abafaraubabebfbnbpbsc1caclcrctcyd2dedidteiemepfufxgagphoidsissj9jilamanroipapdpgpipmpnptspupyrirpscsestsnsospsutctiu1u2utvlwcz9p2vrid
Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits(1,2). Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza saWang, Yuexing; Xiong, Guosheng; Hu, Jiang; Jiang, Liang; Yu, Hong; Xu, Jie; Fang, Yunxia; Zeng, Longjun; Xu, Erbo; Xu, Jing; Ye, Weijun; Meng, Xiangbing; Liu, Ruifang; Chen, Hongqi; Jing, Yanhui; Wang, Yonghong; Zhu, Xudong; Li, Jiayang; Qian, QianWang, YX; Xiong, GS; Hu, J; Jiang, L; Yu, H; Xu, J; Fang, YX; Zeng, LJ; Xu, EB; Xu, J; Ye, WJ; Meng, XB; Liu, RF; Chen, HQ; Jing, YH; Wang, YH; Zhu, XD; Li, JY; Qian, Q944[Wang, Yuexing; Hu, Jiang; Xu, Jie; Fang, Yunxia; Fitzgerald MA, 2009, TRENDS PLANT SCI, V14, P133, DOI 10.1016/j.tplants.2008.12.004; McHale LK, 2012, PLANT PHYSIOL, V159, P1295, DOI 10.1104/pp.112.194605; Qi P, 2012, CELL RES, V22, P1666, DOI 10.1038/cr.2012.151; HIEI Y, 1994, PLANT J, V6, P271, DOI 1010.1038/ngArticle1546-1718ricezxd@126.com; jyli@genetics.ac.cn; qianqian188@hotmail.com+Ministry of Science and Technology of China [2013CBA01400]; National Natural Science Foundation of CWe thank the National Medium Rice Genebank at the China National Rice Research Institute for providiCN8FGORYZA-SATIVA L; GENE; YIELD; ENCODES; WEIGHT; LENGTH; WIDTH; ARABIDOPSIS; QUALITY; PROTEIN8NAT GENETNature Genet.English27Yu, Hong/0000-0002-1748-869375 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USAAUG6NEW YORK26147619JNATURE PUBLISHING GROUP2015Yu, Hong/H-2770-2012Qian, Q (reprint author), China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou, Zhejiang, Peoples R China.Genetics & Heredity1061-4036NATURE GENETICS9Copy number variation at the GL7 locus contributes to grain size diversity in rice5062WOS:00035867410002247Genetics & Heredity1081
The deployment of heterosis in the form of hybrid rice varieties has boosted grain yield, but grain quality improvement still remains a challenge. Here we show that a quantitative trait locus for rice grain quality, qGW7, reflects allelic variation of GW7Wang, Shaokui; Li, Shan; Liu, Qian; Wu, Kun; Zhang, Jianqing; Wang, Shuansuo; Wang, Yi; Chen, Xiangbin; Zhang, Yi; Gao, Caixia; Wang, Feng; Huang, Haixiang; Fu, XiangdongWang, SK; Li, S; Liu, Q; Wu, K; Zhang, JQ; Wang, SS; Wang, Y; Chen, XB; Zhang, Y; Gao, CX; Wang, F; Huang, HX; Fu, XD949[Wang, Shaokui; Li, Shan; Liu, Qian; Wu, Kun; ZhanAHN SN, 1993, THEOR APPL GENET, V87, P27, DOI 10.1007/BF00223739; Yan XM, 2006, MOL BIOL CELL, V17, P634, DOI 10.1091/mbc.E05-08-0810; Patel H, 2005, J CELL SCI, V118, P175, DOI 10.1242/jcs.01600; Xing YZ, 2010, ANNU REV PLANT BIOL, V61, P421, DOI 10.114610.1038/ngArticle1546-1718xdfu@genetics.ac.cn+National Natural Science Foundation of China [91335207, 31130070]; Ministry of Science and TechnologWe thank G. Zhang (South China Agricultural University) for providing the single-segment substitutioCN8FGGREEN-REVOLUTION; ARABIDOPSIS; PROTEIN; GENE; QTL; COMPLEX; ORGANIZATION; ARCHITECTURE; ELONGATION; EXPRESSION8NAT GENETNature Genet.English3275 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USAAUG7NEW YORK26147620JNATURE PUBLISHING GROUP2015Fu, XD (reprint author), Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Beijing, Peoples R China.Genetics & Heredity1061-4036NATURE GENETICS7The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality4150WOS:00035867410002347Genetics & Heredity882
Fragrant rice is favoured worldwide because of its agreeable scent. The presence of a defective badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) results in the synthesis of 2-acetyl-1-pyrroline (2AP), which is a major fragrance compound. Here,Shan, Qiwei; Zhang, Yi; Chen, Kunling; Zhang, Kang; Gao, CaixiaShan, QW; Zhang, Y; Chen, KL; Zhang, K; Gao, CX791[Shan, Qiwei; Zhang, Yi; Chen, Kunling; Zhang, KanLi W, 2013, NAT BIOTECHNOL, V31, P684, DOI 10.1038/nbt.2652; Piganeau M, 2013, GENOME RES, V23, P1182, DOI 10.1101/gr.147314.112; Wang YP, 2014, NAT BIOTECHNOL, V32, P947, DOI 10.1038/nbt.2969; HIEI Y, 1994, PLANT J, V6, P271, DOI 10.1046/j.1365-313X.1994genome edi10.1111/pbArticle1467-7652cxgao@genetics.ac.cn800Ministry of Agriculture of China [2014ZX0801003B]; National Natural Science Foundation of China [312We thank the Core Facility for Metabolomics (IGDB, CAS) for help with the GC-MS assay and Prof. ShaoCM3TIORYZA-SATIVA L.; EFFECTOR NUCLEASES; CRISPR/CAS SYSTEM; DOWN-REGULATION; ZINC-FINGER; GENOME; MULTIPLEX; MUTAGENESIS; MUTATIONS; AROMA6PLANT BIOTECHNOL JPlant Biotechnol. J.English41111 RIVER ST, HOBOKEN 07030-5774, NJ USAAUG10HOBOKEN25599829JWILEY-BLACKWELL2015Gao, CX (reprint author), Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Beijing, Peoples R China.Biotechnology & Applied Microbiology; Plant Sciences1467-7644PLANT BIOTECHNOLOGY JOURNAL5Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology2536WOS:00035760680000613Biotechnology & Applied Microbiology; Plant Sciences683
Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times(1,2). Rice paddies are the largest anthropogenic methane source and produce 7-17Su, J.; Hu, C.; Yan, X.; Jin, Y.; Chen, Z.; Guan, Q.; Wang, Y.; Zhong, D.; Jansson, C.; Wang, F.; Schnurer, A.; Sun, C.Su, J; Hu, C; Yan, X; Jin, Y; Chen, Z; Guan, Q; Wang, Y; Zhong, D; Jansson, C; Wang, F; Schnurer, A; Sun, C602[Su, J.; Hu, C.; Chen, Z.; Guan, Q.; Wang, Y.; ZhoSun CX, 1998, PLANT PHYSIOL, V118, P37, DOI 10.1104/pp.118.1.37; HIEI Y, 1994, PLANT J, V6, P271, DOI 10.1046/j.1365-313X.1994.6020271.x; Narihiro T, 2011, MICROB BIOTECHNOL, V4, P585, DOI 10.1111/j.1751-7915.2010.00239.x; Edwards J, 2015, P NATL ACAD SCI10.1038/naArticle1476-4687wf@fjage.org; Chuanxin.Sun@slu.se+Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas) [219-2Special thanks to S. Stymne. We would also like to thank B. Muller, X. Feng, M. Erikson, L. Sun, S. CN7ZLMETHANOGENIC ARCHAEA; GENE-EXPRESSION; COMMUNITIES; EMISSIONS; SCALES; FLUXES; FIELD; SOIL; PCR7562NATURENatureEnglish29MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND30-Jul19LONDON26200336JNATURE PUBLISHING GROUP2015Sun, C (reprint author), Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Uppsala BioCtr, Dept Plant Biol, POB 7080, SE-75007 Uppsala, Sweden.Science & Technology - Other Topics0028-0836NATURE4Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice5877WOS:000358655200047523Multidisciplinary Sciences484
Leaf erectness is key in determining plant architecture and yield, particularly in cereal crops. Brassinosteroids (BRs) play a unique role in controlling this trait in monocots, but the underlying cellular and molecular mechanisms remain big mysteries. HeSun, Shiyong; Chen, Donghong; Li, Xiaoming; Qiao, Shenglong; Shi, Chaonan; Li, Chengxiang; Shen, Hongyun; Wang, XueluSun, SY; Chen, DH; Li, XM; Qiao, SL; Shi, CN; Li, CX; Shen, HY; Wang, XL220[Sun, Shiyong; Shi, Chaonan; Wang, Xuelu] HuazhongHacham Y, 2011, DEVELOPMENT, V138, P839, DOI 10.1242/dev.061804; Koh S, 2007, PLANT MOL BIOL, V65, P453, DOI 10.1007/s11103-007-9213-4; Yu XF, 2011, PLANT J, V65, P634, DOI 10.1111/j.1365-313X.2010.04449.x; Gonzalez-Garcia MP, 2011, DEVELOPMENT, V138, P8410.1016/j.Article1878-1551xlwang@mail.hzau.edu.cn228Ministry of Science and Technology of China [2012CB114304]; National Natural Science Foundation of CWe thank Makoto Matsuoka (Nagoya University) for providing the rice mutants of d61-1 and d2-2; D. LuCN7FKTOBACCO BY-2 CELLS; LAMINA JOINT; GSK3/SHAGGY-LIKE KINASE; ARABIDOPSIS-THALIANA; GENE-EXPRESSION; GRAIN-SIZE; RICE; YIELD; PHOSPHORYLATION; DIVISION2DEV CELLDev. CellEnglish43600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA27-Jul9CAMBRIDGE26190148JCELL PRESS2015Wang, XL (reprint author), Huazhong Agr Univ, Coll Life Sci & Technol, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China.Cell Biology; Developmental Biology1534-5807DEVELOPMENTAL CELL3Brassinosteroid Signaling Regulates Leaf Erectness in Oryza sativa via the Control of a Specific U-Type Cyclin and Cell Proliferation2233WOS:00035859940001234Cell Biology; Developmental Biology385
Bacterial flagellins are often recognized by the receptor kinase FLAGELLIN SENSITIVE2 (FLS2) and activate MAMP-triggered immunity in dicotyledonous plants. However, the capacity of monocotyledonous rice to recognize flagellins of key rice pathogens and itWang, Shanzhi; Sun, Zhe; Wang, Huiqin; Liu, Lijuan; Lu, Fen; Yang, Jun; Zhang, Min; Zhang, Shiyong; Guo, Zejian; Bent, Andrew F.; Sun, WenxianWang, SZ; Sun, Z; Wang, HQ; Liu, LJ; Lu, F; Yang, J; Zhang, M; Zhang, SY; Guo, ZJ; Bent, AF; Sun, WX1024[Wang, Shanzhi; Sun, Zhe; Wang, Huiqin; Liu, LijuaZipfel C, 2004, NATURE, V428, P764, DOI 10.1038/nature02485; Lindeberg M, 2012, TRENDS MICROBIOL, V20, P199, DOI 10.1016/j.tim.2012.01.003; Kay S, 2009, CURR OPIN MICROBIOL, V12, P37, DOI 10.1016/j.mib.2008.12.006; HAEFELE DM, 1987, APPL ENVIRON MICROB, VOsFLS2; fl10.1016/j.Article1752-9867wxs@cau.edu.cn1037National Natural Science Foundation of China [30971893]; 973 program [2011CB100700]; 111 project [B1The work is supported by the National Natural Science Foundation of China grant 30971893, the 973 prCM3WJPLANT IMMUNE-RESPONSES; PSEUDOMONAS-SYRINGAE; III EFFECTORS; PV. ORYZAE; MICROBE INTERACTIONS; DISEASE RESISTANCE; INNATE IMMUNITY; ARABIDOPSIS; VIRULENCE; TOMATO7MOL PLANTMol. Plant.English68Bent, Andrew/0000-0001-6610-9525600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA6-Jul14CAMBRIDGE25617720JCELL PRESS2015Bent, Andrew/E-5391-2016Sun, WX (reprint author), China Agr Univ, Dept Plant Pathol, 2 West Yuanmingyuan Rd, Beijing 100193, Peoples R China.Biochemistry & Molecular Biology; Plant Sciences1674-2052MOLECULAR PLANT3Rice OsFLS2-Mediated Perception of Bacterial Flagellins Is Evaded by Xanthomonas oryzae pvs. oryzae and oryzicola1220WOS:0003576156000068Biochemistry & Molecular Biology; Plant Sciences386
Stamen is a unique plant organ wherein germ cells or microsporocytes that commit to meiosis are initiated from somatic cells during its early developmental process. While genes determining stamen identity are known according to the ABC model of floral devChen, Rui; Shen, Li-Ping; Wang, Dong-Hui; Wang, Fu-Gui; Zeng, Hong-Yun; Chen, Zhi-Shan; Peng, Yi-Ben; Lin, Ya-Nan; Tang, Xing; Deng, Ming-Hua; Yao, Nan; Luo, Jing-Chu; Xu, Zhi-Hong; Bai, Shu-NongChen, R; Shen, LP; Wang, DH; Wang, FG; Zeng, HY; Chen, ZS; Peng, YB; Lin, YN; Tang, X; Deng, MH; Yao, N; Luo, JC; Xu, ZH; Bai, SN1069[Chen, Rui; Shen, Li-Ping; Wang, Dong-Hui; Chen, ZAffymetrix, 2002, GENECHIP EXPR AN DAT; Affymetrix, 2002, DAT SHEET GENECHIP R; Tang XA, 2010, PLANT PHYSIOL, V154, P1855, DOI 10.1104/pp.110.161661; Haydon MJ, 2013, NATURE, V502, P689, DOI 10.1038/nature12603; Plackett ARG, 2011, TRENDS PLANT SCI, V16, rice; earl10.1016/j.Article1752-9867shunongb@pku.edu.cn1089Ministry of Science and Technology of People's Republic of China [2009CB941502, 2007CB108701]; NatioWe thank Professor Bin Han of the National Center for Gene Research, CAS for his help in ChIP-seq exCM3WJARABIDOPSIS MALE MEIOCYTES; FLORAL HOMEOTIC GENES; PROBE LEVEL DATA; MADS BOX GENES; ANTHER DEVELOPMENT; ORYZA-SATIVA; FLOWER DEVELOPMENT; FUNCTIONAL-ANALYSIS; TAPETUM DEVELOPMENT; AUXIN BIOSYNTHESIS7MOL PLANTMol. Plant.English111Deng, Minghua/0000-0002-9143-1898600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA6-Jul21CAMBRIDGE25684654JCELL PRESS2015Deng, Minghua/B-5430-2012Bai, SN (reprint author), Peking Univ, Ctr Quantitat Biol, Beijing 100871, Peoples R China.Biochemistry & Molecular Biology; Plant Sciences1674-2052MOLECULAR PLANT0A Gene Expression Profiling of Early Rice Stamen Development that Reveals Inhibition of Photosynthetic Genes by OsMADS581621WOS:0003576156000098Biochemistry & Molecular Biology; Plant Sciences187
Sodium transporters play key roles in plant tolerance to salt stress. Here, we report that a member of the High-Affinity K+ Transporter (HKT) family, OsHKT1;1, in rice (Oryza sativa 'Nipponbare') plays an important role in reducing Na+ accumulation in shoWang, Rong; Jing, Wen; Xiao, Longyun; Jin, Yakang; Shen, Like; Zhang, WenhuaWang, R; Jing, W; Xiao, LY; Jin, YK; Shen, L; Zhang, WH1076[Wang, Rong; Jing, Wen; Xiao, Longyun; Jin, YakangBartley LE, 2013, PLANT PHYSIOL, V161, P1615, DOI 10.1104/pp.112.208694; Horie T, 2001, PLANT J, V27, P129, DOI 10.1046/j.1365-313x.2001.01077.x; Sassi A, 2012, PLANT PHYSIOL, V160, P498, DOI 10.1104/pp.112.194936; Hauser F, 2010, PLANT CELL ENVIRON, V33,10.1104/ppArticle1532-2548whzhang@njau.edu.cn+Ministry of Science and Technology in China [2012CB114200]; National Natural Science Foundation of CThis work was supported by the Ministry of Science and Technology in China (grant no. 2012CB114200 tCO6ZPNA+ TRANSPORT; HKT TRANSPORTERS; SODIUM TRANSPORTER; SALINITY TOLERANCE; FUNCTIONAL-ANALYSIS; DNA METHYLATION; GENE-EXPRESSION; HIGHER-PLANTS; K+ TRANSPORT; DURUM-WHEAT3PLANT PHYSIOLPlant Physiol.English6815501 MONONA DRIVE, ROCKVILLE, MD 20855 USAJUL25ROCKVILLE25991736JAMER SOC PLANT BIOLOGISTS2015Zhang, WH (reprint author), Nanjing Agr Univ, Coll Life Sci, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China.Plant Sciences0032-0889PLANT PHYSIOLOGY4The Rice High-Affinity Potassium Transporter1;1 Is Involved in Salt Tolerance and Regulated by an MYB-Type Transcription Factor2733WOS:000359307600027168Plant Sciences488
Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be aHua, Lei; Wang, Diane R.; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Xiao, Langtao; Zhu, Zuofeng; Fu, Qiang; Sun, Xianyou; Gu, Ping; Cai, Hongwei; McCouch, Susan R.; Sun, ChuanqingHua, L; Wang, DR; Tan, LB; Fu, YC; Liu, FX; Xiao, LT; Zhu, ZF; Fu, Q; Sun, XY; Gu, P; Cai, HW; McCouch, SR; Sun, CQ1875[Hua, Lei; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Huang XH, 2012, NATURE, V490, P497, DOI 10.1038/nature11532; Toriba T, 2014, PLANT J, V77, P616, DOI 10.1111/tpj.12411; Luo JH, 2013, PLANT CELL, V25, P3360, DOI 10.1105/tpc.113.113589; Fuller DQ, 2010, ARCHAEOL ANTHROP SCI, V2, P115, DOI 10.1007/s12520-010.1105/tpArticle1532-298Xsuncq@cau.edu.cn1888National Natural Science Foundation of China [31071395, 91335202]; China National High-tech ResearchWe thank Xiaolan Zhang for the help with RNA in situ hybridization, Pengfei Liu for the help with enCO7RILOOP-HELIX PROTEIN; ORYZA-SATIVA L.; ORIGIN; POPULATION; RUFIPOGON; TRAITS; ARCHITECTURE; ARABIDOPSIS; CULTIVATION; TRANSITION7PLANT CELLPlant CellEnglish3715501 MONONA DRIVE, ROCKVILLE, MD 20855 USAJUL14ROCKVILLE26082172JAMER SOC PLANT BIOLOGISTS2015Sun, CQ (reprint author), China Agr Univ, State Key Lab Plant Physiol & Biochem, Beijing Key Lab Crop Genet Improvement, Dept Plant Genet & Breeding,Natl Ctr Evaluat Agr, Beijing 100193, Peoples R China.Biochemistry & Molecular Biology; Plant Sciences; Cell Biology1040-4651PLANT CELL4LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice2222WOS:00035935860000927Biochemistry & Molecular Biology; Plant Sciences; Cell Biology489
Knowledge of arsenic (As) accumulation in rice (Oryza sativa L.) is important for minimizing As transfer to the food chain. The aim of this study was to investigate the role of rice nodes in As storage and distribution. Synchrotron mu X-ray fluorescence (Chen, Yi; Moore, Katie L.; Miller, Anthony J.; McGrath, Steve P.; Ma, Jian Feng; Zhao, Fang-JieChen, Y; Moore, KL; Miller, AJ; McGrath, SP; Ma, JF; Zhao, FJ3717[Chen, Yi; McGrath, Steve P.] Rothamsted Res, DeptSong WY, 2014, P NATL ACAD SCI USA, V111, P15699, DOI 10.1073/pnas.1414968111; Wu ZC, 2011, PLANT PHYSIOL, V157, P498, DOI 10.1104/pp.111.178921; Khan MA, 2010, ENVIRON SCI TECHNOL, V44, P8515, DOI 10.1021/es101952f; KUPPELWIESER H, 1991, PLANT SOIL, V132Arsenic; d10.1093/jxArticle1460-2431fangjie.zhao@njau.edu.cn3724Biotechnology and Biological Sciences Research Council (BBSRC) [BB/H006303/1, BB/JJ004561/1]; NationThe project was funded by Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/H0CN6GVSUBCELLULAR-DISTRIBUTION; GEOGRAPHICAL VARIATION; SILICON TRANSPORTER; PADDY SOILS; ACCUMULATION; GRAIN; ARABIDOPSIS; SHOOTS; BARLEY; PLANTS13J EXP BOTJ. Exp. Bot.English39McGrath, Steve/0000-0003-0952-8947; Miller, Anthony/0000-0003-0572-7607; Zhao, Fang-Jie/0000-0002-0164-169XGREAT CLARENDON ST, OXFORD OX2 6DP, ENGLANDJUL8OXFORD25922485JOXFORD UNIV PRESS2015McGrath, Steve/B-5127-2008; Miller, Anthony/B-5139-2008; Zhao, Fang-Jie/A-8339-2008Zhao, FJ (reprint author), Nanjing Agr Univ, Coll Resources & Environm Sci, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China.Plant Sciences0022-0957JOURNAL OF EXPERIMENTAL BOTANY0The role of nodes in arsenic storage and distribution in rice4461WOS:00035853340000566Plant Sciences090
The early stage of seed germination is the first step in the plant life cycle without visible morphological change, To investigate the mechanism controlling the early stage of rice seed germination, we performed gel-and label free nuclear phosphoproteomicLi, Ming; Yin, Xiaojian; Sakata, Katsumi; Yang, Pingfang; Komatsu, SetsukoLi, M; Yin, XJ; Sakata, K; Yang, PF; Komatsu, S2884[Li, Ming; Yang, Pingfang] Chinese Acad Sci, Key LMILLER J, 1985, EMBO J, V4, P1609; Schuhmann H, 2012, PHYSIOL PLANTARUM, V145, P224, DOI 10.1111/j.1399-3054.2011.01533.x; Shingaki-Wells RN, 2011, PLANT PHYSIOL, V156, P1706, DOI 10.1104/pp.111.175570; LAEMMLI UK, 1970, NATURE, V227, P680, DOI 10.1038/22rice; nuclArticle1535-3907skomatsu@affrc.go.jp2896National Natural Science Foundation of China [31271805]; National Agriculture and Food Research OrgaThe authors thank Dr. K. Sugimoto at the National Institute of Agrobiological Sciences for providingCM3ZQDISEASE RESISTANCE GENES; ZINC-FINGER PROTEINS; DNA-BINDING DOMAIN; ORYZA-SATIVA; ARABIDOPSIS; LOCALIZATION; IDENTIFICATION; PROTEASES; RESPONSES; OXYGEN7J PROTEOME RESJ. Proteome Res.English661155 16TH ST, NW, WASHINGTON, DC 20036 USAJUL13WASHINGTON26035336JAMER CHEMICAL SOC2015Komatsu, S (reprint author), Natl Inst Crop Sci, Natl Agr & Food Res Org, Tsukuba, Ibaraki 3058518, Japan.Biochemistry & Molecular Biology1535-3893JOURNAL OF PROTEOME RESEARCH0Proteomic Analysis of Phosphoproteins in the Rice Nucleus During the Early Stage of Seed Germination1515WOS:00035762440001414Biochemical Research Methods091
High-throughput technology is gradually becoming a powerful tool for routine research in rice. Interpretation of biological significance from the huge amount of data is a critical but non-trivial task, especially for rice, for which gene annotations rely Wang, Jiawei; Qi, Meifang; Liu, Jian; Zhang, YijingWang, JW; Qi, MF; Liu, J; Zhang, YJ359[Wang, Jiawei; Qi, Meifang; Liu, Jian; Zhang, YijiAnders S, 2010, GENOME BIOL, V11, DOI 10.1186/gb-2010-11-10-r106; Fabian-Marwedel T, 2002, PLANT CELL, V14, P197, DOI 10.1105/tpc.010386; Zhang WL, 2012, GENOME RES, V22, P151, DOI 10.1101/gr.131342.111; Trapnell C, 2009, BIOINFORMATICS, V25, P1105, DOI 1CARMO; Ory10.1111/tpArticle1365-313Xzhangyijing@sibs.ac.cn374Chinese Academy of Sciences [XDA01020304]; Shanghai Institutes for Biological Sciences, Chinese AcadWe thank Dr. A. Sugathan from Five Prime Therapeutics for helpful revisions, and Dr. L. Xu from our CM3WXGENOME-WIDE ASSOCIATION; SET ENRICHMENT ANALYSIS; ARABIDOPSIS-THALIANA; ABSCISIC-ACID; GENE NETWORK; EXPRESSION PROFILES; ANALYSIS TOOLKIT; RNA HELICASE; ORYZA-SATIVA; MODULE MAP2PLANT JPlant J.English60111 RIVER ST, HOBOKEN 07030-5774, NJ USAJUL16HOBOKEN26040787JWILEY-BLACKWELL2015Zhang, YJ (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai Inst Plant Physiol & Ecol, Natl Lab Plant Mol Genet, 300 Fenglin Rd, Shanghai 200032, Peoples R China.Plant Sciences0960-7412PLANT JOURNAL0CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data911WOS:00035761720001383Plant Sciences092
Global warming threatens many aspects of human life(1,2), for example, by reducing crop yields(3-5). Breeding heat-tolerant crops using genes conferring thermotolerance is a fundamental way to help deal with this challenge(4-9). Here we identify a major qLi, Xin-Min; Chao, Dai-Yin; Wu, Yuan; Huang, Xuehui; Chen, Ke; Cui, Long-Gang; Su, Lei; Ye, Wang-Wei; Chen, Hao; Chen, Hua-Chang; Dong, Nai-Qian; Guo, Tao; Shi, Min; Feng, Qi; Zhang, Peng; Han, Bin; Shan, Jun-Xiang; Gao, Ji-Ping; Lin, Hong-XuanLi, XM; Chao, DY; Wu, Y; Huang, XH; Chen, K; Cui, LG; Su, L; Ye, WW; Chen, H; Chen, HC; Dong, NQ; Guo, T; Shi, M; Feng, Q; Zhang, P; Han, B; Shan, JX; Gao, JP; Lin, HX827[Li, Xin-Min; Chao, Dai-Yin; Wu, Yuan; Chen, Ke; CHuang XH, 2012, NATURE, V490, P497, DOI 10.1038/nature11532; Mao J, 2005, P NATL ACAD SCI USA, V102, P12270, DOI 10.1073/pnas.0501011102; Gallois JL, 2009, PLANT CELL, V21, P442, DOI 10.1105/tpc.108.062372; Huang WH, 2006, PLANT CELL, V18, P2479, DOI 10.110.1038/ngArticle1546-1718jxshan@sibs.ac.cn; jpgao@sibs.ac.cn; hxlin@sibs.ac.cn+Ministry of Science and Technology of China [2012AA10A302, 2012CB944800]; National Natural Science FWe thank G.Q. Zhang and the National Mid-term Genebank for Rice of China National Rice Research InstCL6PWARABIDOPSIS 26S PROTEASOME; SEGMENT SUBSTITUTION LINES; 19S REGULATORY PARTICLE; QUANTITATIVE TRAIT LOCI; ORYZA-GLABERRIMA; HEAT-STRESS; SPOROPHYTE DEVELOPMENT; CULTIVATED RICE; GENOME; IDENTIFICATION7NAT GENETNature Genet.English5475 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USAJUL10NEW YORK25985140JNATURE PUBLISHING GROUP2015Lin, HX (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai Inst Plant Physiol & Ecol, Natl Key Lab Plant Mol Genet, Shanghai, Peoples R China.Genetics & Heredity1061-4036NATURE GENETICS6Natural alleles of a proteasome alpha 2 subunit gene contribute to thermotolerance and adaptation of African rice3144WOS:00035709030002447Genetics & Heredity793
Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation inHu, Bin; Wang, Wei; Ou, Shujun; Tang, Jiuyou; Li, Hua; Che, Ronghui; Zhang, Zhihua; Chai, Xuyang; Wang, Hongru; Wang, Yiqin; Liang, Chengzhen; Liu, Linchuan; Piao, Zhongze; Deng, Qiyun; Deng, Kun; Xu, Chi; Liang, Yan; Zhang, Lianhe; Li, Legong; Chu, ChengHu, B; Wang, W; Ou, SJ; Tang, JY; Li, H; Che, RH; Zhang, ZH; Chai, XY; Wang, HR; Wang, YQ; Liang, CZ; Liu, LC; Piao, ZZ; Deng, QY; Deng, K; Xu, C; Liang, Y; Zhang, LH; Li, LG; Chu, CC834[Hu, Bin; Wang, Wei; Ou, Shujun; Tang, Jiuyou; Li,Huang XH, 2012, NATURE, V490, P497, DOI 10.1038/nature11532; Alachiotis N, 2012, BIOINFORMATICS, V28, P2274, DOI 10.1093/bioinformatics/bts419; TA TC, 1981, SOIL SCI PLANT NUTR, V27, P347; Gao LZ, 2008, GENETICS, V179, P965, DOI 10.1534/genetics.106.0680710.1038/ngArticle1546-1718ccchu@genetics.ac.cn+Ministry of Science and Technology of China [2014AA10A602-5, 2015CB755702]; Chinese Academy of ScienWe thank H. Xue (Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, ShCL6PWCHLORATE-RESISTANT MUTANTS; ARABIDOPSIS-THALIANA; NITROGEN-UTILIZATION; POSITIVE SELECTION; JAPONICA RICE; TRANSPORTER; PLANTS; AMMONIUM; INDICA; CHL17NAT GENETNature Genet.English34Chu, Chengcai/0000-0001-8097-611575 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USAJUL7NEW YORK26053497JNATURE PUBLISHING GROUP2015Chu, CC (reprint author), Chinese Acad Sci, Inst Genet & Dev Biol, Natl Ctr Plant Gene Res Beijing, State Key Lab Plant Gen, Beijing, Peoples R China.Genetics & Heredity1061-4036NATURE GENETICS3Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies5475WOS:00035709030002547Genetics & Heredity494
OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A transcriptomic analysis of the drought response of transgenic rice plants expressing P (SARK) ::IPT, validated by qPCR, indicated that OsWRKY47 expression waRaineri, Jesica; Wang, Songhu; Peleg, Zvi; Blumwald, Eduardo; Chan, Raquel LiaRaineri, J; Wang, SH; Peleg, Z; Blumwald, E; Chan, RL401[Raineri, Jesica; Chan, Raquel Lia] Inst AgrobioteKlok EJ, 2002, PLANT CELL, V14, P2481, DOI 10.1105/tpc.004747; Chen YF, 2009, PLANT CELL, V21, P3554, DOI 10.1105/tpc.108.064980; Chen H, 2010, BMC PLANT BIOL, V10, DOI 10.1186/1471-2229-10-281; Luo X, 2013, J EXP BOT, V64, P2155, DOI 10.1093/jxb/ert073; P-SARK::IP10.1007/s1Article1573-5028eblumwald@ucdavis.edu413UC Office of the President, UC Discovery Grant [212976]; Agencia Nacional de Promocion Cientifica y This research was supported by funds from the UC Office of the President, UC Discovery Grant # 21297CL6BPDEFENSE SIGNALING PATHWAYS; DNA-BINDING PROTEINS; ARABIDOPSIS-THALIANA; DROUGHT TOLERANCE; LEAF SENESCENCE; NEGATIVE REGULATORS; ESCHERICHIA-COLI; PLANT SENESCENCE; ABIOTIC STRESSES; ENHANCES DROUGHT4月5日PLANT MOL BIOLPlant Mol.Biol.English57Peleg, Zvi/0000-0001-8063-1619VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSJUL13DORDRECHT25957211JSPRINGER2015Peleg, Zvi/A-4662-2012Blumwald, E (reprint author), Univ Calif Davis, Dept Plant Sci, Mail Stop 5,1 Shields Ave, Davis, CA 95616 USA.Biochemistry & Molecular Biology; Plant Sciences0167-4412PLANT MOLECULAR BIOLOGY2The rice transcription factor OsWRKY47 is a positive regulator of the response to water deficit stress2341WOS:00035705210000788Biochemistry & Molecular Biology; Plant Sciences395
Late stage pollen-specific promoters are important tools in crop molecular breeding. Several such promoters, and their functional motifs, have been well characterized in dicotyledonous plants such as tomato and tobacco. However, knowledge about the functiYan, Shuo; Wang, Zhongni; Liu, Yuan; Li, Wei; Wu, Feng; Lin, Xuelei; Meng, ZhengYan, S; Wang, ZN; Liu, Y; Li, W; Wu, F; Lin, XL; Meng, Z415[Yan, Shuo; Wang, Zhongni; Liu, Yuan; Wu, Feng; LiFrewer LJ, 2013, TRENDS FOOD SCI TECH, V30, P142, DOI 10.1016/j.tifs.2013.01.003; Hamilton DA, 1998, PLANT MOL BIOL, V38, P663, DOI 10.1023/A:1006083725102; PAUL W, 1992, PLANT MOL BIOL, V19, P611, DOI 10.1007/BF00026787; Zhang DB, 2009, CHINESE SCI BULL,Pollen-spe10.1007/s1Article1573-5028zhmeng@ibcas.ac.cn428National Natural Science Foundation of China [31270280]; Ministry of Science and Technology of ChinaWe thank Dr. Hualiang Liu and Dr. Wenjing Li for their technical assistance with the GUS activity anCL6BPTISSUE-SPECIFIC EXPRESSION; CIS-REGULATORY ELEMENTS; MALE-STERILITY; TRANSGENIC RICE; GENE-EXPRESSION; MESSENGER-RNAS; PLANTS; ARABIDOPSIS; ANTHER; TOBACCO4月5日PLANT MOL BIOLPlant Mol.Biol.English55VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSJUL14DORDRECHT25991036JSPRINGER2015Meng, Z (reprint author), Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, 20 Nanxincun, Beijing 100093, Peoples R China.Biochemistry & Molecular Biology; Plant Sciences0167-4412PLANT MOLECULAR BIOLOGY0Functional architecture of two exclusively late stage pollen-specific promoters in rice (Oryza sativa L.)1321WOS:00035705210000888Biochemistry & Molecular Biology; Plant Sciences096
Rice allelopathy is a hot topic in the field of allelopathy, and behaviour of donor allelopathic rice has been well documented. However, few study addresses response of receiver barnyardgrass (BYG). We found that expression of miRNAs relevant to plant horFang, Changxun; Li, Yingzhe; Li, Chengxun; Li, Biliang; Ren, Yongjie; Zheng, Haiping; Zeng, Xiaomei; Shen, Lihua; Lin, WenxiongFang, CX; Li, YZ; Li, CX; Li, BL; Ren, YJ; Zheng, HP; Zeng, XM; Shen, LH; Lin, WX1368[Fang, Changxun; Li, Yingzhe; Li, Chengxun; Li, BiKato-Noguchi H, 2013, J CHEM ECOL, V39, P175, DOI 10.1007/s10886-013-0236-9; He HB, 2012, J PLANT PHYSIOL, V169, P1747, DOI 10.1016/j.jplph.2012.06.018; Fitzgerald MA, 2009, TRENDS PLANT SCI, V14, P133, DOI 10.1016/j.tplants.2008.12.004; Michalik L, 2006,allelochem10.1111/pcArticle1365-3040lwx@fafu.edu.cn1381National Natural Science Foundation of China [31271670, 31300336]; National Research Foundation for This work was supported by the National Natural Science Foundation of China (Nos. 31271670, 31300336CJ8MUGENE-EXPRESSION; ORYZA-SATIVA; SMALL RNAS; STRESS; ALLELOCHEMICALS; PLANTS; BIOSYNTHESIS; MYXOBACTERIA; RHIZOSPHERE; MYXOCOCCUS7PLANT CELL ENVIRONPlant Cell Environ.English59111 RIVER ST, HOBOKEN 07030-5774, NJ USAJUL14HOBOKEN25438645JWILEY-BLACKWELL2015Lin, WX (reprint author), Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Agroecol Proc & Safety Monito, Fuzhou 35002, Peoples R China.Plant Sciences0140-7791PLANT CELL AND ENVIRONMENT2Identification and comparative analysis of microRNAs in barnyardgrass (Echinochloa crus-galli) in response to rice allelopathy3046WOS:00035575720001338Plant Sciences297
The phytotoxicity of aluminium (Al) ions can be alleviated by ammonium (NH4+) in rice and this effect has been attributed to the decreased Al accumulation in the roots. Here, the effects of different nitrogen forms on cell wall properties were compared inWang, Wei; Zhao, Xue Qiang; Chen, Rong Fu; Dong, Xiao Ying; Lan, Ping; Ma, Jian Feng; Shen, Ren FangWang, W; Zhao, XQ; Chen, RF; Dong, XY; Lan, P; Ma, JF; Shen, RF1382[Wang, Wei; Zhao, Xue Qiang; Chen, Rong Fu; Dong, De Boer W, 2001, SOIL BIOL BIOCHEM, V33, P853, DOI 10.1016/S0038-0717(00)00247-9; Ma JF, 2014, PLANT SOIL, V381, P1, DOI 10.1007/s11104-014-2073-1; Schubert S, 1997, Z PFLANZ BODENKUNDE, V160, P275, DOI 10.1002/jpln.19971600222; Delhaize E, 2012, TRENDS PAl-binding10.1111/pcArticle1365-3040rfshen@issas.ac.cn1390National Key Basic Research Program of China [2014CB441000]; Chinese Academy of Sciences [XDB1503030This work was supported by the National Key Basic Research Program of China (No. 2014CB441000), 'StrCJ8MUTRITICUM-AESTIVUM L; PINUS-RIGIDA SEEDLINGS; NITROGEN-SOURCE; AL-TOXICITY; NUTRIENT SOLUTIONS; NITRATE NUTRITION; ABC TRANSPORTER; ACID SOILS; L WHEAT; FT-IR7PLANT CELL ENVIRONPlant Cell Environ.English75111 RIVER ST, HOBOKEN 07030-5774, NJ USAJUL9HOBOKEN25444246JWILEY-BLACKWELL2015Shen, RF (reprint author), Chinese Acad Sci, Inst Soil Sci, State Key Lab Soil & Sustainable Agr, Nanjing 210008, Peoples R China.Plant Sciences0140-7791PLANT CELL AND ENVIRONMENT2Altered cell wall properties are responsible for ammonium-reduced aluminium accumulation in rice roots3553WOS:00035575720001438Plant Sciences298
Cellulose, which can be converted into numerous industrial products, has important impacts on the global economy. It has long been known that cellulose synthesis in plants is tightly regulated by various phytohormones. However, the underlying mechanism ofHuang, Debao; Wang, Shaogan; Zhang, Baocai; Shang-Guan, Keke; Shi, Yanyun; Zhang, Dongmei; Liu, Xiangling; Wu, Kun; Xu, Zuopeng; Fu, Xiangdong; Zhou, YihuaHuang, DB; Wang, SG; Zhang, BC; Shang-Guan, KK; Shi, YY; Zhang, DM; Liu, XL; Wu, K; Xu, ZP; Fu, XD; Zhou, YH1681[Huang, Debao; Wang, Shaogan; Zhang, Baocai; Shangde Lucas M, 2008, NATURE, V451, P480, DOI 10.1038/nature06520; Zhao Q, 2011, TRENDS PLANT SCI, V16, P227, DOI 10.1016/j.tplants.2010.12.005; Woodger FJ, 2003, J PLANT GROWTH REGUL, V22, P176, DOI 10.1007/s00344-003-0025-8; Achard P, 2009, CURR BIOL, V19, 10.1105/tpArticle1532-298Xyhzhou@genetics.ac.cn1696Ministry of Sciences and Technology of China [2012CB114501]; National Natural Science Foundation of We thank W. Yang (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences) for CM5HTCELL-WALL BIOSYNTHESIS; SECONDARY WALL; TRANSCRIPTION FACTORS; ARABIDOPSIS-THALIANA; GREEN-REVOLUTION; MOLECULAR-MECHANISM; LIGNIN BIOSYNTHESIS; GENE-EXPRESSION; KEY REGULATOR; DIRECT TARGET6PLANT CELLPlant CellEnglish7115501 MONONA DRIVE, ROCKVILLE, MD 20855 USAJUN16ROCKVILLE26002868JAMER SOC PLANT BIOLOGISTS2015Zhou, YH (reprint author), Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing 100101, Peoples R China.Biochemistry & Molecular Biology; Plant Sciences; Cell Biology1040-4651PLANT CELL2A Gibberellin-Mediated DELLA-NAC Signaling Cascade Regulates Cellulose Synthesis in Rice3638WOS:00035771880001127Biochemistry & Molecular Biology; Plant Sciences; Cell Biology299
In plants, auxin signalling is initiated by the auxin-promoted interaction between the auxin receptor TIR1, an E3 ubiquitin ligase, and the Aux/IAA transcriptional repressors, which are subsequently degraded by the proteasome. Gain-of-function mutations iJing, Hongwei; Yang, Xiaolu; Zhang, Jian; Liu, Xuehui; Zheng, Huakun; Dong, Guojun; Nian, Jinqiang; Feng, Jian; Xia, Bin; Qian, Qian; Li, Jiayang; Zuo, Jianru7395Jing, HW; Yang, XL; Zhang, J; Liu, XH; Zheng, HK; Dong, GJ; Nian, JQ; Feng, J; Xia, B; Qian, Q; Li, JY; Zuo, JR[Jing, Hongwei; Yang, Xiaolu; Zhang, Jian; Zheng, Liscum E, 2002, PLANT MOL BIOL, V49, P387, DOI 10.1023/A:1015255030047; Li BB, 2010, J PROTEOME RES, V9, P4242, DOI 10.1021/pr100560v; Park SW, 2013, P NATL ACAD SCI USA, V110, P9559, DOI 10.1073/pnas.1218872110; Tian Q, 2003, PLANT J, V36, P643, DOI 10.110.1038/ncArticlejrzuo@genetics.ac.cnNational Natural Science Foundation of China [91217302]; Ministry of Science and Technology of ChinaWe thank Dr Xiaorong Mo for cyp2-2 mutant seeds; Dr Ping Wu for osiaa11 mutant seeds; Dr Yoshiaki InCL7TTLATERAL ROOT INITIATION; OF-FUNCTION MUTATION; BOX PROTEIN TIR1; PLANT DEVELOPMENT; ARABIDOPSIS; CYCLOPHILIN; GENE; RECEPTOR; DIAGEOTROPICA; PERCEPTIONNAT COMMUNNat. Commun.English60MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLANDJUN10LONDON26096057JNATURE PUBLISHING GROUP2015Zuo, JR (reprint author), Chinese Acad Sci, State Key Lab Plant Genom, Beijing 100101, Peoples R China.Science & Technology - Other Topics2041-1723NATURE COMMUNICATIONS3Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling1218WOS:0003571753000286Multidisciplinary Sciences4100