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genome editing opens a new era of genetic improvement in polyploid crops

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The Crop Journal 2019年第2期7卷 141-150页

作者： Qamar U.Zaman Chao Li Hongtao Cheng Qiong Hu Oil Crops Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture Graduate School of Chinese Academy of Agricultural Sciences

Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.

关键词： genome editing CRISPR Site-specific mutagenesis Polyploid Crop improvement

genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis

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Virologica Sinica 2015年第6期30卷 417-424页

作者： Shan Zhang Zheng Zhu Shifeng Sun Qijin Chen Fei Deng Kai Yang State Key Laboratory of Biocontrol Sun Yat-sen University State Key Laboratory of Virology and China Center for Virus Culture Collection Wuhan Institute of Virology Chinese Academy of Sciences Guangdong Haina Agriculture Co. Ltd

The complete genome of Cnaphalocrocis medinalis granulovirus(CnmeGV) from a serious migratory rice pest, Cnaphalocrocis medinalis(Lepidoptera: Pyralidae), was sequenced using the Roche 454 genome Sequencer FLX system(GS FLX) with shotgun strategy and assembled by Roche GS De Novo assembler software. Its circular double-stranded genome is 111,246 bp in size with a high A+T content of 64.8% and codes for 118 putative open reading frames(ORFs). It contains 37 conserved baculovirus core ORFs, 13 unique ORFs, 26 ORFs that were found in all Lepidoptera baculoviruses and 42 common ORFs. The analysis of nucleotide sequence repeats revealed that the CnmeGV genome differs from the rest of sequenced GVs by a 23 kb and a 17 kb gene block inversions, and does not contain any typical homologous region(hr) except for a region of non-hr-like sequence. Chitinase and cathepsin genes, which are reported to have major roles in the liquefaction of the hosts, were not found in the CnmeGV genome, which explains why CnmeGV infected insects do not show the phenotype of typical liquefaction. Phylogenetic analysis,based on the 37 core baculovirus genes, indicates that CnmeGV is closely related to Adoxophyes orana granulovirus. The genome analysis would contribute to the functional research of CnmeGV,and would benefit to the utilization of CnmeGV as pest control reagent for rice production.

关键词： baculovirus granulovirus Cnaphalocrocis medinalis granulovirus(CnmeGV) genome sequencing

genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

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Chinese Journal of Oceanology and Limnology 2014年第1期32卷 8-21页

作者：王家丰亓海刚李莉张国范 Institute of Oceanology Chinese Academy of Sciences University of Chinese Academy of Sciences

Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the fi rst genome-wide investigation of microsatellites in the Pacifi c oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacifi c oyster genome is rich in microsatellites. A total of 604 653 repeats were identifi ed, in average of one locus per 815 base pairs(bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of(A)n and(C)n repeats and abundant long(C)n repeats(≥24 bp); 3) large average length of(AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-fl anking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identifi ed. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the fi eld of oyster genetics, particularly for molecular-based selection and breeding.

关键词： microsatellites genome Pacific oyster Crassostrea gigas

genome-wide detection of selective signatures in a Jinhua pig population

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Journal of Integrative Agriculture 2020年第5期19卷 1314-1322页

作者： XU Zhong SUN Hao ZHANG Zhe Zhao Qing-bo Babatunde Shittu Olasege Li Qiu-meng Yue Yang Ma Pei-pei Zhang Xiang-zhe Wang Qi-shan Pan Yu-chun Department of Animal Science School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240P.R.China Shanghai Key Laboratory of Veterinary Bio-technology Shanghai 200240P.R.China

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig *** results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production *** the present study,we performed extended haplotype homozygosity(EHH)tests to identify significant core regions in 202 Jinhua pigs.A total of 26161 core regions spanning 636.42 Mb were identified,which occupied approximately 28%of the genome across all autosomes,and 1158 significant(Pgenome-wide map of selection signature in the pig genome,and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.

关键词： pig genome selection signatures extended haplotype homozygosity(EHH) candidate genes

genome of Wild Mandarin and Domestication History of Mandarin

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Molecular Plant 2018年第8期11卷 1024-1037页

作者： Lun Wang Fa He Yue Huang Jiaxian He Shuizhi Yang Jiwu Zeng Chongling Deng Xiaolin Jiang Yiwen Fang Shaohua Wen Rangwei Xu Huiwen Yu Xiaoming Yang Guangyan Zhong Chuanwu Chen Xiang Yan Changfu Zhou Hongyan Zhang Zongzhou Xie Robert M. Larkin Xiuxin Deng Qiang Xu Key Laboratory of Horticultural Plant Biotogy (Ministry of Education) Huazhong Agricultural University Wuhan 430070 P.R. China Horticulture institute Hunan Academy of Agricultural Sciences Changsha 410125 P.R. China Fruit Tree Research Institute Guangdong Academy of Agricultural Sciences Guangzhou 510640 P.R. China Guangxi Key Laboratory of Citrus Biology Guangxi Academy of Specialty Crops Guilin 541000 P.R. China Institute of Citrus Science Research of Ganzheu City Ganzhou 341000 P.R. China

Mandarin （Citrus reticulata） is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins （MD1 and MD2） in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase （ACO） gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.

关键词： Citrus Citric acid Domestication genome Wild mandarin

genome Sequence of a Marine Carotenoid Producing Yeast Rhodotorula mucilaginosa CYJ03

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Journal of Ocean University of China 2020年第2期19卷 466-472页

作者： TANG Wei WANG Yue CAI Yali LIU Shibo ZHANG Jun HE Zengguo School of Medicine and Pharmacy Ocean University of ChinaQingdao 266000China Marine Microbiological Engineering&Research Center Marine Biomedical Research Institute of QingdaoQingdao 266000China

Carotenoids are valuable pigments that have been widely used in food,pharmaceutical,animal breeding and cosmetics *** to the increasing demand for carotenoids of natural origin,the trend for production of carotenoids by red yeast has become *** Rhodotorula mucilaginosa CYJ03 was isolated from northern Yellow Sea of China for its carotenoid producing *** was found that the whole genome of CYJ03 was 19.03 Mb in size and contained 6301 protein-coding genes including a gene cluster for the carotenoids *** genome sequence would be valuable for exploring the potential biological properties of CYJ03,as well as for facilitating the molecular genetic analysis and the manipulation of carotenoids accumulation in this strain,and for the development of it as an engineered host for carotenoid production.

关键词： Rhodotorula mucilaginosa CYJ03 genome carotenoid biosynthesis pathway gene cluster

Mutation analyses of integrated HBV genome in hepatitis B patients

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Journal of Genetics and Genomics 2008年第2期35卷 85-90页

作者： Peilin Wang Xiuhai Wang Shuying Cong Hongming Ma Xuecheng Zhang Laboratory of Medical Genetics Medical College of Qingdao University Qingdao 266021 China Laboratory of Molecular Genetics College of Marine Life Science Ocean University of China Qingdao 266003 China

Little has been learnt in the last 30 years about detection of HBV genome as well as its mutation analysis between hepatitis B fathers （HBF） and their children. In this study, we used nest polymerase chain reaction （PCR）, fluorescence in situ hybridization （FISH）, and DNA sequencing analysis, to examine the integrated HBV genome in paraffin-embedded testis tissues, which were taken as samples from HBE and in peripheral blood mononuclear cells （PBMC） from 74 cases of HBFs and their children who were born after their fathers＇ HBV infection （caHBF）. We found that HBV DNA existed in testis tissues, mainly in the basilar parts of the seminiferous tubules, and also in PBMC of HBE It was also documented that there were point mutations of poly-loci, insertions and deletions of nucleotides in integrated HBV genomes, and the types of gene mutations in the HBFs were similar to those in caHBE This study addresses the major types of gene mutations in integrated HBV genome in human patients and also presents reliable evidence of possible genetic transmission of hepatitis B.

关键词： genome hepatitis B virus (HBV) gene mutation vertical transmission

genome editing in Bombyx mori: New opportunities for silkworm functional genomics and the sericulture industry

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Insect Science 2019年第6期26卷 964-972页

作者： San-Yuan Ma Guy Smagghe Qing-You Xia State Key Laboratory of Silkworm genome Biology Southwest University ChongqingChina Chongqing Engineering and Technology Research Center for Novel Silk Materials Southwest University Chongqing China Department of Crop Protection Faculty of Bioscience Engineering Ghent University Ghent Belgium

In recent years, research in life sciences has been remarkably revolutionized owing to the establishment, development and application of genome editing technologies. genome editing has not only accelerated fundamental research but has also shown promising applications in agricultural breeding and therapy. In particular, the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology has become an indispensable tool in molecular biology owing to its high efficacy and simplicity. genome editing tools have also been established in silkworm (Bombyx mori), a model organism of Lepidoptera insects with high economic importance. This has remarkably improved the level and scope of silkworm research and could reveal new mechanisms or targets in basic entomology and pest management studies. In this review, we summarize the progress and potential of genome editing in silkworm and its applications in functional genomic studies for generating novel genetic materials.

关键词： CRISPR genome editing silkworm TALEN ZFN

genome-editing technologies: the gap between application and policy

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Science China(Life Sciences) 2019年第11期62卷 1534-1538页

作者： Gousi Li Yao-Guang Liu Yuanling Chen State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhou 510642China Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions South China Agricultural UniversityGuangzhou 510642China College of Life Sciences South China Agricultural UniversityGuangzhou 510642China

genome editing is a new technology for manipulating genomic DNA sequences at specific sites,and researchers worldwide are rapidly developing new variants of genomeediting applications that target mRNAs,viruses,chromat... 详细信息

关键词： genome processes. editing