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The Crop Journal 2014年第4期2卷 244-254页

作者： Yuange Wang Huaihua Liu Qingguo Xin Institute of genetics and Developmental Biology Chinese Academy of Sciences Postdoctoral Research Center of Shandong Shengfeng Seeds Co. Ltd. Yantai Academy of Agricultural Sciences

Cytokinin oxidase/dehydrogenase(CKX; EC.1.***.99.12) regulates cytokinin(CK) level in plants and plays an essential role in CK regulatory processes. CKX proteins are encoded by a small gene family with a varying number of members in different plants. In spite of their physiological importance, systematic analyses of SiCKX genes in foxtail millet have not yet been examined. In this paper, we report the genome wide isolation and characterization of SiCKXs using bioinformatic methods. A total of 11 members of the family were identified in the foxtail millet genome. SiCKX genes were distributed in seven chromosomes(chromosome 1, 3, 4, 5, 6, 7, and 11). The coding sequences of all the SiCKX genes were disrupted by introns, with numbers varying from one to four. These genes expanded in the genome mainly due to segmental duplication events. Multiple alignment and motif display results showed that all SiCKX proteins share FAD- and CK-binding domains. Putative cis-elements involved in Ca2+-response, abiotic stress response, light and circadian rhythm regulation, disease resistance and seed development were present in the promoters of SiCKX genes. Expression data mining suggested that SiCKX genes have diverse expression patterns. Real-time PCR analysis indicated that all 11 SiCKX genes were up-regulated in embryos under 6-BA treatment, and some were NaCl or PEG inducible. Collectively, these results provide molecular insights into CKX research in plants.

关键词： Foxtail millet CKX gene family Phylogenetic analysis Real-time PCR analysis

Myofiber development during embryonic to neonatal development in duck breeds differing in muscle growth rates

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Journal of Integrative Agriculture 2016年第2期15卷 403-413页

作者： LI Hui-fang SHU Jing-ting SHAN Yan-ju CHEN Wen-feng SONG Chi XU Wen-juan Key Laboratory for Poultry genetics and Breeding of Jiangsu Province Institute of Poultry Science Chinese Academy of Agricultural Science Yangzhou 225125 P.R. China Jiangsu Tengdayuan Co. ltd. Jiangyan 225538 P.R. China

Little is known about the muscle developmental patterns during embryonic to neonatal development in *** investigated the developmental patterns in the lateral gastrocnemius muscles of Gaoyou and Jinding ducks differing in their muscle growth rates during the final stages of egg incubation and the first week after *** of the MyoD gene was quantified by quantitative real-time PCR（qRT-PCR）.The average cross-sectional area and diameter of the fibers increased from embryonic day 21（E21）,peaking at E27,and then declining slightly 7 d after *** density of the fibers decreased initially but increased after hatching in both breeds and *** within-breed variation in muscle fiber-type composition was greater than the average variation between the ***,the percentage of type Ⅰ fibers increased and that of type lIb fibers decreased ***,the percentage of type lla fibers was almost constant as development proceeded in both duck *** profiles of MyoD mRNA expression were similar in both breeds,and a significantly positive relationship was observed between the expression of MyoD and the percentage of type lIb *** study firstly revealed the characteristics of duck muscle development and differences between the two breeds differing in growth ***,type lIb fibers might convert to type Ⅰ fibers in the lateral gastrocnemius,while MyoD may potentially function in controlling the muscle fiber phenotype during the secondary myogenesis of muscle development.

关键词： duck myofiber development MyoD gene gene expression

Genetic relationship between purebred and crossbred sow longevity

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Journal of Animal Science and Biotechnology 2017年第1期8卷 24-29页

作者： C.E.Abell R.L.Fernando T.V.Serenius M.F.Rothschild K.A.Gray K.J.Stalder Department of Animal Science Iowa State University Ames IA 50011-3150 USA Figen ltd. PO Box 31960101 Seinajoki Finland Smithfield Premium genetics 316 W. Charity Rd Rose Hill NC 28458 USA

Background： The overall breeding objective for a nucleus swine selection program is to improve crossbred commercial performance. Most genetic improvement programs are based on an assumed high degree of positive relationship between purebred performance in a nucleus herd and their relatives＇ crossbred performance in a commercial herd. The objective of this study was to examine the relationship between purebred and crossbred sow longevity performance. Sow longevity was defined as a binary trait with a success occurring if a sow remained in the herd for a certain number of parities and including the cumulative number born alive as a measure of reproductive success. Heritabilities, genetic correlations, and phenotypic correlations were estimated using ***： Results indicated little to no genetic correlations between crossbred and purebred reproductive *** indicates that selection for longevity or lifetime performance at the nucleus level may not result in improved longevity and lifetime performance at the crossbred level. Early parity performance was highly correlated with lifetime performance indicating that an indicator trait at an early parity could be used to predict lifetime performance. This would allow a sow to have her own record for the selection trait before she has been removed from the ***： Results from this study aid in quantifying the relationship between purebred and crossbred performance and provide information for genetic companies to consider when developing a selection program where the objective is to improve crossbred sow performance. Utilizing crossbred records in a selection program would be the best way to improve crossbred sow productivity.

关键词： Binary traits Sow longevity Threshold model

Current and future editing reagent delivery systems for plant genome editing

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Science China(Life Sciences) 2017年第5期60卷 490-505页

作者： Yidong Ran Zhen Liang Caixia Gao Genovo Biotechnology Co. Ltd. Tianjin 301700 China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China

Many genome editing tools have been developed and new ones are anticipated; some have been extensively applied in plant genetics, biotechnology and breeding, especially the CRISPR/Cas9 system. These technologies have opened up a new era for crop improvement due to their precise editing of user-specified sequences related to agronomic traits. In this review, we will focus on an update of recent developments in the methodologies of editing reagent delivery, and consider the pros and cons of current delivery systems. Finally, we will reflect on possible future directions.

关键词： genome editing DNA RNA RNP and virus delivery Agrobacterium-mediated transformation biolistic method protoplast transfeetion ttransgene-free genome edited plant

Untargeted LC–MS Data Preprocessing in Metabolomics

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Journal of Analysis and Testing 2017年第3期1卷 187-192页

作者： He Tian Bowen Li Guanghou Shui State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China LipidALL Technologies ltd. Changzhou 213000China

Liquid chromatography–mass spectrometry(LC–MS)has enabled the detection of thousands of metabolite features from a single biological sample that produces large and complex *** of the key issues in LC–MS-based metabolomics is comprehensive and accurate analysis of enormous amount of *** free data preprocessing tools,such as XCMS,MZmine,MAVEN,and MetaboAnalyst,as well as commercial software,have been developed to facilitate data ***,researchers are challenged by the inevitable and unconquerable yields of numerous false-positive peaks,and human errors while manually removing such false *** with continuous improvements of data processing tools,there can still be many mistakes generated during data *** addition,many data preprocessing software exist,and every tool has its own advantages and ***,a researcher needs to judge what kind of software or tools to choose that most suit their vendor proprietary formats and goal of downstream ***,we provided a brief introduction of the general steps of raw MS data processing,and properties of automated data processing ***,characteristics of mainly free data preprocessing software were summarized for researchers’consideration in conducting metabolomics study.

关键词： Metabolomics Data preprocessing LC-MS Free software/tools

Decoding the chromatin accessibility in Andrographis paniculata genome,a case study of genome-wide investigation of the cis-regulatory elements in medicinal plants

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Acta Pharmaceutica Sinica B 2024年第9期14卷 4179-4182页

作者： Mingkun Huang Yufang Hu Ling Zhang Hua Yang Chen Feng Chunhong Jiang Ning Xie Difa Liu Shilin Chen Jihua Wang Wei Sun Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization Lushan Botanical GardenChinese Academy of SciencesJiujiang 332900China Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine China Academy of Chinese Medical SciencesInstitute of Chinese Materia Medic1Beijing 100070China State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Institute of Chinese Materia Medic1China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Guangdong Provincial Key Laboratory of Crops genetics and Improvement Crop Research InstituteGuangdong Academy of Agriculture SciencesGuangzhou 510640China State Key Laboratory of Innovative Natural Medicine and TCM Injections Jiangxi Qingfeng Pharmaceutical Co.Ltd.Ganzhou 341008China

To the Editor:Medicinal plants have the ability to synthesize a large number of pharmaceutical metabolites,the production and regulation of which are influenced by both intrinsic signals(e.g.,the spatial and temporal stage)and extrinsic environmental conditions(e.g.,temperature,light availability,and water availability)*** to the Encyclopedia of DNA Elements(ENCODE)project2,accessible chromatin regions(ACRs)served essential roles in maintaining the genome architecture and gene regulation in both mammals and ***,identifying ACRs within medicinal plant genomes remains a challenge,as genomic sequences have been determined for numerous species yet the characterization of such functional elements *** this study,we selected Andrographis paniculata(APA)3 as a model system to map ACRs genome-wide by the assay for transposase-accessible chromatin with sequencing(ATAC-seq)*** aimed to uncover the genomic features of ACRs as well as their association with the expression of genes involved in secondary metabolite biosynthesis(e.g.,andrographolide)within medicinal plants(Supporting Information Fig.S1).

关键词： Andrographis paniculata Chromatin accessibility Medicinal plant Epigenetics ENCODE cis-regulatory elements

Antimicrobial peptides act on the rumen the performance of castrated bulls

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Journal of Animal Science and Biotechnology 2023年第3期14卷 1218-1234页

作者： Jinping Shi Yu Lei Jianping Wu Zemin Li Xiao Zhang Li Jia Ying Wang Yue Ma Ke Zhang Qiang Cheng Zhao Zhang Yannan Ma Zhaomin Lei College of Animal Science and Technology Gansu Agricultural UniversityLanzhou 730070China Key Laboratory of Animal genetics Breeding and Reproduction of Shanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Institute of Rural Development Northwest Normal UniversityLanzhou 730070China Jingchuan Xu Kang Food Co. Ltd.Pingliang 744300China Gansu Huarui Agriculture Co. Ltd.Zhangye 734500China

Background Many countries have already banned the use of antibiotics in animal husbandry,making it extremely difficult to maintain animal health in livestock *** the livestock industry,there is an urgent need to develop alternatives to antibiotics which will not lead to drug resistance on prolonged *** this study,eighteen castrated bulls were randomly divided into two *** control group(CK)was fed the basal diet,while the antimicrobial peptide group(AP)was fed the basal diet supplemented with 8 g of antimicrobial peptides in the basal diet for the experimental period of 270 *** were then slaughtered to measure production performance,and the ruminal contents were isolated for metagenomic and metabolome sequencing *** The results showed that antimicrobial peptides could improve the daily weight,carcass weight,and net meat weight of the experimental ***,the rumen papillae diameter and the micropapillary density in the AP were significantly greater than those in the ***,the determination of digestive enzymes and fermentation parameters showed that the contents of protease,xylanase,andβ-glucoside in the AP were greater than those in the ***,lipase content in the CK was greater than that in the ***,the content of acetate,propionate,butyrate,and valerate was found to be greater in AP than those in *** metagenomic analysis annotated 1993 differential microorganisms at the species *** KEGG enrichment of these microorganisms revealed that the enrichment of drug resistance-related pathways was dramatically decreased in the AP,whereas the enrichment of immune-related pathways was significantly *** was also a significant reduction in the types of viruses in the AP.187 probiotics with significant differences were found,135 of which were higher in AP than in *** was also found that the antimicrobial mechanism of the antimicrobial peptides was quite *** low-abundance microor

关键词： Antimicrobial peptides Castrated bull Growth performance Metabolites Microorganisms Rumen

Strategy for Public Service for Less or Zero Pesticide Residual in Fresh Vegetables （Learning by Doing and Demand-supply）

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Journal of Life Sciences 2016年第7期10卷 328-333页

作者： Dr. M.L. Anothai Choomsai Green World genetics (Thailand) Co. Ltd. Maesuai Chaing Rai Thailand

The government must seriously consider the casualty in health due to pesticide residual in vegetables.

关键词：蔬菜农药残留服务策略新鲜蔬菜

The transcription factor GATA10 regulates fertility conversion of a two-line hybrid tms5 mutant rice via the modulation of UbL40 expression^∞

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Journal of Integrative Plant Biology 2020年第7期62卷 1034-1056页

作者： Jing Jin Songtao Gui Qian Li Ying Wang Hongyuan Zhang Zhixuan Zhu Hao Chen Yueyang Sun Yu Zou Xingguo Huang Yi Ding State Key Laboratory of Hybrid Rice Department of GeneticsCollege of Life SciencesWuhan UniversityWuhan 430072China Institute of Vegetable Wuhan Academy of Agricultural SciencesWuhan 430072China Wuhan Wuda Tianyuau Bio-Tech Co. Ltd.Wuhan 430070China

The thermosensitive genic male sterile 5(tms5)mutation causes thermosensitive genic male sterility in rice(Oryza sativa)through loss of RNase ZS1 function,which influences ubiquitin fusion ribosomal protein L40(UbL40)messenger RNA levels during male ***,we used ATAC-seq,combined with analysis of H3K9ac and H3K4me2,to identify changes in accessible chromatin during fertility conversion of the two-line hybrid rice Wux-iang S(WXS)derived from a mutant tms5 ***-thermore,RNA-seq and bioinformatic analyses identified specific transcription factors(TFs)in differentially accessible chromatin *** these TFs,only GATA10 targeted ***10 knockout mutations,which resulted in low expression of UbL40 and a tendency toward male fertility,confirmed that GATA10 regulated fertility conversion via themodulation of ***,GATA10 acted as a medi-ator for interactions with ERF65,which revealed that tran-scriptional regulation is a complex process involving multiple complexes of TFs,namely TF *** appears that the ERF141/MADS7/MADS50/MYB modules affect metabolic processes that control anther and pollen development,es-pecially cell wall *** analysis revealed that these modules directly or indirectly affect metabolic pathway-re-lated genes to coordinate plant growth with proper anther development,and furthermore,that GATA10 regulates fer-tility conversion via the modulation of UbL40 expression.

关键词： sativa fertility sterile

Genome-wide screening of long non-coding RNAs involved in rubber biosynthesis in Eucommia ulmoides

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Journal of Integrative Plant Biology 2018年第11期60卷 1070-1082页

作者： Huimin Liu Yan Lu Juan Wang Jingjing Hu Tana Wuyun State Key Laboratory of Tree genetics and Breeding Non-timber Forest Research and Development CenterChinese Academy of ForestryZhengzhou 450003China State Key Laboratory of Tree genetics and Breeding Research Institute of ForestryChinese Academy of ForestryBeijing 100091China Chemistry department University of Missouri-ColumbiaColumbia MO 65201USA Inertia Shanghai Biotechnology Co. Ltd.Shanghai 200335China

Increasing evidence indicates that long non- coding RNAs （IncRNAs） play pivotal roles in regulatory networks controlling plant and animal gene expression. However, IncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber （Eu-rubber）, are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,1o3 IncRNAs and 9,048 transcripts of uncertain coding potential （TUCPs） were *** differentially expressed （DE）TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis （GIEBs）, as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which ＂commanders＂（DE TUCPs） direct the ＂builders＂（DE genes） to construct a ＂storehouse＂ of materials needed for Eu-rubber synthesis, and the ＂workers＂（GIEBs） to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.

关键词： RNA Genome-wide screening of long non-coding RNAs involved in rubber biosynthesis in Eucommia ulmoides Eu