[1]

Sreenivasulu N, Schnurbusch T. 2012. A genetic playground for enhancing grain number in cereals. Trends in Plant Science 17:91−101

doi: 10.1016/j.tplants.2011.11.003
[2]

Zhang D, Yuan Z. 2014. Molecular control of grass inflorescence development. Annual Review of Plant Biology 65:553−78

doi: 10.1146/annurev-arplant-050213-040104
[3]

Schilling S, Pan S, Kennedy A, Melzer R. 2018. MADS-box genes and crop domestication: the jack of all traits. Journal of Experimental Botany 69:1447−69

doi: 10.1093/jxb/erx479
[4]

Yan W, Chen D, Kaufmann K. 2016. Molecular mechanisms of floral organ specification by MADS domain proteins. Current Opinion in Plant Biology 29:154−62

doi: 10.1016/j.pbi.2015.12.004
[5]

Xie P, Wu Y, Xie Q. 2023. Evolution of cereal floral architecture and threshability. Trends in Plant Science 28:1438−50

doi: 10.1016/j.tplants.2023.08.003
[6]

Wu F, Shi X, Lin X, Liu Y, Chong K, et al. 2017. The ABCs of flower development: mutational analysis of AP1/FUL-like genes in rice provides evidence for a homeotic (A)-function in grasses. Plant Journal 89:310−24

doi: 10.1111/tpj.13386
[7]

Li N, Liu Y, Zhong M, Jiang M, Li H. 2014. Thinking out of the box: MADS-box genes and maize spikelet development. African Journal of Biotechnology 13:4673−79

doi: 10.5897/ajb11.3885
[8]

Dreni L, Zhang D. 2016. Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes. Journal of Experimental Botany 67:1625−38

doi: 10.1093/jxb/erw046
[9]

Gao X, Liang W, Yin C, Ji S, Wang H, et al. 2010. The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiology 153:728−40

doi: 10.1104/pp.110.156711
[10]

Gao H, Suo X, Zhao L, Ma X, Cheng R, et al. 2023. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. Plant Cell Reports 42:1003−24

doi: 10.1007/s00299-023-03009-6
[11]

Hirakawa Y. 2021. CLAVATA3, a plant peptide controlling stem cell fate in the meristem. Peptides 142:170579

doi: 10.1016/j.peptides.2021.170579
[12]

Somssich M, Je BI, Simon R, Jackson D. 2016. CLAVATA-WUSCHEL signaling in the shoot meristem. Development 143:3238−48

doi: 10.1242/dev.133645
[13]

Mayer KFX, Schoof H, Haecker A, Lenhard M, Jürgens G, et al. 1998. Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95:805−15

doi: 10.1016/S0092-8674(00)81703-1
[14]

Fletcher JC. 2018. The CLV-WUS stem cell signaling pathway: a roadmap to crop yield optimization. Plants 7:87

doi: 10.3390/plants7040087
[15]

Nemec-Venza Z, Madden C, Stewart A, Liu W, Novák O, et al. 2022. CLAVATA modulates auxin homeostasis and transport to regulate stem cell identity and plant shape in a moss. New Phytologist 234:149−63

doi: 10.1111/nph.17969
[16]

Shinohara H, Matsubayashi Y. 2015. Reevaluation of the CLV3-receptor interaction in the shoot apical meristem: dissection of the CLV3 signaling pathway from a direct ligand‐binding point of view. The Plant Journal 82:328−36

doi: 10.1111/tpj.12817
[17]

Xu W, Tao J, Chen M, Dreni L, Luo Z, et al. 2017. Interactions between FLORAL ORGAN NUMBER4 and floral homeotic genes in regulating rice flower development. Journal of Experimental Botany 68:483−98

doi: 10.1093/jxb/erw459
[18]

Je BI, Gruel J, Lee YK, Bommert P, Arevalo ED, et al. 2016. Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits. Nature Genetics 48:785−91

doi: 10.1038/ng.3567
[19]

Long JA, Moan EI, Medford JI, Barton MK. 1996. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 379:66−69

doi: 10.1038/379066a0
[20]

Zhuang H, Li YH, Zhao XY, Zhi JY, Chen H, et al. 2024. STAMENLESS1 activates SUPERWOMAN1 and FLORAL ORGAN NUMBER 1 to control floral organ identities and meristem fate in rice. The Plant Journal 118:802−22

doi: 10.1111/tpj.16637
[21]

Tsago Y, Chen Z, Cao H, Sunusi M, Khan AU, et al. 2020. Rice gene, OsCKX2-2, regulates inflorescence and grain size by increasing endogenous cytokinin content. Plant Growth Regulation 92:283−94

doi: 10.1007/s10725-020-00637-w
[22]

Chuck G, Muszynski M, Kellogg E, Hake S, Schmidt RJ. 2002. The control of spikelet meristem identity by the branched silkless1 gene in maize. Science 298:1238−41

doi: 10.1126/science.1076920
[23]

Chandler JW. 2018. Class VIIIb APETALA2 ethylene response factors in plant development. Trends in Plant Science 23:151−62

doi: 10.1016/j.tplants.2017.09.016
[24]

Xie W, Ding C, Hu H, Dong G, Zhang G, et al. 2022. Molecular events of rice AP2/ERF transcription factors. International Journal of Molecular Sciences 23:12013

doi: 10.3390/ijms231912013
[25]

Hussin SH, Wang H, Tang S, Zhi H, Tang C, et al. 2021. SiMADS34, an E-class MADS-box transcription factor, regulates inflorescence architecture and grain yield in Setaria italica. Plant Molecular Biology 105:419−34

doi: 10.1007/s11103-020-01097-6
[26]

Wang H, Tang S, Zhi H, Xing L, Zhang H, et al. 2022. The boron transporter SiBOR1 functions in cell wall integrity, cellular homeostasis, and panicle development in foxtail millet. The Crop Journal 10:342−53

doi: 10.1016/j.cj.2021.05.002
[27]

Zhang H, Zhi H, Di Y, Liang H, Zhang W, et al. 2024. Identification and characterization of a no grain mutant (nog1) in foxtail millet. Journal of Integrative Agriculture 23:4263−66

doi: 10.1016/j.jia.2024.06.016
[28]

Yang J, Thames S, Best NB, Jiang H, Huang P, et al. 2018. Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis. The Plant Cell 30:48−66

doi: 10.1105/tpc.17.00816
[29]

Yang J, Bertolini E, Braud M, Preciado J, Chepote A, et al. 2021. The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis. Plant Physiology 187:1202−20

doi: 10.1093/plphys/kiab169
[30]

Tang S, Zhao Z, Liu X, Sui Y, Zhang D, et al. 2023. An E2-E3 pair contributes to seed size control in grain crops. Nature Communications 14:3091

doi: 10.1038/s41467-023-38812-y
[31]

Zhu C, Liu L, Crowell O, Zhao H, Brutnell TP, et al. 2021. The CLV3 homolog in Setaria viridis selectively controls inflorescence meristem size. Frontiers in Plant Science 12:636749

doi: 10.3389/fpls.2021.636749
[32]

Huang P, Jiang H, Zhu C, Barry K, Jenkins J, et al. 2017. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize. Nature Plants 3:17054

doi: 10.1038/nplants.2017.54
[33]

Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357−60

doi: 10.1038/nmeth.3317
[34]

Anders S, Pyl PT, Huber W. 2015. HTSeq − a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166−69

doi: 10.1093/bioinformatics/btu638
[35]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/gb-2014-15-1-r1
[36]

Kanehisa M, Araki M , Goto S, Hattori M, Hirakawaet M al. 2007. KEGG for linking genomes to life and the environment. Nucleic Acids Research 36:D480−D484

doi: 10.1093/nar/gkm882
[37]

Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, et al. 2017. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nature Protocols 12:1659−72

doi: 10.1038/nprot.2017.055
[38]

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−20

doi: 10.1093/bioinformatics/btu170
[39]

Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26:589−95

doi: 10.1093/bioinformatics/btp698
[40]

Doust AN, Devos KM, Gadberry MD, Gale MD, Kellogg EA. 2005. The genetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics 169:1659−72

doi: 10.1534/genetics.104.035543
[41]

Liu H, Li G, Yang X, Kuijer HNJ, Liang W, et al. 2020. Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence. The Crop Journal 8:71−86

doi: 10.1016/j.cj.2019.04.005
[42]

Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, et al. 2014. Chromatin meets the cell cycle. Journal of Experimental Botany 65:2677−89

doi: 10.1093/jxb/ert433
[43]

Wu H, Qu X, Dong Z, Luo L, Shao C, et al. 2020. WUSCHEL triggers innate antiviral immunity in plant stem cells. Science 370:227−31

doi: 10.1126/science.abb7360
[44]

Schoof H, Lenhard M, Haecker A, Mayer KF, Jürgens G, Laux T. 2000. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100:635−44

doi: 10.1016/S0092-8674(00)80700-X
[45]

Mizukami Y, Fischer RL. 2000. Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis. Proceedings of the National Academy of Sciences of the United States of America 97:942−47

doi: 10.1073/pnas.97.2.942
[46]

Klucher KM, Chow H, Reiser L, Fischer RL. 1996. The AINTEGUMENTA gene of Arabidopsis required for ovule and female gametophyte development is related to the floral homeotic gene APETALA2. The Plant Cell 8:137−53

doi: 10.1105/tpc.8.2.137
[47]

Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, et al. 1996. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. The Plant Cell 8:155−68

doi: 10.1105/tpc.8.2.155
[48]

Nonomura KI, Miyoshi K, Eiguchi M, Suzuki T, Miyao A, et al. 2003. The MSP1 gene is necessary to restrict the number of cells entering into male and female sporogenesis and to initiate anther wall formation in rice. The Plant Cell 15:1728−39

doi: 10.1105/tpc.012401
[49]

Liu X, Shangguan Y, Zhu J, Lu Y, Han B. 2013. The rice OsLTP6 gene promoter directs anther-specific expression by a combination of positive and negative regulatory elements. Planta 238:845−57

doi: 10.1007/s00425-013-1934-9
[50]

Zhang Y, Shen C, Li G, Shi J, Yuan Y, et al. 2024. MADS1-regulated lemma and awn development benefits barley yield. Nature Communications 15:301

doi: 10.1038/s41467-023-44457-8
[51]

Hu Y, Liang W, Yin C, Yang X, Ping B, et al. 2015. Interactions of OsMADS1 with floral homeotic genes in rice flower development. Molecular Plant 8:1366−84

doi: 10.1016/j.molp.2015.04.009
[52]

Ito Y, Hirochika H, Kurata N. 2002. Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice. Gene 288:41−47

doi: 10.1016/S0378-1119(02)00460-2
[53]

Jia P, Wang Y, Sharif R, Dong QL, Liu Y, et al. 2023. KNOTTED1-like homeobox (KNOX) transcription factors-Hubs in a plethora of networks: a review. International Journal of Biological Macromolecules 253:126878

doi: 10.1016/j.ijbiomac.2023.126878
[54]

Parenicová L, de Folter S, Kieffer M, Horner DS, Favalli C, et al. 2003. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. The Plant Cell 15:1538−51

doi: 10.1105/tpc.011544
[55]

Arora R, Agarwal P, Ray S, Singh AK, Singh VP, et al. 2007. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242

doi: 10.1186/1471-2164-8-242
[56]

Malcomber ST, Kellogg EA. 2005. SEPALLATA gene diversification: brave new whorls. Trends in Plant Science 10:427−35

doi: 10.1016/j.tplants.2005.07.008
[57]

Litt A, Kramer EM. 2010. The ABC model and the diversification of floral organ identity. Seminars in Cell & Developmental Biology 21:129−37

doi: 10.1016/j.semcdb.2009.11.019
[58]

Rijpkema AS, Vandenbussche M, Koes R, Heijmans K, Gerats T. 2010. Variations on a theme: changes in the floral ABCs in angiosperms. Seminars in Cell & Developmental Biology 21:100−7

doi: 10.1016/j.semcdb.2009.11.002
[59]

Prasad K, Sriram P, Kumar SC, Kushalappa K, Vijayraghavan U. 2001. Ectopic expression of rice OsMADS1 reveals a role in specifying the lemma and palea, grass floral organs analogous to sepals. Development Genes and Evolution 211:281−90

doi: 10.1007/s004270100153
[60]

Lee S, Choi SC, An G. 2008. Rice SVP-group MADS-box proteins, OsMADS22 and OsMADS55, are negative regulators of brassinosteroid responses. The Plant Journal 54:93−105

doi: 10.1111/j.1365-313X.2008.03406.x
[61]

Yadav SR, Prasad K, Vijayraghavan U. 2007. Divergent regulatory OsMADS2 functions control size, shape and differentiation of the highly derived rice floret second-whorl organ. Genetics 176:283−94

doi: 10.1534/genetics.107.071746
[62]

Schuster C, Gaillochet C, Medzihradszky A, Busch W, Daum G, et al. 2014. A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals. Developmental Cell 28:438−49

doi: 10.1016/j.devcel.2014.01.013
[63]

Gremski K, Ditta G, Yanofsky MF. 2007. The HECATE genes regulate female reproductive tract development in Arabidopsis thaliana. Development 134:3593−601

doi: 10.1242/dev.011510
[64]

Gaillochet C, Jamge S, van der Wal F, Angenent G, Immink R, et al. 2018. A molecular network for functional versatility of HECATE transcription factors. Plant Journal 95:57−70

doi: 10.1111/tpj.13930