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Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice

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Journal of Genetics and Genomics 2022年第5期49卷 448-457页

作者： Pengfei Wang Feixiang Qi Honglin Yao Xingbing Xu Wenjun Li Jianghu Meng Qinglu Zhang weibo xie Yongzhong Xing National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

In rice,the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance,as shown by their extremely high ***,the mechanisms underlying the success of these rice hybrids are *** this study,three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific *** constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies,respectively,although introgression of 20%of the Xian ancestry and 14%of the Geng ancestry are ***-five percent of the hybrid genomes carries homozygous Xian or Geng fragments,which harbors hybrid sterility genes such as Sd,Sc,f5,and q S12 and favorable alleles of key yield-related genes,including NAL1,Ghd7,and *** of the parents carries the S5+killer of the S5 killer-protector *** allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific *** effects of favorable alleles of yield-related genes fixed in both parents enhances midparent *** QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to *** factors result in an extremely high yield of the *** findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.

关键词： Intersubspecific hybrid Heterosis Fertility Introgression Favorable alleles Dominance

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A Nonresonant Hybridized Electromagnetic-Triboelectric Nanogenerator for Irregular and Ultralow Frequency Blue Energy Harvesting

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Research 2021年第1期2021卷 304-315页

作者： weibo xie Lingxiao Gao Lingke Wu Xin Chen Fayang Wang Daqiao Tong Jian Zhang Jianyu Lan Xiaobin He Xiaojing Mu Ya Yang State Key Laboratory of Mechanical Transmissions Chongqing UniversityChongqing 400044China Key Laboratory of Optoelectronic Technology&Systems Ministry of Education International R&D Center of Micro-Nano Systems and New Materials TechnologyChongqing UniversityChongqing 400044China CAS Center for Excellence in Nanoscience Beijing Key Laboratory of Micro-Nano Energy and SensorBeijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing 100083China College of Aerospace Engineering Chongqing UniversityChongqing 400044China Shanghai Academy of Spaceflight Technology Shanghai Institute of Space Power SourceShanghai 200245China School of Nanoscience and Technology University of Chinese Academy of SciencesBeijing 100049China Center on Nanoenergy Research School of Physical Science and TechnologyGuangxi UniversityNanningGuangxi 530004China

As a promising renewable energy source,it is a challenging task to obtain blue energy,which is irregular and has an ultralow frequency,due to the limitation of ***,a nonresonant hybridized electromagnetic-triboelectric nanogenerator was presented to efficiently obtain the ultralow frequency *** instrument adopted the flexible pendulum structure with a precise design and combined the working principle of electromagnetism and triboelectricity to realize the all-directional vibration energy acquisition *** results confirmed that the triboelectric nanogenerator(TENG)had the potential to deliver the maximum power point of about 470μW while the electromagnetic nanogenerator(EMG)can provide 523 mW at *** conversion efficiency of energy of the system reached 48.48%,which exhibited a remarkable improvement by about 2.96 times,due to the elastic buffering effect of the TENG with the double helix ***,its ability to collect low frequency wave energy was successfully proven by a buoy in Jialing *** woke provides an effective candidate to harvest irregular and ultralow frequency blue energy on a large scale.

关键词： generator precise instrument

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Genome-and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

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Molecular Plant 2021年第3期14卷 470-487页

作者： Shan Tang Hu Zhao Shaoping Lu Liangqian Yu Guofang Zhang Yuting Zhang Qing-Yong Yang Yongming Zhou Xuemin Wang Wei Ma weibo xie Liang Guo National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina Department of Biology University of Missouri-St.LouisSt.LouisMO 63121USA Donald Danforth Plant Science Center St.LouisMO 63132USA School of Biological Sciences Nanyang Technological UniversitySingapore 637551Singapore

Seed oil content(SOC)is a highly important and complex trait in oil ***,we decipher the genetic basis of natural variation in SOC of Brassica napus by genome-and transcriptome-wide association studies using 505 inbred *** mapped reliable quantitative trait loci(QTLs)that control SOC in eight environments,evaluated the effect of each QTL on SOC,and analyzed selection in QTL regions during ***-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds.A gene prioritization framework,POCKET(prioritizing the candidate genes by incorporating information on knowledge-based gene sets,effects of variants,genome-wide association studies,and transcriptome-wide association studies),was implemented to determine the causal genes in the QTL regions based on multi-omic datasets.A pair of homologous genes,BnPMT6s,in two QTLs were identified and experimentally demonstrated to negatively regulate *** study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of *** and other oil crops.

关键词： Brassica napus seed oil content QTL GWAS TWAS gene module

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An inferred functional impact map of genetic variants in rice

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Molecular Plant 2021年第9期14卷 1584-1599页

作者： Hu Zhao Jiacheng Li Ling Yang Gang Qin Chunjiao Xia Xingbing Xu Yangmeng Su Yinmeng Liu Luchang Ming Ling-Ung Chen Lizhong Xiong weibo xie National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanningChina

Interpreting the functional impacts of genetic variants(GVs)is an important challenge for functional genomic studies in crops and next-generation *** studies in rice(Oryza sativa)have focused mainly on the identification of GVs,whereas systematic functional annotation of GVs has not yet been ***,we present a functional impact map of GVs in *** curated haplotype information for 17397026 GVs from sequencing data of 4726 rice *** quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918848 non-redundant missense ***,we generated high-quality chromatin accessibility(CA)data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5067405 GVs for CA in regulatory *** characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different ***,we demonstrated how the functional impact map could be used to prioritize causal variants in mapping *** impact map will be a useful resource for accelerating gene cloning and functional studies in rice,and can be freely queried in RiceVarMap V2.0(http://***).

关键词： ricegenetic variantschromatin accessibilityfunctional impact mapdeep learning

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Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

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Molecular Plant 2015年第6期8卷 946-957页

作者： Quanxiu. Wang weibo xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu Xingming Lian Sibin Yu Yongzhong Xing Gongwei Wang National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070China

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photo- synthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice （Oryza sativa） and the extent of variations explored is very limited. We con- ducted a genome-wide association study （GWAS） using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demon- strated that Grain number, plant height, andheading date7 （GhdT） was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down- regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 （NAL1） corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5＇ UTR and four non-synonymous SNPs in the cod- ing region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes iden- tified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

关键词： chlorophyll GWAS Ghd7 NAL 1 pleiotropic effect Oryza sativa

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Comparative genomic analysis of the parents of an elite rice hybrid

Comparative genomic analysis of the parents of an elite rice...

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第十四届全国植物基因组学大会

作者： Wen Yao weibo xie Qifa Zhang National Key Laboratory of Crop Genetic Improvement National Centre of Plant Gene Research(Wuhan)Huazhong Agricultural University

Rice is a staple food crop and an ideal model for functional genome research of *** of heterosis has contributed tremendously to the increased productivity of *** report the next generation sequencing of Zhenshan 97 a... 详细信息

关键词： genome sequencing SNPs indels structural variations

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RNA-Directed DNA Methylation Is Involved in Regulating Photoperiod-Sensitive Male Sterility in Rice

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Molecular Plant 2012年第6期5卷 1210-1216页

作者： Jihua Ding Jianqiang Shen Hailiang Mao weibo xie Xianghua Li Qifa Zhang National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research(Wuhan) I-luazhong Agriculture UniversityWuhan 430070China

Photoperiod-sensitive male sterility （PSMS） is a valuable germplasm for hybrid rice breeding. Recently, we cloned pros3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions. Increased methylation in the promoter of LDMAR in the PSMS rice （Nongken 58S） relative to the wild-type （Nongken 58） reduced expression of LDMAR leading to male sterility under long-day conditions. In this study, we identified a siRNA named Psi-LDMAR in the LDMAR promoter region that was more abundant in Nongken 58S than in Nongken 58. We showed that Psi-LDMAR was likely derived from AKl11270, a transcript obtained from the sense strand of the LDMAR promoter with its 3＇-end having a 110-base overlap with the 5＇-end of LDMAR. Overexpressing AKl11270 in Nongken 58S greatly enriched Psi-LDMAR, which induced RNA-directed DNA methylation in the LDMAR promoter and repressed the expression of LDMAR. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS.

关键词： Oryza sativa siRNA Psi-LDMAR epigenetics hybrid rice.

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Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13, a Positive Regulator of Disease Resistance

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Molecular Plant 2008年第3期1卷 538-551页

作者： Deyun Qiu Jun Xiao weibo xie Hongbo Liu Xianghua Li Lizhong Xiong Shiping Wang National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural UniversityWuhan 430070 China

Accumulating information indicates that plant disease resistance signaling pathways frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, appears to function as a convergent point for crosstalk among the pathogen-induced salicylate-dependent defense pathway and five other physiologic pathways. Genome-wide analysis of the expression profiles of OsWRKY13-overexpressing lines suggests that OsWRKY13 directly or indirectly regulates the expression of more than 500 genes that are potentially involved in different physiologic processes according to the classification of the Gene Ontology database. By comparing the expression patterns of genes functioning in known pathways or cellular processes of pathogen infection and the phenotypes between OsWRKY13-overexpressing and wildtype plants, our data suggest that OsWRKY13 is also a regulator of other physiologic processes during pathogen infection. The OsWRKY13-associated disease resistance pathway synergistically interacts via OsWRKY13 with the glutathione/ glutaredoxin system and flavonoid biosynthesis pathway to monitor redox homeostasis and to putatively enhance the biosynthesis of antimicrobial flavonoid phytoalexins, respectively, in OsWRKY13-overexpressing lines. Meanwhile, the OsWRKY13-associated disease resistance pathway appears to interact antagonistically with the SNACl-mediated abiotic stress defense pathway, jasmonic acid signaling pathway, and terpenoid metabolism pathway via OsWRKY13 to suppress salt and cold defense responses as well as to putatively retard rice growth and development.

关键词： abiotic stress bacterial blight microarray Oryza sativa signal transduction.

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Rice Information GateWay： A Comprehensive Bioinformatics Platform for Indica Rice Genomes

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Molecular Plant 2018年第3期11卷 505-507页

作者： Jia-Ming,Song Yang,Lei Cheng-Cheng,Shu Yuduan,Ding Feng,Xing Hao,Liu Jia,Wang weibo,xie Jianwei,Zhang Ling-Ling,Chen National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 P. R. China Agricultural Bioinformatics Key Laboratory of Hubei Province College of Informatics Huazhong Agricultural University Wuhan 430070 China [∗]Corresponding author [∗∗]Corresponding author

Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB）（Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP）（Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS）（Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;

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Complete Dissection of the Genetic Basis of Heterosis in a Highly Heterotic Rice Hybrid Based on a Ultra-high Density Linkage Map

Complete Dissection of the Genetic Basis of Heterosis in a H...

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2010全国植物生物学研讨会

作者： Gang Zhou weibo xie Yongzhong Xing Caiguo Xu Qifa Zhang National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural University

We have been investigating genetic and molecular bases of yield and heterosis in rice using a combination of approaches,with the ultimate goal to achieve a comprehensive understanding of the biology of yield and *** focused the effort in yield traits of Shanyou 63,a cross between Zhenshan 97 and Minghui 63,which is the most widely

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