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植物功能基因组学与生物信息学研究组

研究组简介

 

植物功能基因组学(Plant Functional Genomics)是后基因组时代兴起的以组学策略作为研究手段的学科。本课题组以植物功能基因组学、生物信息学作为基础研究手段,定位挖掘农作物、园艺植物与药用植物中关键的植物性状遗传因子,进而采用植物遗传转化、基因编辑等常用分子育种技术对植物性状进行改良。

研究方向:

1. 植物非编码DNA调控元件(Cis-regulatory elements),如启动子(Promoter)、增强子(Enhancer)的生物学功能解析;

2. 多组学联用, 如ChIP-seq、ATAC-seq、三代长读长测序技术等在解析植物转录调控的分子机制中的应用;

3. 园艺植物、药用植物基因编辑。


研究组长

姓 名

黄铭坤

性 别

职 务

研究组长

职 称

副研究员

通讯地址

江西省南昌市溪霞镇溪霞农业园科研中心

邮政编码

330114

电子邮箱

huangmk@lsbg.cn

学习经历(由近及远):

2012.9-2016.1 中国科学院华南植物园 博士

2009.9-2012.6 华南农业大学 硕士

2005.9-2009.6 华南农业大学 学士 

工作经历(由近及远):

2022.1-今 江西省、中国科学院庐山植物园

2018.3-2021.12 香港中文大学

2016.3-2018.2 北京中药研究所/北京诺禾致源生物科技公司

获奖及荣誉:

国家博士奖学金

中国科学院优秀博士论文 

研究领域:

1.植物功能基因组学、生物信息学(Dry lab);

2.植物分子生物学、植物基因编辑(Wet lab); 

承担科研项目情况:

1.庐山植物园专项基金(主持);

2.香港中文大学优秀博士后基金项目 (Impact Postdoctoral Fellowship Scheme of The Chinese University of Hong Kong) (主持);

3.香港AoE 项目(Hong Kong Research Grants Council Area of Excellence Scheme, AoE/M-403/16) (参与);

4.香港罗桂祥基金项目(Lo Kwee-Seong Biomedical Research Fund) (参与);

5.中国博士后创新计划(BX201600155) 基金项目(主持)。 

论文及论著:

1.Huang,M.,Zhang,L.,Zhou,L.,Wang,M.,Yung,W.-S.,Wang,Z.,Duan,S.,Xiao,Z.,Wang,Q.,Wang,X.,and Lam, H.M#.(2022).Identification of the accessible chromatin regions in six tissues in the soybean. Genomics [Accepted]

2.Zhang,L.,Zhou,L.,Yung,W.S.,Su,W.,and Huang,M.#(2022)Genome-wide characterization of Nuclear Factor Y transcription factors in Fagopyrum tataricum. Physiol Plant [Accepted]

3.Huang,M.,Li,M.W.,and Lam,H.M#.(2021).How noncoding open chromatin regions shape soybean domestication. Trends Plant Sci 10.1016/j.tplants.2021.06.008.

4.Huang,M.,Zhang,L.,Zhou,L.,Wang,M.,Yung,W.-S.,Wang,Z.,Duan,S.,Xiao,Z.,Wang,Q.,Wang,X.,and Lam, H.M#.(2021). An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts. Genomics 113:344-355.

5.Huang,M.,Zhang,L.,Zhou,L.,Yung,W,Li,M.,and Lam,H.M#.(2021).Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions.Genes 1210.3390/genes12050640.

6.Zhang,L.,Zhou,L.,Yung,W.S.,Su,W.,and Huang,M.#(2021).Ectopic expression of Torenia fournieri TCP8 and TCP13 alters the leaf and petal phenotypes in Arabidopsis thaliana.Physiol Plant 10.1111/ppl.13479.

7.Huang,M.,Hu,Y.,Liu,X.,Li,Y.,and Hou, X#.(2015).Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development.Front Plant Sci 6:955.10.3389/fpls.2015.00955.

8.Huang,M.,Ma,C.,Yu,R.,Mu,L.,Hou,J.,Yu,Y.,and Fan,Y#.(2015).Concurrent changes in methyl jasmonate emission and the expression of its biosynthesis-related genes in Cymbidium ensifolium flowers. Physiol Plant 153:503-512.10.1111/ppl.12275.

9.Huang,M.,Hu,Y.,Liu,X.,Li,Y.,and Hou,X#.(2015).Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4.Plant Cell 27:3099-3111.

10.Yung,W.,Wang,Q.,Huang,M.,Wong,F.,Liu,A.,Ng,M.S.,Li,M.W.,and Lam,H.M#.(2022)Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress. Plant J [Accepted]

11.Wang,G.,Li,X.,Ye,N.,Huang,M.,Feng,L.,Li,H.,and Zhang, J#.(2021).OsTPP1 regulates seed germination through the crosstalk with abscisic acid in rice.New Phytol 10.1111/nph.17300.

12.Sun,W.,Leng,L.,Yin,Q.,Xu,M.,Huang,M.,Xu,Z.,Zhang,Y.,Yao,H.,Wang,C.,Xiong,C.,and Chen,S#.(2019). The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide.Plant J 97:841-857.

13.Hu,Y.,Zhou,L.,Huang,M.,He,X.,Yang,Y.,Liu,X.,Li,Y.,and Hou, X#.(2018).Gibberellins play an essential role in late embryogenesis of Arabidopsis.Nature Plants 4:289-298.

14.Liu,X.,Hu,P.,Huang,M.,Tang,Y.,Li,Y.,Li,L.,and Hou,X#.(2016).The NF-YC–RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis.Nature Communications 7:12768.


研究组员

姓 名

张玲

性 别

职 务

研究组员

职 称

副研究员

通讯地址

江西省南昌市溪霞镇溪霞农业园科研中心

邮政编码

330114

电子邮箱

zhangl@lsbg.cn

学习经历:

2013.9-2016.6 华南农业大学 博士 园艺学院果树学专业;

2009.9-2012.6 华南农业大学 硕士 园艺学院果树学专业;

2005.9-2009.6 武汉科技学院 本科 生物工程专业。 

工作经历:

2016.8-2021.7 深圳大学 博士后 生命与海洋科学学院植物表观遗传课题组;

2012.7-2013.7 华南植物园 研究助理 植物代谢课题组。 

任职经历:

2021.8至今 江西省中国科学院庐山植物园 组员 植物功能基因组学研究组。 

获奖及荣誉:

2014.5 获 2013-2014 学年度优秀博士研究生二等奖;

2016.5 获 2015-2016 学年度优秀博士研究生一等奖。 

研究领域:

植物转录因子功能研究;植物基因编辑; 

承担科研项目情况:

1.中国科学院庐山植物园,庐山植物园专项,2021ZWZX31,园艺植物转录因子预测及功能分析,2021/12-2023/12,在研,主持;

2.国家自然科学基金委员会,面上项目,31772322,microRNA399调控番茄缺磷胁迫响应的机理研究,2018/1-2021/12,在研,参与。 

论文及论著:

1.Zhang L,Yung W,Sun W,Li MW,Huang M*.Genome-wide characterization of nuclear factor Y transcription factors in Fagopyrum tataricum. Physiol Plant.2022.

2.Zhang L,Zhou L,Yung WS,Su W*,Huang M*.Ectopic expression of Torenia fournieri TCP8 and TCP13 alters the leaf and petal phenotypes in Arabidopsis thaliana. Physiol Plant. 2021, 173(3):856-866.

3.Yu H#,Zhang L#,Wang W,Tian P,Wang W,Wang K,Gao Z,Liu S,Zhang Y,Irish VF,Huang T*.TCP5 controls leaf margin development by regulating the KNOX and BEL-like transcription factors in Arabidopsis. Journal of experimental botany. 2021, 72(5):1809-1821.

4.Huang M,Zhang L,Zhou L,Wang M,Yung WS,Wang Z,Duan S,Xiao Z,Wang Q,Wang X,Li MW,Lam HM*.An expedient survey and characterization of the soybean JAGGED 1(GmJAG1)transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts. Genomics.2021,113: 344-355.

5.Huang M,Zhang L,Zhou LM,Yung WS,Li MW,Lam HM*.Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions. Genes. 2021, 12(5):640.

6.Peng Z,Wang M,Zhang L,Jiang Y,Zhao C,Shahid MQ,Bai Y,Hao J,Peng J,Gao Y,Su W*,Yang X*. EjRAV1/2 Delay Flowering Through Transcriptional Repression of EjFTs and EjSOC1s in Loquat. Frontiers in plant science,2021,12:816086.

7.Su W, Jing Y, Lin S, Yue Z, Yang X, Xu J, Wu J, Zhang Z, Xia R, Zhu J, An N, Chen H, Hong Y, Yuan Y, Long T, Zhang L, Jiang Y, Liu Z, Zhang H, Gao Y, Liu Y, Lin H, Wang H, Yant L, Lin S*, Liu Z*. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe.Proc Natl Acad Sci. 2021, 118(20):e2101767118.

8.Jiang Y,Zhu Y,Zhang L,Su W,Peng J,Yang X,Song H,Gao Y*,Lin S*.EjTFL1 genes promote growth but inhibit flower bud differentiation in loquat. Frontiers in plant science,2020, 11.

9.Zhang L,Jiang Y,Zhu Y,Su W,Long T,Huang T,Peng J,Yu H,Lin S*,Gao Y*.Functional Characterization of GI and CO Homologs from Eriobotrya deflexa Nakai forma koshunensis.Plant cell reports, 2019, 38(5): 533-543.

10.Su W,Yuan Y,Zhang L,Jiang Y,Gan X,Bai Y,Peng J,Wu J,Liu Y*,Lin S*.Selection of the optimal reference genes for expression analyses in different materials of Eriobotrya japonica.Plant Methods,2019,15:7.

11.Jiang Y,Peng J,Zhu Y,Su W,Zhang L,Jing Y,Lin S,Gao Y*.The Role of EjSOC1s in Flower Initiation in Eriobotrya japonica.Frontiers in plant science,2019, 10:253.

12.Su W,Zhu Y,Zhang L,Yang X,Gao Y,Lin S*.The cellular physiology of loquat (Eriobotrya japonica Lindl.) fruit with a focus on how cell division and cell expansion processes contribute to pome morphogenesis. Scientia Horticulturae,2017,224: 142-149.

13.Zhang L,Yu H,Lin S*,Gao Y*.Molecular Characterization of FT and FD Homologs from Eriobotrya deflexa Nakai forma koshunensis. Frontiers in plant science,2016, 7.

14.Zhou Y,Zhang L,Gui J,Dong F,Cheng S,Mei X,Zhang L,Li Y,Su X,Baldermann S,Watanabe N,Yang Z*. Molecular cloning and characterization of a short chain dehydrogenase showing activity with volatile compounds isolated from Camellia sinensis. Plant Molecular Biology Reporter, 2015, 33(2): 253-263.