Rice Functional Genomics Research: Past Decade and Future

被引：104

作者：

Li, Yan ^{[1
]}

Xiao, Jinghua ^{[1
]}

Chen, Lingling ^{[1
]}

Huang, Xuehui ^{[2
]}

Cheng, Zhukuan ^{[3
]}

Han, Bin ^{[4
]}

Zhang, Qifa ^{[1
]}

Wu, Changyin ^{[1
]}

机构：

[1] Huazhong Agr Univ, Natl Ctr Plant Gene Res Wuhan, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Hubei, Peoples R China

[2] Shanghai Normal Univ, Coll Life & Environm Sci, Shanghai 200234, Peoples R China

[3] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Natl Ctr Plant Gene Res, Beijing 100101, Peoples R China

[4] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Ctr Gene Res, Shanghai 200233, Peoples R China

来源：

MOLECULAR PLANT | 2018年 / 11卷 / 03期

基金：

中国国家自然科学基金;

关键词：

functional genomics; gene identification; green super rice; Oryza sativa; NITROGEN-USE EFFICIENCY; CONFERS BROAD-SPECTRUM; CYTOPLASMIC MALE-STERILITY; QUANTITATIVE TRAIT LOCUS; SENSITIVE MALE-STERILITY; ZINC-FINGER PROTEIN; GRAIN-SIZE; NATURAL VARIATION; WIDE ASSOCIATION; GENE-EXPRESSION;

D O I：

10.1016/j.molp.2018.01.007

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding 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 monocotyledons. 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 characterized. 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.

引用

页码：359 / 380

页数：22

共 254 条

[31] Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica [J].

Du, Zhou ;

Li, Hui ;

Wei, Qiang ;

Zhao, Xin ;

Wang, Chunchao ;

Zhu, Qilin ;

Yi, Xin ;

Xu, Wenying ;

Liu, X. Shirley ;

Jin, Weiwei ;

Su, Zhen .

MOLECULAR PLANT, 2013, 6 (05) :1463-1472

[32]

Duan PG, 2016, NAT PLANTS, V2, DOI [10.1038/NPLANTS.2015.203, 10.1038/nplants.2015.203]

[33] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[34] GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein [J].

Fan, CH ;

Xing, YZ ;

Mao, HL ;

Lu, TT ;

Han, B ;

Xu, CG ;

Li, XH ;

Zhang, QF .

THEORETICAL AND APPLIED GENETICS, 2006, 112 (06) :1164-1171

[35] Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields [J].

Fan, Xiaorong ;

Tang, Zhong ;

Tan, Yawen ;

Zhang, Yong ;

Luo, Bingbing ;

Yang, Meng ;

Lian, Xingming ;

Shen, Qirong ;

Miller, Anthony John ;

Xu, Guohua .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (26) :7118-7123

[36] Over-expression of OsPTR6 in rice increased plant growth at different nitrogen supplies but decreased nitrogen use efficiency at high ammonium supply [J].

Fan, Xiaorong ;

Xie, Dan ;

Chen, Jingguang ;

Lu, Haiyan ;

Xu, Yanling ;

Ma, Cui ;

Xu, Guohua .

PLANT SCIENCE, 2014, 227 :1-11

[37] PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice [J].

Fan, Yourong ;

Yang, Jiangyi ;

Mathioni, Sandra M. ;

Yu, Jinsheng ;

Shen, Jianqiang ;

Yang, Xuefei ;

Wang, Lei ;

Zhang, Qinghua ;

Cai, Zhaoxia ;

Xu, Caiguo ;

Li, Xianghua ;

Xiao, Jinghua ;

Meyers, Blake C. ;

Zhang, Qifa .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (52) :15144-15149

[38] Control of Leaf Senescence by an MeOH-Jasmonates Cascade that Is Epigenetically Regulated by OsSRT1 in Rice [J].

Fang, ChuanYing ;

Zhang, Hua ;

Wan, Jian ;

Wu, YangYang ;

Li, Kang ;

Jin, Cheng ;

Chen, Wei ;

Wang, ShouChuang ;

Wang, WenSheng ;

Zhang, HaiWei ;

Zhang, Pan ;

Zhang, Fei ;

Qu, LiangHuan ;

Liu, Xianqing ;

Zhou, Dao-Xiu ;

Luo, Jie .

MOLECULAR PLANT, 2016, 9 (10) :1366-1378

[39] Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice [J].

Fang, Zhongming ;

Xia, Kuaifei ;

Yang, Xin ;

Grotemeyer, Marianne Suter ;

Meier, Stefan ;

Rentsch, Doris ;

Xu, Xinlan ;

Zhang, Mingyong .

PLANT BIOTECHNOLOGY JOURNAL, 2013, 11 (04) :446-458

[40] The ENCODE (ENCyclopedia of DNA elements) Project [J].

Feingold, EA ;

Good, PJ ;

Guyer, MS ;

Kamholz, S ;

Liefer, L ;

Wetterstrand, K ;

Collins, FS ;

Gingeras, TR ;

Kampa, D ;

Sekinger, EA ;

Cheng, J ;

Hirsch, H ;

Ghosh, S ;

Zhu, Z ;

Pate, S ;

Piccolboni, A ;

Yang, A ;

Tammana, H ;

Bekiranov, S ;

Kapranov, P ;

Harrison, R ;

Church, G ;

Struhl, K ;

Ren, B ;

Kim, TH ;

Barrera, LO ;

Qu, C ;

Van Calcar, S ;

Luna, R ;

Glass, CK ;

Rosenfeld, MG ;

Guigo, R ;

Antonarakis, SE ;

Birney, E ;

Brent, M ;

Pachter, L ;

Reymond, A ;

Dermitzakis, ET ;

Dewey, C ;

Keefe, D ;

Denoeud, F ;

Lagarde, J ;

Ashurst, J ;

Hubbard, T ;

Wesselink, JJ ;

Castelo, R ;

Eyras, E ;

Myers, RM ;

Sidow, A ;

Batzoglou, S .

SCIENCE, 2004, 306 (5696) :636-640

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