Cheng C-Y, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD (2017) Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J 89(4):789–804. https://doi.org/10.1111/tpj.13415
Article
CAS
PubMed
Google Scholar
Fu X-D (2014) Non-coding RNA: a new frontier in regulatory biology. Natl Sci Rev 1(2):190–204. https://doi.org/10.1093/nsr/nwu008
Article
CAS
PubMed
Google Scholar
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155–159. https://doi.org/10.1038/nrg2521
Article
CAS
PubMed
Google Scholar
Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP (2014) Science forum considerations when investigating lncRNA function in vivo. Elife 3:e03058. https://doi.org/10.7554/eLife.03058
Article
PubMed
PubMed Central
Google Scholar
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166. https://doi.org/10.1146/annurev-biochem-051410-092902
Article
CAS
PubMed
Google Scholar
Caixia G, Xiuwen Z, Hubo L, Mlekwa UA, Yu G, Jie X (2020) Role of lncRNAs in rice: advances and challenges. Rice Sci 27(5):384–395. https://doi.org/10.1016/j.rsci.2020.03.003
Article
Google Scholar
Wang Y, Luo X, Sun F, Hu J, Zha X, Su W, Yang J (2018) Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice. Nat Commun 9(1):1–9. https://doi.org/10.1038/s41467-018-05829-7
Article
CAS
Google Scholar
Jabnoune M, Secco D, Lecampion C, Robaglia C, Shu Q, Poirier Y (2013) A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25(10):4166–4182. https://doi.org/10.1105/tpc.113.116251
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu X, Li D, Zhang D, Yin D, Zhao Y, Ji C, Zhao X, Li X, He Q, Chen R, Hu S, Zhu L (2018) A novel antisense long noncoding RNA, TWISTED LEAF, maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice. New Phytol 218(2):774–788. https://doi.org/10.1111/nph.15023
Article
CAS
PubMed
Google Scholar
Fang J, Zhang F, Wang H, Wang W, Zhao F, Li Z, Sun C, Chen F, Xu F, Chang S, Wu L, Bu Q, Wang P, Xie J, Chen F, Huang X, Zhang Y, Zhu X, Han B, Deng X, Chu C (2019) Ef-cd locus shortens rice maturity duration without yield penalty. Proc Natl Acad Sci USA 116(37):18717–18722. https://doi.org/10.1073/pnas.181503011
Article
CAS
PubMed
PubMed Central
Google Scholar
Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci USA 109(7):2654–2659. https://doi.org/10.1073/pnas.1121374109
Article
PubMed
PubMed Central
Google Scholar
Yu Y, Zhou Y-F, Feng Y-Z, He H, Lian J-P, Yang Y-W, Lei M-Q, Zhang Y-C, Chen Y-Q (2020) Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistance. Plant Biotechnol J 18(3):679–690. https://doi.org/10.1111/pbi.13234
Article
CAS
PubMed
Google Scholar
Zhou Y-F, Zhang Y-C, Sun Y-M, Yu Y, Lei M-Q, Yang Y-W, Lian J-P, Feng Y-Z, Zhang Z, Yang L, He R-R, Huang J-H, Cheng Y, Liu Y-W, Chen Y-Q (2021) The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 12:6525. https://doi.org/10.1038/s41467-021-26795-7
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Xiao S, Li W, Feng W, Li J, Wu Z, Gao X, Liu F, Shao M (2011) Overexpression of a Harpin-encoding gene hrf1 in rice enhances drought tolerance. J Exp Bot 62(12):4229–4238. https://doi.org/10.1093/jxb/err131
Article
CAS
PubMed
PubMed Central
Google Scholar
Lafitte HR, Ismail A, Bennett J (2004) Abiotic stress tolerance in rice for Asia progress and the future. In: Fischer T, Turner N, Angus J, McIntyre L, Robertson M, Borrell A, Lloyd D (eds) New directions for a diverse planet Proceedings of the 4th International Crop Science Congress, Crop Science Society of America, Brisbane, 1337
Kawahara Y, Oono Y, Wakimoto H, Ogata J, Kanamori H, Sasaki H, Mori S, Matsumoto T, Itoh T (2016) TENOR: Database for comprehensive mRNA-seq experiments in rice. Plant Cell Physiol 57(1):e7. https://doi.org/10.1093/pcp/pcv179
Article
CAS
PubMed
Google Scholar
Kang Y-J, Yang D-C, Kong L, Hou M, Meng Y-Q, Wei L, Gao G (2017) CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res 45(W1):W12–W16. https://doi.org/10.1093/nar/gkx428
Article
CAS
PubMed
PubMed Central
Google Scholar
Seo JS, Sun H-X, Park BS, Huang C-H, Yeh S-D, Jung C, Chua N-H (2017) ELF18-INDUCED LONG-NONCODING RNA associates with mediator to enhance expression of innate immune response genes in Arabidopsis. Plant Cell 29(5):1024–1038. https://doi.org/10.1105/tpc.16.00886
Article
CAS
PubMed
PubMed Central
Google Scholar
Shim JS, Oh N, Chung PJ, Kim YS, Choi YD, Kim J-K (2018) Overexpression of OsNAC14 improves drought tolerance in rice. Front Plant Sci 9:310. https://doi.org/10.3389/fpls.2018.00310
Article
PubMed
PubMed Central
Google Scholar
Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133(4):1755–1767. https://doi.org/10.1104/pp.103.025742
Article
CAS
PubMed
PubMed Central
Google Scholar
Ward M, McEwan C, Mills JD, Janitz M (2015) Conservation and tissue-specific transcription patterns of long noncoding RNAs. J Hum Transcr 1(1):2–9. https://doi.org/10.3109/23324015.2015.1077591
Article
PubMed
PubMed Central
Google Scholar
Iwamoto M, Higo K, Takano M (2009) Circadian clock-and phytochrome-regulated Dof-like gene, Rdd1, is associated with grain size in rice. Plant Cell Environ 32(5):592–603. https://doi.org/10.1111/j.1365-3040.2009.01954
Article
CAS
PubMed
Google Scholar
Fedak H, Palusinska M, Krzyczmonik K, Brzezniak L, Yatusevich R, Pietras Z, Kaczanowski S, Swiezewski S (2016) Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript. Proc Natl Acad Sci USA 113(48):E7846–E7855. https://doi.org/10.1073/pnas.1608827113
Article
CAS
PubMed
PubMed Central
Google Scholar
Ohnuma M, Yokoyama T, Inouye T, Sekine Y, Tanaka K (2008) Polyethylene glycol (PEG)—mediated transient gene expression in a red alga, Cyanidioschyzon merolae 10D. Plant Cell Physiol 49(1):117–120. https://doi.org/10.1093/pcp/pcm157
Article
CAS
PubMed
Google Scholar
Chen S, Tao L, Zeng L, Vega-Sanchez ME, Umemura K, Wang G-L (2006) A highly efficient transient protoplast system for analyzing defence gene expression and protein-protein interactions in rice. Mol Plant Pathol 7(5):417–427. https://doi.org/10.1111/j.1364-3703.2006.00346.x
Article
CAS
PubMed
Google Scholar