traits of eight homozygous lines with various combinations of Hd1,Ghd7,and DTH8 alleles in the prr37 background under long-day(LD)and short-day(SD)conditions,respectively.We find that Hd1 alone promotes heading,regardless of the day length.However,under LDs,Hd1 suppresses flowering,in coordination with functional Ghd7 or with Ghd7 and DTH8.These loci cooperate to negatively regulate the Ehd1-Hd3 a/RFT1 pathway and delay heading.Under SDs,Hd1 competes with various heading suppressors to promote heading.Therefore,the dual function of Hd1 is vital for PS.The lines carrying Hd1 alone show reduced plant height with fewer primary and secondary branches in panicles.Lines carrying Ghd7 and DTH8(with hd1)show delayed heading and improve agronomic traits.Overall,our results reveal the regulation of rice PS flowering by the core heading date genes and their effects on agronomic traits,providing valuable information for the selection of rice varieties for adaptation to different light and temperature conditions.

关键词： rice Photoperiod sensitivity Heading date Hd1 Agronomic traits

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OsDMI3-mediated OsUXS3 phosphorylation improves oxidative stress tolerance by modulating OsCATB protein abundance in rice

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Journal of Integrative Plant Biology 2022年第5期64卷 1087-1101页

作者： Lan Ni Qingwen Wang Chao Chen Shuang Wang Tao Shen Jingjing Jiang Zhenzhen Cui Kaiyue Li Qiqing Yang Mingyi Jiang College of Life Sciences National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Crop Physiology Ecology and Production ManagementMinistry of AgricultureNanjing Agricultural UniversityNanjing 210095China Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China Hunan Agricultural UniversityChangsha 410128China

Calcium(Ca^(2+))/calmodulin(CaM)-dependent protein kinase(CCaMK)is an important positive regulator of antioxidant defenses and tolerance against oxidative stress.However,the underlying molecular mechanisms are largely unknown.Here,we report that the rice(Oryza sativa)CCa MK(OsDMI3)physically interacts with and phosphorylates OsUXS3,a cytosol-localized UDP-xylose synthase.Genetic and biochemical evidence demonstrated that OsUXS3 acts downstream of OsDMI3 to enhance the oxidative stress tolerance conferred by higher catalase(CAT)activity.Indeed,OsUXS3 interacted with CAT isozyme B(OsCATB),and this interaction was required to increase OsCATB protein abundance under oxidative stress conditions.Furthermore,we showed that OsDMI3 phosphorylates OsUXS3 on residue Ser-245,thereby further promoting the interaction between OsUXS3 and OsCATB.Our results indicate that OsDMI3 promotes the association of OsUXS3 with OsCATB to enhance CAT activity under oxidative stress.These findings reveal OsUXS3 as a direct target of OsDMI3 and demonstrate its involvement in antioxidant defense.

关键词： Ca2+/calmodulin-dependent protein kinase catalase oxidative stress rice UDP-xylose synthase

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RID1 sets rice heading date by balancing its binding with SLR1 and SDG722

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Journal of Integrative Plant Biology 2022年第1期64卷 149-165页

作者： Shuo Zhang Li Deng Rui Cheng Jie Hu Chang-Yin Wu National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China

rice(Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time(heading date). Loss of rice INDETERMINATE1(RID1) function causes plants not to flower;thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition.Here, we revealed that the chromatin accessibilityand H3 K9 ac, H3 K4 me3, and H3 K36 me3 levels at Heading date 3 a(Hd3 a) and rice FLOWERING LOCUS T1(RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722(SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3 K4 me2/3 and H3 K36 me2/3, and promotes flowering primarily through the Early heading date1-Hd3 a/RFT1 pathway. We further established that rice DELLA protein SLENDER rice1(SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.

关键词： heading date histone modification rice RID1 SDG722 SLR1

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An epi-allele of SMS causes Sanming dominant genic male sterility in rice

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Science China(Life Sciences) 2023年第12期66卷 2701-2710页

作者： Yachun Yang Cheng Zhang Hao Li Zeyuan Yang Zuntao Xu Dewei Tai Dahu Ni Pengcheng Wei Chengxin Yi Jianbo Yang Yong Ding rice Research Institute Anhui Academy of Agricultural SciencesHefei 230036China Institute of Health and Medicine Hefei Comprehesive National Science CenterHefei 230031China Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China

Male sterility is an important trait in rice for hybrid rice(Oryza sativa)breeding.However,the factors involved in dominant male sterility are largely unknown.Here,we identified a gene from Sanming dominant genic male sterile rice,named Sanming dominant male sterility(SMS),and reported that an epi-allele of this locus contributes to male sterility.Segregation analysis attributed dominant male sterility to a single locus,SMS,which we characterized using a male-sterile near isogenic line(NIL)of rice cultivar 93-11.The SMS locus was heterozygous in the male-sterile 93-11 NIL,containing an epi-allele identical to that in 93-11,and an epi-allele identical to that in rice cultivar Nipponbare,which we refer to as SMS9 and SMSN,respectively.SMS9is silent and hyper-methylated,whereas SMSNis expressed and hypo-methylated in the 93-11 NIL.Overexpressing SMSNled to male sterility.Mutations in SMS rescued the male sterility of the 93-11 NIL.Interestingly,we observed the duplication of SMSN in Nipponbare,but did not observe the duplication of SMS9in 93-11.Together,these findings suggest that the reduced methylation and enhanced expression of the SMSNepi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.

关键词： male sterility rice epi-allele Sanming DNA methylation

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Mediator complex subunit MED25 physically interacts with DST to regulate spikelet number in rice

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Journal of Integrative Plant Biology 2022年第4期64卷 871-883页

作者： Lihao Lin Minmin Du Shuyu Li Chuanlong Sun Fangming Wu Lei Deng Qian Chen Chuanyou Li State Key Laboratory of Plant Genomics National Centre for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignThe Chinese Academy of SciencesBeijing 100101China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTaian 271018China

Grain number is a flexible trait and contributes significantly to grain yield.In rice,the zinc finger transcription factor DROUGHT AND SALT TOLERANCE(DST)controls grain number by directly regulating cytokinin oxidase!dehydrogenase 2(OsCKX2)expression.Although specific upstream regulators of the DST-OsCKX2 module have been identified,the mechanism employed by DST to regulate the expression of OsCKX2 remains unclear.Here,we demonstrate that DST-interacting protein 1(DIP1),known as Mediator subunit OsMED25,acts as an interacting coactivator of DST.Phenotypic analyses revealed that OsMED25-RNAi and the osmed25 mutant plants exhibited enlarged panicles,with enhanced branching and spikelet number,similar to the dst mutant.Genetic analysis indicated that OsMED25 acts in the same pathway as the DST-OsCKX2 module to regulate spikelet number per panicle.Further biochemical analysis showed that OsMED25 physically interacts with DST at the promoter region of OsCKX2,and then recruits RNA polymerase II(Pol II)to activate OsCKX2 transcription.Thus,OsMED25 was involved in the communication between DST and Pol II general transcriptional machinery to regulate spikelet number.In general,our findings reveal a novel function of OsMED25 in DST-OsCKX2 modulated transcriptional regulation,thus enhancing our un derstanding of the regulatory mechanism underlying DST-OsCKX2-mediated spikelet number.

关键词： DST MED25 OsCKX2 rice spikelet number

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