Abe M, Katsumata H, Komeda Y, Takahashi T (2003) Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Dev 130:635–643
Article
CAS
Google Scholar
Abe Y, Mieda K, Ando T, Kono I, Yano M, Kitano H, Iwasaki Y (2010) The SMALL AND ROUND SEED1 (SRS1/DEP2) gene is involved in the regulation of seed size in rice. Genes Genet Syst 85:327–339
Article
CAS
Google Scholar
Ahmadi N, Audebert A, Bennett MJ, Bishopp A, de Oliveira AC, Courtois B, Diedhiou A, Diévart A, Gantet P, Ghesquière A, Guiderdoni E, Henry A, Inukai Y, Kochian L, Laplaze L, Lucas M, Luu DT, Manneh B, Mo X, Muthurajan R, Périn C, Price A, Robin S, Sentenac H, Sine B, Uga Y, Véry AA, Wissuwa M, Wu P, Xu J (2014) The roots of future rice harvests. Rice 7:29
Article
PubMed
PubMed Central
Google Scholar
Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinform 22:195–201
Article
CAS
Google Scholar
Bai MY, Zhang LY, Gampala SS, Zhu SW, Song WY, Chong K, Wang ZY (2007) Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice. Proc Natl Acad Sci U S A 104:13839–13844
Article
CAS
PubMed
PubMed Central
Google Scholar
Becraft P, Stinard P, McCarty D (1996) CRINKLY4: a TNFR-like receptor kinase involved in maize epidermal differentiation. Sci 273:1406–1409
Article
CAS
Google Scholar
Becraft PW, Kang SH, Suh SG (2001) The maize CRINKLY4 receptor kinase controls a cell-autonomous differentiation response. Plant Physiol 127:486–496
Article
CAS
PubMed
PubMed Central
Google Scholar
Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinform 27:343–350
Article
CAS
Google Scholar
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo Cassarino T, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258
Article
CAS
PubMed
PubMed Central
Google Scholar
Büttner M, Singh KB (1997) Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein. Proc Natl Acad Sci U S A 94:5961–5966
Article
CAS
Google Scholar
Cao X, Li K, Suh S, Guo T, Becraft (2005) Molecular analysis of the CRINKLY4 gene family in Arabidopsis thaliana. Planta 220:645–657
Article
PubMed
CAS
Google Scholar
Chen CK, Chan NL, Wang AH (2011) The many blades of the β-propeller proteins: conserved but versatile. Trends Biochem Sci 36:553–561
Article
CAS
PubMed
Google Scholar
Chen J, Gao H, Zheng XM, Jin M, Weng JF, Ma J, Ren Y, Zhou K, Wang Q, Wang J, Wang JL, Zhang X, Cheng Z, Wu C, Wang H, Wan JM (2015) An evolutionarily conserved gene, FUWA, plays a role in determining panicle architecture, grain shape and grain weight in rice. Plant J 83:427–438
Article
CAS
PubMed
Google Scholar
Cock JM, Vanoosthuyse V, Gaude T (2002) Receptor kinase signalling in plants and animals: distinct molecular systems with mechanistic similarities. Curr Opin Cell Biol 14:230–236
Article
CAS
PubMed
Google Scholar
Demko V, Ako E, Perroud PF, Quatrano R, Olsen OA (2016) The phenotype of the CRINKLY4 deletion mutant of Physcomitrella patens suggests a broad role in developmental regulation in early land plants. Planta 244:1–10
Article
CAS
Google Scholar
Dikic I, Giordano S (2003) Negative receptor signalling. Curr Opin Cell Biol 15:128–135
Article
CAS
PubMed
Google Scholar
Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G, Huang K, Huang L, Xu R, Ge S, Qian Q, Li Y (2017) Natural variation in the promoter of GSE5 contributes to grain size diversity in rice. Mol Plant 10:685–694
Article
CAS
PubMed
Google Scholar
Ebine K, Fujimoto M, Okatani Y, Nishiyama T, Goh T, Ito E, Dainobu T, Nishitani A, Uemura T, Sato MH, Thordal-Christensen H, Tsutsumi N, Nakano A, Ueda T (2011) A membrane trafficking pathway regulated by the plant-specific RAB GTPase ARA6. Nat Cell Biol 13:853–859
Article
CAS
PubMed
Google Scholar
Fu FF, Xue HW (2010) Coexpression analysis identifies rice starch regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol 154:927–938
Article
CAS
PubMed
PubMed Central
Google Scholar
Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12:393–404
CAS
PubMed
PubMed Central
Google Scholar
Gifford ML, Dean S, Ingram GC (2003) The Arabidopsis ACR4 gene plays a role in cell layer organisation during ovule integument and sepal margin development. Dev 130:4249–4258
Article
CAS
Google Scholar
Gifford ML, Robertson FC, Soares DC, Ingram GC (2005) ARABIDOPSIS CRINKLY4 function, internalization, and turnover are dependent on the extracellular CRINKLY repeat domain. Plant Cell 17:1154–1166
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo T, Chen K, Dong NQ, Shi CL, Ye WW, Gao JP, Shan JX, Lin HX (2018) GRAIN SIZE AND NUMBER1 negatively regulates the OsMKKK10-OsMKK4-OsMPK6 cascade to coordinate the trade-off between grain NUMBER per panicle and grain size in rice. Plant Cell 30:871–888
Article
CAS
PubMed
PubMed Central
Google Scholar
Hong Z, Ueguchi-Tanaka M, Shimizu-Sato S, Inukai Y, Fujioka S, Shimada Y, Takatsuto S, Agetsuma M, Yoshida S, Watanabe Y, Uozu S, Kitano H, Ashikari M, Matsuoka M (2002) Loss-of-function of a rice brassinosteroid biosynthetic enzyme, C-6 oxidase, prevents the organized arrangement and polar elongation of cells in the leaves and stem. Plant J 32:495–508
Article
CAS
PubMed
Google Scholar
Hu X, Qian Q, Xu T, Zhang Y, Dong G, Gao T, Xie Q, Xue Y (2013) The U-box E3 ubiquitin ligase TUD1 functions with a heterotrimeric G α subunit to regulate Brassinosteroid-mediated growth in rice. PLoS Genet 9:e1003391
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226
Article
CAS
PubMed
Google Scholar
Huo X, Wu S, Zhu Z, Liu F, Fu Y, Cai H, Sun X, Gu P, Xie D, Tan L, Sun C (2017) NOG1 increases grain production in rice. Nat Commun 8:1497
Article
PubMed
PubMed Central
CAS
Google Scholar
Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901–3907
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang L, Li G, Chern M, Jian R, Pham NT, Martin JA, Schackwitz WS, Zhao J, Ruan D, Huang R, Zheng J, Ronald PC (2019a) Whole-genome sequencing identifies a rice grain shape mutant, gs9–1. Rice 12:52
Jiang L, Ma X, Zhao S, Tang Y, Liu F, Gu P, Fu Y, Zhu Z, Cai H, Sun C, Tan L (2019b) The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size. Plant Cell 31:17–36
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang Y, Bao L, Jeong SY, Kim SK, Xu C, Li X, Zhang Q (2012) XIAO is involved in the control of organ size by contributing to the regulation of signaling and homeostasis of brassinosteroids and cell cycling in rice. Plant J 70:398–408
Article
CAS
PubMed
Google Scholar
Jin P, Guo T, Becraft PW (2000) The maize CR4 receptor-like kinase mediates a growth factor-like differentiation response. Genesis 27:104–116
Article
CAS
PubMed
Google Scholar
Jofuku KD, Omidyar PK, Gee Z, Okamuro JK (2005) Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc Natl Acad Sci U S A 102:3117–3122
Article
CAS
PubMed
PubMed Central
Google Scholar
Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I, Yano M, Kitano H, Iwasaki Y (2010) A novel kinesin 13 protein regulating rice seed length. Plant Cell Physiol 51:1315–1329
Article
CAS
PubMed
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549
Article
CAS
PubMed
PubMed Central
Google Scholar
Li F, Liu W, Tang J, Chen J, Tong H, Hu B, Li C, Fang J, Chen M, Chu C (2010) Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation. Cell Res 20:838–849
Article
PubMed
Google Scholar
Li N, Li Y (2016) Signaling pathways of seed size control in plants. Curr Opin Plant Biol 33:23–32
Article
PubMed
CAS
Google Scholar
Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269
Article
CAS
PubMed
Google Scholar
Liu L, Tong H, Xiao Y, Che R, Xu F, Hu B, Liang C, Chu J, Li J, Chu C (2015) Activation of Big Grain1 significantly improves grain size by regulating auxin transport in rice. Proc Natl Acad Sci U S A 112:11102–11107
Article
CAS
PubMed
PubMed Central
Google Scholar
Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci U S A 107:19579–19584
Article
CAS
PubMed
PubMed Central
Google Scholar
Marmor MD, Yarden Y (2004) Role of protein ubiquitylation in regulating endocytosis of receptor tyrosine kinases. Oncogene 23:2057–2070
Article
CAS
PubMed
Google Scholar
Mori M, Nomura T, Ooka H, Ishizaka M, Yokota T, Sugimoto K, Okabe K, Kajiwara H, Satoh K, Yamamoto K, Hirochika H, Kikuchi S (2002) Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis. Plant Physiol 130:1152–1161
Article
CAS
PubMed
PubMed Central
Google Scholar
Nan J, Feng X, Wang C, Zhang X, Wang R, Liu J, Yuan Q, Jiang G, Lin S (2018) Improving rice grain length through updating the GS3 locus of an elite variety Kongyu 131. Rice 11:21
Article
PubMed
PubMed Central
Google Scholar
Ogawa E, Yamada Y, Sezaki N, Kosaka S, Kondo H, Kamata N, Abe M, Komeda Y, Takahashi T. (2015) ATML1 and PDF2 play a redundant and essential role in Arabidopsis embryo development. Plant Cell Physiol 56:1183–1192
Article
CAS
PubMed
Google Scholar
Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7:173–182
CAS
PubMed
PubMed Central
Google Scholar
Ohto MA, Fischer RL, Goldberg RB, Nakamura K, Harada JJ (2005) Control of seed mass by APETALA2. Proc Natl Acad Sci U S A 102:3123–3128
Article
CAS
PubMed
PubMed Central
Google Scholar
Pu C, Ma Y, Wang J, Zhang Y, Jiao X, Hu Y, Wang L, Zhu Z, Sun D, Sun Y (2012) Crinkly4 receptor-like kinase is required to maintain the interlocking of the palea and lemma, and fertility in rice, by promoting epidermal cell differentiation. Plant J 70:940–953
Article
CAS
PubMed
Google Scholar
Pu CX, Han YF, Zhu S, Song FY, Zhao Y, Wang CY, Zhang YC, Yang Q, Wang J, Bu SL, Sun LJ, Zhang SW, Zhang SQ, Sun DY, Sun Y (2017) The rice receptor-like kinases DWARF AND RUNTISH SPIKELET1 and 2 repress cell death and affect sugar utilization during reproductive development. Plant Cell 29:70–89
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin Y, Yang L, Sun Z, Wang X, Wang Y, Zhang J, Rehman AU, Chen Z, Qi J, Wang B, Song CP, Yang S, Gong Z (2019) Redox-mediated endocytosis of a receptor-like kinase during distal stem cell differentiation depends on its tumor necrosis factor receptor domain. Plant Physiol doi. https://doi.org/10.1104/pp.19.00616
Article
CAS
PubMed
PubMed Central
Google Scholar
San-Bento R, Farcot E, Galletti R, Creff A, Ingram G (2014) Epidermal identity is maintained by cell-cell communication via a universally active feedback loop in Arabidopsis thaliana. Plant J 77:46–58
Article
CAS
PubMed
Google Scholar
Segami S, Kono I, Ando T, Yano M, Kitano H, Miura K, Iwasaki Y (2012) Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice. Rice 5:4
Article
PubMed
PubMed Central
Google Scholar
Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, Weng Q, Wang Y, Zhan Q, Liu K, Wei X, An K, An G, Han B (2015) OsSPL13 controls grain size in cultivated rice. Nat Genet 48:447–456
Article
CAS
Google Scholar
Song XJ (2017) Crop seed size: BR matters. Mol Plant 10:668–669
Article
CAS
PubMed
Google Scholar
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630
Article
CAS
PubMed
Google Scholar
Tan YF, Xing YZ, Li JX, Yu SB, Xu CG, Zhang QF (2000) Genetic bases of appearance quality of rice grains in shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829
Article
CAS
Google Scholar
Tanabe S, Mieda K, Ashikari M, Kitano H, Iwasaki Y (2007) Mapping of Small and Round Seed 1 gene in rice. Rice Genet Newsletters 23:44–47
Google Scholar
Tanaka A, Nakagawa H, Tomita C, Shimatani Z, Ohtake M, Nomura T, Jiang CJ, Dubouzet JG, Kikuchi S, Sekimoto H, Yokota T, Asami T, Kamakura T, Mori M (2009) BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice. Plant Physiol 151:669–680
Article
CAS
PubMed
PubMed Central
Google Scholar
Tanaka H, Watanabe M, Sasabe M, Hiroe T, Tanaka T, Tsukaya H, Ikezaki M, Machida C, Machida Y (2007) Novel receptor-like kinase ALE2 controls shoot development by specifying epidermis in Arabidopsis. Dev 134:1643–1652
Article
CAS
Google Scholar
Tanaka H, Watanabe M, Watanabe D, Tanaka T, Machida C, Machida Y (2002) ACR4, a putative receptor kinase gene of Arabidopsis thaliana, that is expressed in the outer cell layers of embryos and plants, is involved in proper embryogenesis. Plant and Cell Physiol 43:419–428
Article
CAS
Google Scholar
Tian Q, Olsen L, Sun B, Lid S, Brown R, Lemmon B, Fosnes K, Gruis D, Opsahl-Sorteberg H, Otegui M, Olsen O (2007) Subcellular localization and functional domain studies of DEFECTIVE KERNEL1 in maize and Arabidopsis suggest a model for aleurone cell fate specification involving CRINKLY4 and SUPERNUMERARY ALEURONE LAYER1. Plant Cell 19:3127–3145
Article
CAS
PubMed
PubMed Central
Google Scholar
Tichtinsky G, Vanoosthuyse V, Cock JM, Gaude T (2003) Making inroads into plant receptor kinase signalling pathways. Trends Plant Sci 8:231–237
Article
CAS
PubMed
Google Scholar
Tong H, Chu C (2018) Functional specificities of brassinosteroid and potential utilization for crop improvement. Trends Plant Sci 23:1016–1028
Article
CAS
PubMed
Google Scholar
Tsutsui T, Nakano A, Ueda T (2015) The plant-specific RAB5 GTPase ARA6 is required for starch and sugar homeostasis in Arabidopsis thaliana. Plant Cell Physiol 56:1073–1083
Article
CAS
PubMed
Google Scholar
Ueda T, Yamaguchi M, Uchimiya H, Nakano A (2001) Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana. The EMBO J 20:4730–4741
Article
CAS
PubMed
Google Scholar
Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374
Article
CAS
PubMed
Google Scholar
Wang S, Li S, Liu Q, Wu K, Zhang J, Wang S, Wang Y, Chen X, Zhang Y, Gao C, Wang F, Huang H, Fu X (2015b) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet 47:949–954
Article
CAS
PubMed
Google Scholar
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557:43–49
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W, Meng X, Liu R, Chen H, Jing Y, Wang Y, Zhu X, Li J, Qian Q (2015a) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–948
Article
CAS
PubMed
Google Scholar
Watanabe M, Tanaka H, Watanabe D, Machida C, Machida Y (2004) The ACR4 receptor-like kinase is required for surface formation of epidermis-related tissues in Arabidopsis thaliana. Plant J 39:298–308
Article
CAS
PubMed
Google Scholar
Xia T, Li N, Dumenil J, Li J, Kamenski A, Bevan MW, Gao F, Li Y (2013) The ubiquitin receptor DA1 interacts with the E3 ubiquitin ligase DA2 to regulate seed and organ size in Arabidopsis. Plant Cell 25:3347–3359
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu R, Duan P, Yu H, Zhou Z, Zhang B, Wang R, Li J, Zhang G, Zhuang S, Lyu J, Li N, Chai T, Tian Z, Yao S, Li Y (2018a) Control of grain size and weight by the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway in Rice. Mol Plant 11:860–873
Article
CAS
PubMed
Google Scholar
Xu R, Yu H, Wang J, Duan P, Zhang B, Li J, Li Y, Xu J, Lyu J, Li N, Chai T, Li Y (2018b) A mitogen-activated protein kinase phosphatase influences grain size and weight in rice. Plant J 95:937–946
Article
CAS
PubMed
Google Scholar
Ying JZ, Ma M, Bai C, Huang XH, Liu JL, Fan YY, Song XJ (2018) TGW3, a major QTL that negatively modulates grain length and weight in rice. Mol Plant 11:750–753
Article
CAS
PubMed
Google Scholar
Zafar SA, Hameed A, Nawaz MA, Wei M, Noor MA, Hussain M, Rehman M (2018) Mechanisms and molecular approaches for heat tolerance in rice (Oryza sativa L.) under climate change scenario. J INTEGR AGR 17(4):726–738
Article
CAS
Google Scholar
Zafar SA, Patil SB, Uzair M, Fang J, Zhao J, Yuan S, Uzair M, Luo Q, Shi J, Schreiber L, Li X (2020) DEGENERATED PANICLE AND PARTIAL STERILITY 1 (DPS1) encodes a CBS domain containing protein required for anther cuticle and panicle development in rice. New Phytol 225:356–375
Zeng X, Ren Z, Wu Q, Fan J, Peng PP, Tang K, Zhang R, Zhao KH, Yang X (2015) Dynamic crystallography reveals early signalling events in ultraviolet photoreceptor UVR8. Nat Plants. https://doi.org/10.1038/nplants
Zhang C, Bai MY, Chong K (2014) Brassinosteroid-mediated regulation of agronomic traits in rice. Plant Cell Rep 33:683–696
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou J, Tang X, Martin GB (1997) The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes. The EMBO J 16:3207–3218
Article
CAS
PubMed
Google Scholar
Zou L, Sun X, Zhang Z, Liu P, Wu J, Tian C, Qiu J, Lu T (2011) Leaf rolling controlled by the homeodomain leucine zipper class IV gene Roc5 in rice. Plant Physiol 156(3):1589–1602
Article
CAS
PubMed
PubMed Central
Google Scholar