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Journal of Integrative Agriculture 2018年第10期17卷 2215-2221页

作者： CHEN Hua-tao LIU Xiao-qing ZHANG Hong-mei YUAN Xing-xing GU He-ping CUI Xiao-yan CHEN Xin Institute of Industrial Crops Jiangsu Academy of Agricultural Sciences

Salt stress is one of the major abiotic stresses affecting soybean growth. genetic improvement for salt tolerance is an effective way to protect soybean yield under salt stress conditions. Successful improvement of salt tolerance in soybean relies on identifying genetic variation that confers tolerance in soybean germplasm and subsequently incorporating these genetic resources into cultivars. In this review, we summarize the progress in genetic diversity and genetics of salt tolerance in soybean, which includes identifying genetic diversity for salt tolerant germplasm; mapping QTLs conferring salt tolerance; map-based cloning; and conducting genome-wide association study（GWAS） analysis in soybean. Future research avenues are also discussed, including high throughput phenotyping technology, the CRISPR/Cas9 Genome-Editing System, and genomic selection technology for molecular breeding of salt tolerance.

关键词： soybean genetic variation heredity gene identification salinity improvement

The ethanol response gene Cab45 can modulate the impairment elicited by ethanol and ultraviolet in PC12 cells

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Journal of genetics and Genomics 2008年第3期35卷 153-161页

作者： Yunfeng Zhu Quanli Wang Wangru Xu Sha Li Department of Oncology in Beijing 307 Hospital Fengtai District Beijing 100071 China Department of Transfusion in Beijing 307 Hospital Fengtai District Beijing 100071 China

High consumption of ethanolic beverages facilitates neurodegeneration, but the mechanism of this process still remained elusive. Suppression subtractive hybridization （SSH） is a technique for detection of rare transcripts. With SSH approach, we identified one ethanol response gene Cab45, which was down-regulated by ethanol with time-dependent manner in B104 cells. The full-length sequence of Cab45 gene was obtained by 5＇-RACE （5＇Rapid Amplification of cDNA Ends） for the first time in rat. Based on the sequence of deduced amino acid of rat Cab45, the alignment was conducted with its counterparts in different species and displayed a high conservation. Using different tissues in rat and cell lines, Cab45 was characterized by a ubiquitous expression and differentiation dependent down-regulation. Given that ethanol facilitates some cell differentiation, we hypothesize that Cab45 is involved in ethanol-mediated differentiation. With transient transfection, the function of Cab45 was investigated by up-regulation and down-regulation in PC12 cells. Ethanol treatment and UV exposure were conducted subsequently and cell proliferations were detected by MTT （Methyl Thiazolyl Tetrazolium） approach. It revealed that the up-regulation of Cab45 modulated the impairment elicited by ethanol and UV in transfected cells. As a member of new calcium binding protein family, the exact role of Cab45 still remains unclear.

关键词： ethanol Cab45 calcium-binding protein gene identification subtractive hybridization

Genome-wide identification and co-expression analysis of GDSL genes related to suberin formation during fruit russeting in pear

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Horticultural Plant Journal 2022年第2期8卷 153-170页

作者： Pujuan Zhang Hong Zhang Jianke Du Yushan Qiao Laboratory of Fruit Crop Biotechnology College of HorticultureNanjing Agricultural UniversityNanjing 210095China

Glycine-aspartic acid–serine-leucine(GDSL)type lipases/esterases genes play critical roles in plant development and are related to the responses to abiotic and biotic stress.However,little is known about the GDSL family in pear(Pyrus spp.).Studies have shown GDSL-domain proteins play key roles in suberin deposition.Suberin deposition in the fruit epidermis,also called russeting,is an important defect that negatively affects consumer's appeal in some fruit species,such as pear,apple and grapevine.Fruit russeting is mainly associated with cuticle microcracking and suberin accumulation in the inner part of the epidermal cell walls.To gain insight into the role of the GDSL gene family in suberin deposition and russet development in pear,we performed a genome-wide characterization of the GDSL family,including their identification,chromosomal localization,phylogenetic relationships,and expression patterns,in different tissues/organs in pear.One hundred and thirteen GDSL-type lipases/esterases genes were identified in the pear genome,and a phylogenetic analysis revealed that GDSL family can be classified into four distinct groups.Thirty GDSL genes were co-expressed with five homolog pear genes of three well-known suberin biosynthesis Arabidopsis genes(AtGPAT5,AtASFT,and AtCYP86B1)in the transcriptional co-expression network during pear fruit development.Among the 30 co-expressed GDSL genes,twelve genes were further analyzed by quantitative Real-time PCR,and the results showed the expression levels of the 12 genes were different between the russet exocarp and green exocarp of sand pear at different fruit development stages.Our study provides a detailed overview of the GDSL gene family and lays the foundation for future functional characterization of GDSL genes in P.bretschneideri.

关键词： Pear gene identification GDSL-type lipases/esterases Pyrus bretschneideri Russeting

Characterization and functional divergence of genes encoding sucrose transporters in oilseeds castor bean

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Oil Crop Science 2022年第1期7卷 31-39页

作者： Pei Jin Di Wu Huan Dai Rui Sun Aizhong Liu Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of EducationSouthwest Forestry UniversityKunmingChina Key Laboratory of Economic Plants and Biotechnology Yunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina

Castor bean(Ricinus communis L.)is an economically important non-edible oilseed crop.Its seed oils are rich in hydroxy fatty acid,which are highly valuable with a wide range of industrial applications.Sucrose transportation is critical in regulating the growth,development and oilseed yield in castor bean.The transporters or carriers(SUTs or SUCs)play a central role in orchestrating sucrose allocation and aiding in plant adaptation to diverse stresses.In this study,based on castor bean genome,three RcSUCs(RcSUC2,RcSUC3 and RcSUC4)were identified and characterized.The expressional profiles of RcSUCs in different tissues such as leaf,stem,root,phloem and seed tissues exhibited a distinct divergence of gene expression,suggesting that the functions of RcSUC2,RcSUC3 and RcSUC4 are differentiated into long or short-distance transportation among tissues.Additionally,under abiotic stresses including hot temperature,low temperature,drought and salt stresses,the sugar allocation among leaf,stem and roots was tested.The expressional changes of Rc SUCs in leaf,stem and root tissues were associated with sugar transportation and allocation.Taken together,the differential expression of Rc SUCs among tissues responsing to abiotic stress suggested functional differences in sucrose transport and redistribution in different tissues.This study is helpful to understand the physiological and molecular mechanisms of sucrose transportation and allocation among tissues in heterotrophic oilseeds,and could provide clues for genetic improvement and optimization of cultivation practices.

关键词： Sucrose transporter Castor bean gene identification Expression profile Abiotic stress

EST-based Analysis of gene Expression in the Porcine Brain

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Genomics, Proteomics & Bioinformatics 2004年第4期2卷 237-244页

作者： BingZhang WUJin YanwuZeng ZhixiSu SongnianHu JunYu JamesD.WatsonInstituteofGenomeSciences ZhejiangUniversity／HangzhouGenomicsInstituteHangzhou310008China TheSecondAffiliatedHospitalofChinaMedicalUniversity Shenyang110004China JamesD.WatsonInstituteofGenomeSciences ZhejiangUniversity／HangzhouGenomicsInstituteHangzhou310008China／／BeijingGenomicsInstituteChineseAcademyofSciencesBeijing101300China

Since pig is an important livestock species worldwide, its gene expressionhas been investigated intensively, but rarely in brain. In order to study gene expression profilesin the pig central nervous system, we sequenced and analyzed 43,122 high-quality 5'' end expressedsequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries,involving several different prenatal and postnatal developmental stages. The initial ESTs wereassembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Ofthese sequences, 30.6% clusters matched protein databases and represented function known sequences;75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3%matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used thecategories defined by the gene Ontology to survey gene expression in the porcine brain.

关键词： pig brain expressed sequence tags gene identification

Rice Functional Genomics Research： Past Decade and Future

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Molecular Plant 2018年第3期11卷 359-380页

作者： Yan Li Jinghua Xiaot Lingling Chen Xuehui Huang Zhukuan Cheng Bin Han Qifa Zhang Changyin Wu National Key Laboratory of Crop genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China College of Life and Environment Sciences Shanghai Normal University Shanghai 200234 China National Center for Plant gene Research State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy ofSciences Beijing 100101 China National Center for gene Research Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200233 China

Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

关键词： functional genomics gene identification green super rice Oryza sativa

Conditional optimization of transient gene manipulation in strawberry fruits and the percentage difference of phenotype（PDP） method to evaluate gene function in fruit ripening

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Conditional optimization of transient gene manipulation in s...

Exploring the metabolic diversity in major crops-from functional genomics to functional metabolomics

第三届全国植物开花·衰老与采后生物学大会

作者： Yaoyao Zhao College of Horticulture China Agriculture University

Strawberry is increasingly used as a model plant for research on fruit growth and development. The transient gene manipulation（TGM） technique is widely used to determine the function of plant genes, including those in strawberry fruits. However, its reliable application for precise identification of gene function has been difficult, owing to the lack of conditional optimization. In this study, we found that successful TGM requires optimization, with the vector type, temperature, and fruit developmental stage being three major factors determining success. Notably, we found that TGM was feasible only at the large green fruit stage and later, making it especially suitable for identifying genes involved in strawberry fruit ripening. Furthermore, we established a method called ’percentage difference of phenotype’（PDP）, in which the functional effect of a gene could be precisely and efficiently identified in strawberry fruits. The PDP method can be used to estimate the functional effect of a gene as a value from 0 to 100%, such that different genes can be quantitatively compared for their relative abilities to regulate fruit ripening. This study provides a useful tool to accelerate research into the molecular basis of strawberry fruit ripening.

关键词： FaMYB10 fruit ripening gene identification manipulation strawberry transient gene

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Exploring the metabolic diversity in major crops-from functi...