[1]

Zeng D, Tian Z, Rao Y, Dong G, Yang Y, et al. 2017. Rational design of high-yield and superior-quality rice. Nature Plants 3:17031

doi: 10.1038/nplants.2017.31
[2]

Ma GH, Yuan LP. 2015. Hybrid rice achievements, development and prospect in China. Journal of Integrative Agriculture 14:197−205

doi: 10.1016/S2095-3119(14)60922-9
[3]

Tilman D, Balzer C, Hill J, Befort BL. 2011. Global food demand and the sustainable intensification of agriculture. Proceedings of the National Academy of Sciences of the United States of America 108:20260−64

doi: 10.1073/pnas.1116437108
[4]

Zhou G, Chen Y, Yao W, Zhang C, Xie W, et al. 2012. Genetic composition of yield heterosis in an elite rice hybrid. Proceedings of the National Academy of Sciences of the United States of America 109:15847−52

doi: 10.1073/pnas.1214141109
[5]

Liu J, Wu MW, Liu CM. 2022. Cereal endosperms: development and storage product accumulation. Annual Review of Plant Biology 73:255−91

doi: 10.1146/annurev-arplant-070221-024405
[6]

Huang L, Tan H, Zhang C, Li Q, Liu Q. 2021. Starch biosynthesis in cereal endosperms: An updated review over the last decade. Plant Communications 2:100237

doi: 10.1016/j.xplc.2021.100237
[7]

Huang B, Hennen-Bierwagen TA, Myers AM. 2014. Functions of multiple genes encoding ADP-glucose pyrophosphorylase subunits in maize endosperm, embryo, and leaf. Plant Physiology 164:596−611

doi: 10.1104/pp.113.231605
[8]

Wei X, Jiao G, Lin H, Sheng Z, Shao G, et al. 2017. GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development. Journal of Integrative Plant Biology 59:134−53

doi: 10.1111/jipb.12510
[9]

Shure M, Wessler S, Fedoroff N. 1983. Molecular identification and isolation of the Waxy locus in maize. Cell 35:225−33

doi: 10.1016/0092-8674(83)90225-8
[10]

Wang ZY, Wu ZL, Xing YY, Zheng FG, Guo XL, et al. 1990. Nucleotide sequence of rice waxy gene. Nucleic Acids Research 18:5898

doi: 10.1093/nar/18.19.5898
[11]

Liu DR, Huang WX, Cai XL. 2010. Oligomerization of rice granule-bound starch synthase 1 modulates its activity regulation. Plant Science 210:141−50

doi: 10.1016/j.plantsci.2013.05.019
[12]

Wang W, Wei X, Jiao G, Chen W, Wu Y, et al. 2020. GBSS-BINDING PROTEIN, encoding a CBM48 domain-containing protein, affects rice quality and yield. Journal of Integrative Plant Biology 62:948−66

doi: 10.1111/jipb.12866
[13]

Zhang G, Cheng Z, Zhang X, Guo X, Su N, et al. 2011. Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch. Genome 54:448−59

doi: 10.1139/g11-010
[14]

Crofts N, Satoh Y, Miura S, Hosaka Y, Abe M, et al. 2022. Active-type starch synthase (SS) IIa from indica rice partially complements the sugary-1 phenotype in japonica rice endosperm. Plant Molecular Biology 108:325−42

doi: 10.1007/s11103-021-01161-9
[15]

Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F. 2001. A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif. Journal of Biological Chemistry 276:14139−52

doi: 10.1074/jbc.M007405200
[16]

Kawakatsu T, Yamamoto MP, Touno SM, Yasuda H, Takaiwa F. 2009. Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. The Plant Journal 59:908−20

doi: 10.1111/j.1365-313X.2009.03925.x
[17]

Wang JC, Xu H, Zhu Y, Liu QQ, Cai XL. 2013. OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm. Journal of Experimental Botany 64:3453−66

doi: 10.1093/jxb/ert187
[18]

Xu H, Li X, Zhang H, Wang L, Zhu Z, et al. 2020. High temperature inhibits the accumulation of storage materials by inducing alternative splicing of OsbZIP58 during filling stage in rice. Plant, Cell & Environment 43:1879−96

doi: 10.1111/pce.13779
[19]

Niu B, Deng H, Li T, Sharma S, Yun Q, et al. 2020. OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa). Journal of Integrative Plant Biology 62:1983−96

doi: 10.1111/jipb.12989
[20]

Wang JD, Wang J, Huang LC, Kan LJ, Wang CX, et al. 2024. ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module. Nature Communications 15:4493

doi: 10.1038/s41467-024-48760-w
[21]

Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, et al. 2020. SUPER STARCHY1/ONAC025 participates in rice grain filling. Plant Direct 4:e00249

doi: 10.1002/pld3.249
[22]

Ren Y, Huang Z, Jiang H, Wang Z, Wu F, et al. 2021. A heat stress responsive NAC transcription factor heterodimer plays key roles in rice grain filling. Journal of Experimental Botany 72:2947−64

doi: 10.1093/jxb/erab027
[23]

Wang J, Chen Z, Zhang Q, Meng S, Wei C. 2020. The NAC transcription factors OsNAC20 and OsNAC26 regulate starch and storage protein synthesis. Plant Physiology 184:1775−91

doi: 10.1104/pp.20.00984
[24]

Niu B, Zhang Z, Zhang J, Zhou Y, Chen C. 2021. The rice LEC1-like transcription factor OsNF-YB9 interacts with SPK, an endosperm-specific sucrose synthase protein kinase, and functions in seed development. Plant Journal 106:1233−46

doi: 10.1111/tpj.15230
[25]

Bello BK, Hou Y, Zhao J, Jiao G, Wu Y, et al. 2019. NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.). Plant Biotechnology Journal 17:1222−35

doi: 10.1111/pbi.13048
[26]

E Z, Li T, Zhang H, Liu Z, Deng H, et al. 2018. A group of nuclear factor Y transcription factors are sub-functionalized during endosperm development in monocots. Journal of Experimental Botany 69:2495−510

doi: 10.1093/jxb/ery087
[27]

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 Physiology 154:927−38

doi: 10.1104/pp.110.159517
[28]

Zhang H, Xu H, Feng M, Zhu Y. 2018. Suppression of OsMADS7 in rice endosperm stabilizes amylose content under high temperature stress. Plant Biotechnology Journal 16:18−26

doi: 10.1111/pbi.12745
[29]

Yin LL, Xue HW. 2012. The MADS29 transcription factor regulates the degradation of the nucellus and the nucellar projection during rice seed development. The Plant Cell 24:1049−65

doi: 10.1105/tpc.111.094854
[30]

Zhang J, Nallamilli BR, Mujahid H, Peng Z. 2010. OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa). The Plant Journal 64:604−17

doi: 10.1111/j.1365-313X.2010.04354.x
[31]

Oikawa A, Matsuda F, Kusano M, Okazaki Y, Saito K. 2008. Rice metabolomics. Rice 1:63−71

doi: 10.1007/s12284-008-9009-4
[32]

Concepcion JCT, Calingacion M, Garson MJ, Fitzgerald MA. 2020. Lipidomics reveals associations between rice quality traits. Metabolomics 16:54

doi: 10.1007/s11306-020-01670-6
[33]

Cho K, Evans BS, Wood BM, Kumar R, Erb TJ, et al. 2014. Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. Metabolomics 11:503−17

doi: 10.1007/s11306-014-0713-3
[34]

Sun J, Schmitt T, Schnackenberg LK, Pence L, Ando Y, et al. 2014. Comprehensive analysis of alterations in lipid and bile acid metabolism by carbon tetrachloride using integrated transcriptomics and metabolomics. Metabolomics 10:1293−304

doi: 10.1007/s11306-014-0665-7
[35]

Chen J, Le XC, Zhu L. 2019. Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2′, 4,4′-tetrabromodiphenyl ether. Environment International 133:105154

doi: 10.1016/j.envint.2019.105154
[36]

Li Y, Zong Y, Li W, Guo G, Zhou L, et al. 2023. Transcriptomics integrated with metabolomics reveals the effect of cold stress on rice microspores. BMC Plant Biology 23:521

doi: 10.1186/s12870-023-04530-2
[37]

Ranjitha HP, Gowda R, Nethra N, Amruta N, Kandikattu HK. 2019. Biochemical and metabolomics on rice cultivars. Rice Science 26:189−94

doi: 10.1016/j.rsci.2018.08.007
[38]

Zhang Z, Zhang F, Deng Y, Sun L, Mao M, et al. 2022. Integrated metabolomics and transcriptomics analyses reveal the metabolic differences and molecular basis of nutritional quality in landraces and cultivated rice. Metabolites 12:384

doi: 10.3390/metabo12050384
[39]

Zhou Y, Ju C, Xu G, Xie P, Gao M. 2008. Liangyou 287, a New Two-line Early-cropping Super Hybrid Rice Combination with Fine Grain Quality. Hybrid Rice 23:71−72 (in Chinese)

doi: 10.16267/j.cnki.1005-3956.2008.01.026
[40]

Qiu XJ, Peng B, Yu SB. 2018. Rice grain quality analysis. Bio-101 2018:e1010163 (in Chinese)

doi: 10.21769/BioProtoc.1010163
[41]

Chen T, Chen X, Zhang S, Zhu J, Tang B, et al. 2021. The genome sequence archive family: toward explosive data growth and diverse data types. Genomics, Proteomics & Bioinformatics 19:578−83

doi: 10.1016/j.gpb.2021.08.001
[42]

CNCB-NGDC Members and Partners. 2022. Database resources of the national genomics data center, China national center for bioinformation in 2022. Nucleic Acids Research 50:D27−D38

doi: 10.1093/nar/gkab951
[43]

Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, et al. 2016. MetaboLights: an open-access database repository for metabolomics data. Current Protocols in Bioinformatics 53:14.13.1−14.13.18

doi: 10.1002/0471250953.bi1413s53
[44]

Zhang H, Li M, He D, Wang K, Yang P. 2020. Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice. PLoS Genetics 16:e1008562

doi: 10.1371/journal.pgen.1008562
[45]

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. 2000. Gene ontology: tool for the unification of biology. Nature Genetics 25:25−29

doi: 10.1038/75556
[46]

The Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, et al. 2023. The gene ontology knowledgebase in 2023. Genetics 224:iyad031

doi: 10.1093/genetics/iyad031
[47]

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. 1999. KEGG kyoto encyclopedia of genes and genomes. Nucleic Acids Research 27:29−34

doi: 10.1093/nar/27.1.29
[48]

Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. 2023. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research 51:D587−D592

doi: 10.1093/nar/gkac963
[49]

Qin P, Zhang G, Hu B, Wu J, Chen W, et al. 2021. Leaf-derived ABA regulates rice seed development via a transporter-mediated and temperature-sensitive mechanism. Science Advances 7:eabc8873

doi: 10.1126/sciadv.abc8873
[50]

Krishnan S, Dayanandan P. 2003. Structural and histochemical studies on grain-filling in the caryopsis of rice (Oryza sativa L.). Journal of Biosciences 28:455−69

doi: 10.1007/BF02705120
[51]

Li F, Cui C, Li C, Yu Y, Zeng Q, et al. 2024. Cytology, metabolomics, and proteomics reveal the grain filling process and quality difference of wheat. Food Chemistry 457:140130

doi: 10.1016/j.foodchem.2024.140130
[52]

Yin B, Jia J, Sun X, Hu X, Ao M, et al. 2024. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. Plant Communications 5:100792

doi: 10.1016/j.xplc.2024.100792
[53]

Yang C, Shen S, Zhou S, Li Y, Mao Y, et al. 2022. Rice metabolic regulatory network spanning the entire life cycle. Molecular Plant 15:258−75

doi: 10.1016/j.molp.2021.10.005
[54]

Li K, Wang D, Gong L, Lyu Y, Guo H, et al. 2019. Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population. Plant Journal 100:908−22

doi: 10.1111/tpj.14482
[55]

Chen Y, Wang Z, Wang C, Li H, Huang D, et al. 2022. Comparisons of metabolic profiles for carbohydrates, amino acids, lipids, fragrance and flavones during grain development in indica rice cultivars. Rice Science 29:155−65

doi: 10.1016/j.rsci.2022.01.004
[56]

Cao R, Zhao S, Jiao G, Duan Y, Ma L, et al. 2022. OPAQUE3, encoding a transmembrane bZIP transcription factor, regulates endosperm storage protein and starch biosynthesis in rice. Plant Communications 3:100463

doi: 10.1016/j.xplc.2022.100463
[57]

Impa SM, Raju B, Hein NT, Sandhu J, Vara Prasad PV, et al. 2021. High night temperature effects on wheat and rice: Current status and way forward. Plant, Cell & Environment 44:2049−65

doi: 10.1111/pce.14028
[58]

Nallamilli BRR, Zhang J, Mujahid H, Malone BM, Bridges SM, et al. 2013. Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genetics 9:e1003322

doi: 10.1371/journal.pgen.1003322
[59]

Gui J, Liu C, Shen J, Li L. 2014. Grain setting defect1, encoding a remorin protein, affects the grain setting in rice through regulating plasmodesmatal conductance. Plant Physiology 166:1463−78

doi: 10.1104/pp.114.246769
[60]

Wu X, Liu J, Li D, Liu CM. 2016. Rice caryopsis development II: Dynamic changes in the endosperm. Journal of Integrative Plant Biology 58:786−98

doi: 10.1111/jipb.12488
[61]

Schnyder H. 1993. The role of carbohydrate storage and redistribution in the source‐sink relations of wheat and barley during grain filling − a review. New Phytologist 123:233−45

doi: 10.1111/j.1469-8137.1993.tb03731.x
[62]

Ma B, Zhang L, He Z. 2023. Understanding the regulation of cereal grain filling: The way forward. Journal of Integrative Plant Biology 65:526−47

doi: 10.1111/jipb.13456
[63]

Sivaramakrishnan M, Veeraganti Naveen Prakash C, Chandrasekar B. 2024. Multifaceted roles of plant glycosyl hydrolases during pathogen infections: more to discover. Planta 259:113

doi: 10.1007/s00425-024-04391-5
[64]

Kong H, Song J, Ma S, Yang J, Shao Z, et al. 2024. Genome-wide identification and expression analysis of the glycosyl hydrolase family 1 genes in Medicago sativa revealed their potential roles in response to multiple abiotic stresses. BMC Genomics 25:20

doi: 10.1186/s12864-023-09918-w
[65]

Zhang XF, Tong JH, Bai AN, Liu CM, Xiao LT, et al. 2020. Phytohormone dynamics in developing endosperm influence rice grain shape and quality. Journal of Integrative Plant Biology 62:1625−37

doi: 10.1111/jipb.12927
[66]

Liu X, Zhong X, Liao J, Ji P, Yang J, et al. 2023. Exogenous abscisic acid improves grain filling capacity under heat stress by enhancing antioxidative defense capability in rice. BMC Plant Biology 23:619

doi: 10.1186/s12870-023-04638-5