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A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean

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Journal of Integrative Plant Biology 2023年第6期65卷 1536-1552页

作者： Baocheng Sun Yu Wang Qun Yang Han Gao Haiyu Niu Yansong Li Qun Ma Qing Huan Wenfeng Qian Bo Ren State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Although root nodules are essential for biological nitrogen fixation in legumes,the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes,such as soybean(Glycine max),remain incompletely ***,we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation(dpi)and annotated 17 major cell types,including six that are specific to *** identified the specific cell types responsible for each step in the ureides synthesis pathway,which enables spatial compartmentalization of biochemical reactions during soybean nitrogen *** utilizing RNA velocity analysis,we reconstructed the differentiation dynamics of soybean nodules,which differs from those of indeterminate nodules in Medicago ***,we identified several putative regulators of soybean nodulation and two of these genes,GmbHLH93 and GmSCL1,were as-yet uncharacterized in *** of each gene in soybean hairy root systems validated their respective roles in ***,enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor,GmCRE1,as a prominent component of the nodulation ***1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and depletion of leghemoglobins,accompanied by downregulation of nodule-specific gene expression,as well as almost complete abrogation of biological nitrogen *** summary,this study provides a comprehensive perspective of the cellular landscape during soybean nodulation,shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation.

关键词： cytokinin determinate nodule nitrogen fixation nodulation RNA velocity single nucleus RNA sequencing(snRNA-seq) soybean ureide

The impact of genotyping strategies and statistical models on accuracy of genomic prediction for survival in pigs

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Journal of Animal Science and Biotechnology 2023年第3期14卷 908-916页

作者： Tianfei Liu Bjarne Nielsen Ole F.Christensen Mogens SandøLund Guosheng Su institute of Animal Science Guangdong Academy of Agricultural SciencesGuangzhou 510640China Center for Quantitative genetics and genomics Aarhus University8830 TjeleDenmark Pig Research Centre SEGES1609 CopenhagenDenmark

Background:Survival from birth to slaughter is an important economic trait in commercial pig *** survival can improve both economic efficiency and animal *** aim of this study is to explore the impact of genotyping strategies and statistical models on the accuracy of genomic prediction for survival in pigs during the total growing period from birth to ***:We simulated pig populations with different direct and maternal heritabilities and used a linear mixed model,a logit model,and a probit model to predict genomic breeding values of pig survival based on data of individual survival records with binary outcomes(0,1).The results show that in the case of only alive animals having genotype data,unbiased genomic predictions can be achieved when using variances estimated from pedigreebased *** using genomic information achieved up to 59.2%higher accuracy of estimated breeding value compared to pedigree-based model,dependent on genotyping *** scenario of genotyping all individuals,both dead and alive individuals,obtained the highest *** an equal number of individuals(80%)were genotyped,random sample of individuals with genotypes achieved higher accuracy than only alive individuals with *** linear model,logit model and probit model achieved similar ***:Our conclusion is that genomic prediction of pig survival is feasible in the situation that only alive pigs have genotypes,but genomic information of dead individuals can increase accuracy of genomic prediction by 2.06%to 6.04%.

关键词： Genomic prediction Genotyping strategy Simulation Statistical models Survival

Oryza pan-genomics: A new foundation for future rice research and improvement

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The Crop Journal 2021年第3期9卷 622-632页

作者： Chao Huang Zhuo Chen Chengzhi Liang State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice ***-genomics has revolutionized genomic research in ***,rice pan-genomic studies so far have been limited mostly to cultivated accessions,with only a few close wild *** in sequencing technologies have permitted the assembly of highquality rice genome sequences at low cost,making it possible to construct genus-level pan-genomes across all *** this review,we summarize progress in current research on genetic and genomic resources in Oryza,and in sequencing and computational technologies used for rice genome and pangenome *** future work,we discuss the approaches and challenges in the construction of,and data access to,Oryza pan-genomes based on representative high-quality genome *** Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.

关键词： Oryza Pan-genome De novo assembly Genetic diversity Wild rice

OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa)

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Journal of Integrative Plant Biology 2020年第12期62卷 1983-1996页

作者： Baixiao Niu Hui Deng Tingting Li Sandeep Sharma Qianbin Yun Qianru Li Zhiguo E Chen Chen Jiangsu Key Laboratory of Crop genetics and Physiology/Key Laboratory of Plant Functional genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop genomics and Molecular Breeding/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Agricultural College of Yangzhou UniversityYangzhou 225009China Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310000China Department of genetics and Plant Breeding Institute of Agricultural SciencesBHUVaranasi 221005India

Following double fertilization,plant endosperm nuclei undergo syncytial divisions,followed by synchro-nous *** is a key event during endosperm development,but our understanding of its regulation is limited to *** this study we show that OsbZIP76 regulates cellularization in rice(Oryza sativa).Activation of OsbZIP76 coincided with the initiation of cellularization,and its knockdown or knockout mutants exhibited precocious *** involved in en-dosperm development or starch biosynthesis were pre-maturely activated in the osbzip76 *** a putative transcription factor,OsbZIP76 alone lacked transcriptional activation activity;however,it interacted with the nuclear factor Y(NF-Y)family transcription factors OsNF-YB9 and OsNF-YB1 in yeast and in ***76 and OsNF-YB9 were predominantly expressed in the endosperm and the proteins *** of osnf-yb1 and osbzip76 mu-tants showed reduced size and reduced apparent amylose *** parent-of-origin-dependent expression of OsbZIP76 is variable in different rice *** sum-mary,OsbZIP76 is an endosperm-expressed imprinted gene that regulates endosperm development in rice.

关键词： sativa) (Oryza endosperm

Towards Transgenic Primates:What can we learn from mouse genetics?

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Science China(Life Sciences) 2009年第6期52卷 506-514页

作者： WANG Phillip L. TSIEN Joe Z. Brain and Behavior Discovery institute School of MedicineMedical College of Georgia Yunnan Banna Primate Disease Model Research Center and Shanghai Institute of Brain Functional GenomicsKey Laboratory of Brain Functional GenomicsMOE & STCSMEast China Normal University

Considering the great physiological and behavioral similarities with humans,monkeys represent the ideal models not only for the study of complex cognitive behavior but also for the preclinical research and development of novel therapeutics for treating human *** powerful genetic tech-nologies initially developed for making mouse models are being explored for generating transgenic primate *** review the latest genetic engineering technologies and discuss the potentials and limitations for systematic production of transgenic primates.

关键词： Non-human primate Mouse Transgene genetics Learning Memory disease model

DsMTOPVIB Promotes Meiotic DNA Double-Strand Break Formation in Rice

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Molecular Plant 2016年第11期9卷 1535-1538页

作者： Zhihui Xue Yafei Li LeiZhang Wenqing Shi Chao Zhang Mengshi Feng Fanfan Zhang Ding Tang Hengxiu Yu Minghong Gu Zhukuan Cheng State Key Laboratory of Plant genomics and Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Key Laboratory of Crop genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional genomics of Ministry of Education Yangzhou University Yangzhou 225009 China These authors contribute equally to this article

Dear Editor,Meiotic recombination is initiated by the generation of DNA double-strand breaks （DSBs）, which are catalyzed by the Spo11 protein （de Massy, 2013）. Two key findings point to the role of Spo11 as the initiator of DSB formation in budding yeast：（1） Spo11 is linked to the 5＇ termini of the broken DNA molecules in rad50s mutants, whose meiosis has been blocked at the stage of the cleavaqe reaction （＇Keenev et al., 1997）.

关键词： DNA双链断裂减数分裂 DNA分子芽殖酵母引发剂 DSB 蛋白突变

Histone modifications and their regulatory roles in plant development and environmental memory

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Journal of genetics and genomics 2019年第10期46卷 467-476页

作者： Ting Zhao Zhenping Zhan Danhua Jiang State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China University of Chinese Academy of Sciences Beijing100101China

Plants grow in dynamic environments where they receive diverse environmental *** and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating *** on histones serve as histone code" to specify chromatin and gene *** modifications execute distinct functions on the chromatin,promoting either active transcription or gene *** writers,erasers,and readers mediate the regulation of histone modifications by catalyzing,removing,and recognizing modifications,*** evidence indicates the important function of histone modifications in plant development and environmental *** modifications also serve as environmental memory for plants to adapt to environmental *** we review recent progress on the regulation of histone modifications in plants,the impact of histone modifications on environment-controlled developmental transitions including germination and flowering,and the role of histone modifications in environmental memory.

关键词： Histone modification Transcription Germination Flowering Plant-environmental response Environmental memory

Rice receptor-like kinase OsSI-RLK2 inhibits internode elongation

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Chinese Science Bulletin 2007年第19期52卷 2657-2663页

作者： WURIYANGHAN Hada CHEN LiJuan DONG Yi LEI Gang JIA FaXing ZHANG JinSong CHEN ShouYi National Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100039 China

Receptor-like kinase participates in the early events of plant signal transduction pathways. Previously, we screened the receptor-like kinase genes in rice and performed phylogenetic analyses. In this study, we isolated a receptor-like kinase gene, OsSI-RLK2, from rice. Expression of OsSI-RLK2 was induced by ABA treatment. In vitro analysis indicates that OsSI-RLK2 has Mn2+ dependent autophosphorylation activity, but does not have this activity in the presence of Ca2+ and Mg2+. Transgenic rice with over-expressed OsSI-RLK2 displayed shortened internodes resulting in a dwarf phenotype. Taken together, these results suggest that OsSI-RLK2 may represent a new type of functional RLK in rice that can inhibit the elongation of the internode.

关键词：受体样激活酶 OsSI-RLK2 节间伸长大米

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

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Journal of genetics and genomics 2021年第12期48卷 1111-1121页

作者： Changshuo Wei Ke-Jia Shan Weiguang Wang Shuya Zhang Qing Huan Wenfeng Qian State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of hostjumping. The molecular spectrum of mutations(i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host,then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

关键词： SARS-CoV-2 Omicron Evolutionary origins Molecular spectrum of mutations Spike-ACE2 interaction Receptor-binding domain