|
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Matsuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science, 309, 741–745.
Best N B, Hartwig T, Budka J, Fujioka S, Johal G, Schulz B, Dilkes B P. 2016. nana plant2 encodes a maize ortholog of the Arabidopsis brassinosteroid biosynthesis gene DWARF1, identifying developmental interactions between brassinosteroids and gibberellins. Plant Physiology, 171, 2633–2647.
Bostick M, Lochhead S R, Honda A, Palmer S, Callis J. 2004. Related to ubiquitin 1 and 2 are redundant and essential and regulate vegetative growth, auxin signaling, and ethylene production in Arabidopsis. The Plant Cell, 16, 2418–2432.
Brookbank B P, Patel J, Gazzarrini S, Nambara E. 2021. Role of basal ABA in plant growth and development. Genes (Basel), 12, 1936.
Chai G, Qi G, Wang D, Zhuang Y, Xu H, Bai Z, Bai MY, Hu R, Wang Z Y, Zhou G, Kong Y. 2022. The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling. Plant Physiology, 189, 285–300.
Chen Y, Liu B, Zhao Y, Yu W, Si W. 2021. Whole-genome duplication and purifying selection contributes to the functional redundancy of auxin response factor (ARF) genes in foxtail millet (Setaria italica L.). International Journal of Genomics, 2021, 2590665.
Christians M J, Rottier A, Wiersma C. 2018. Light regulates the RUBylation levels of individual cullin proteins in Arabidopsis thaliana. Plant Molecular Biology Reporter, 36, 123–134.
Chu J, Fang S, Xin P, Guo Z, Chen Y. 2017. Quantitative analysis of plant hormones based on LC-MS/MS. In: Li J, Li C, Smith S M, eds., Hormone Metabolism and Signaling in Plants. Elsevier, London. pp. 471–537.
Chu L, Yan Z, Sheng X, Liu H, Wang Q, Zeng R, Hu C, Zhang J. 2023. Citrus ACC synthase CiACS4 regulates plant height by inhibiting gibberellin biosynthesis. Plant Physiology, 192, 1947–1968.
Diao X, Jia G. 2017. Foxtail millet breeding in China. In: Doust A, Diao X, eds., Genetics and Genomics of Setaria. Springer, Cham. pp. 93–113.
Diao X, Schnable J, Bennetzen L J, Li J. 2014. Initiation of Setaria as a model plant. Frontiers of Agricultural Science and Engineering, 1, 16–20.
Dong H, Li D, Yang R, Zhang L, Zhang Y, Liu X, Kong X, Sun J. 2023. GSK3 phosphorylates and regulates the green revolution protein Rht-B1b to reduce plant height in wheat. The Plant Cell, 35, 1970–1983.
Enchev R I, Schulman B A, Peter M. 2015. Protein neddylation: Beyond cullin–RING ligases. Nature Reviews Molecular Cell Biology, 16, 30–44.
Fan X, Tang S, Zhi H, He M, Ma W, Jia Y, Zhao B, Jia G, Diao X. 2017. Identification and fine mapping of SiDWARF3(D3), a pleiotropic locus controlling environment-independent dwarfism in foxtail millet. Crop Science, 57, 2431–2442.
Ford B A, Foo E, Sharwood R, Karafiatova M, Vrana J, MacMillan C, Nichols D S, Steuernagel B, Uauy C, Dolezel J, Chandler P M, Spielmeyer W. 2018. Rht18 Semidwarfism in wheat is due to increased GA 2-oxidaseA9 expression and reduced GA content. Plant Physiology, 177, 168–180.
Gui J, Zheng S, Liu C, Shen J, Li J, Li L. 2016. OsREM4.1 interacts with OsSERK1 to coordinate the interlinking between abscisic acid and brassinosteroid signaling in rice. Developmental Cell, 38, 201–213.
Guo F, Huang Y, Qi P, Lian G, Hu X, Han N, Wang J, Zhu M, Qian Q, Bian H. 2021. Functional analysis of auxin receptor OsTIR1/OsAFB family members in rice grain yield, tillering, plant height, root system, germination, and auxinic herbicide resistance. New Phytologist, 229, 2676–2692.
Guo G, Li N. 2011. Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA). Phytochemistry, 72, 1028–1039.
Gupta R, Ting J T, Sokolov L N, Johnson S A, Luan S. 2002. A tumor suppressor homolog, AtPTEN1, is essential for pollen development in Arabidopsis. The Plant Cell, 14, 2495–2507.
Hartwig T, Chuck G S, Fujioka S, Klempien A, Weizbauer R, Potluri D P, Choe S, Johal G S, Schulz B. 2011. Brassinosteroid control of sex determination in maize. Proceedings of the National Academy of Sciences of the United States of America, 108, 19814–19819.
He Q, Tang S, Zhi H, Chen J, Zhang J, Liang H, Alam O, Li H, Zhang H, Xing L, Li X, Zhang W, Wang H, Shi J, Du H, Wu H, Wang L, Yang P, Xing L, Yan H, et al. 2023. A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics, 55, 1232–1242.
He Q, Zhi H, Tang S, Xing L, Wang S, Wang H, Zhang A, Li Y, Gao M, Zhang H, Chen G, Dai S, Li J, Yang J, Liu H, Zhang W, Jia Y, Li S, Liu J, Qiao Z, et al. 2021. QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theoretical and Applied Genetics, 134, 557–572.
Huo C, Zhang B, Wang H, Wang F, Liu M, Gao Y, Zhang W, Deng Z, Sun D, Tang W. 2016. Comparative study of early cold-regulated proteins by two-dimensional difference gel electrophoresis reveals a key role for Phospholipase Dα1 in mediating cold acclimation signaling pathway in rice. Molecular & Cellular Proteomics, 15, 1397–1411.
Iliev E A, Xu W, Polisensky D H, Oh M H, Torisky R S, Clouse S D, Braam J. 2002. Transcriptional and posttranscriptional regulation of Arabidopsis TCH4 expression by diverse stimuli. Roles of cis regions and brassinosteroids. Plant Physiology, 130, 770–783.
Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, et al. 2013. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nature Genetics, 45, 957–961.
Kir G, Ye H, Nelissen H, Neelakandan A K, Kusnandar A S, Luo A, Inzé D, Sylvester A W, Yin Y, Becraft P W. 2015. RNA interference knockdown of BRASSINOSTEROID INSENSITIVE1 in maize reveals novel functions for brassinosteroid signaling in controlling plant architecture. Plant Physiology, 169, 826–839.
Lata C, Gupta S, Prasad M. 2013. Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses. Critical Reviews in Biotechnology, 33, 328–343.
Li H, Wang L, Liu M, Dong Z, Li Q, Fei S, Xiang H, Liu B, Jin W. 2020. Maize plant architecture is regulated by the ethylene biosynthetic gene ZmACS7. Plant Physiology, 183, 1184–1199.
Miao L, Wang X, Yu C, Ye C, Yan Y, Wang H. 2024. What factors control plant height? Journal of Integrative Agriculture, 23, 1803–1824.
Li P, Liu J. 2021. Protein phosphorylation in plant cell signaling. Methods in Molecular Biology, 2358, 45–71.
Li Z, Zhang X, Zhao Y, Li Y, Zhang G, Peng Z, Zhang J. 2018. Enhancing auxin accumulation in maize root tips improves root growth and dwarfs plant height. Plant Biotechnology Journal, 16, 86–99.
Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X. 2023. Identification and haplotype analysis of SiCHLI: A gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. Theoretical and Applied Genetics, 136, 24.
Liu F, Wang P, Zhang X, Li X, Yan X, Fu D, Wu G. 2018. The genetic and molecular basis of crop height based on a rice model. Planta, 247, 1–26.
Liu X, Tang S, Jia G, Schnable J C, Su H, Tang C, Zhi H, Diao X. 2016. The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv). Journal of Experimental Botany, 67, 3237–3249.
Liu Y H, Sun T, Li Y Y, Huang J Q, Wang X J, Bai H M, Hu J Y, Zhang Z F, Wang S, Zhang D M, Li X X, Wang Z H, Zheng H K, Lin G F. 2025. Proteomic analysis revealed the function of PoElp3 in development, pathogenicity, and autophagy through the tRNA-mediated translation efficiency in the rice blast fungus. Journal of Integrative Agriculture, 24, 1515–1528.
Mergner J, Kuster B, Schwechheimer C. 2017. DENEDDYLASE1 protein counters automodification of neddylating enzymes to maintain NEDD8 protein homeostasis in Arabidopsis. Journal of Biological Chemistry, 292, 3854–3865.
Neris D, Mattiello L, Zuñiga G, Purgatto E, Menossi M. 2022. Reduction of ethylene biosynthesis in sugarcane induces growth and investment in the non-enzymatic antioxidant apparatus. Plant Cell Reports, 41, 979–993.
Nibau C, Tao L, Levasseur K, Wu H M, Cheung A Y. 2013. The Arabidopsis small GTPase AtRAC7/ROP9 is a modulator of auxin and abscisic acid signalling. Journal of Experimental Botany, 64, 3425–3437.
Nolan T M, Vukašinović N, Liu D, Russinova E, Yin Y. 2019. Brassinosteroids: Multi-dimensional regulators of plant growth, development, and stress responses. The Plant Cell, 32, 295–318.
Pan J, Li Z, Wang Q, Garrell A K, Liu M, Guan Y, Zhou W, Liu W. 2018. Comparative proteomic investigation of drought responses in foxtail millet. BMC Plant Biology, 18, 315.
Pan J, Li Z, Wang Q, Guan Y, Li X, Huangfu Y, Meng F, Li J, Dai S, Liu W. 2021. Phosphoproteomic profiling reveals early salt-responsive mechanisms in two foxtail millet cultivars. Frontiers in Plant Science, 12, 712257.
Panchal A, Singh R K, Prasad M. 2023. Recent advancements and future perspectives of foxtail millet genomics. Plant Growth Regulation, 99, 11–23.
Pellegrino N E, Guven A, Gray K, Shah P, Kasture G, Nastke M D, Thakurta A, Gesta S, Vishnudas V K, Narain N R, Kiebish M A. 2022. The next frontier: Translational development of Ubiquitination, SUMOylation, and NEDDylation in cancer. International Journal of Molecular Sciences, 23, 3480.
Peng J, Richards D E, Hartley N M, Murphy G P, Devos K M, Flintham J E, Beales J, Fish L J, Worland A J, Pelica F, Sudhakar D, Christou P, Snape J W, Gale M D, Harberd N P. 1999. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature, 400, 256–261.
Pribat A, Sormani R, Rousseau-Gueutin M, Julkowska M M, Testerink C, Joubès J, Castroviejo M, Laguerre M, Meyer C, Germain V, Rothan C. 2012. A novel class of PTEN protein in Arabidopsis displays unusual phosphoinositide phosphatase activity and efficiently binds phosphatidic acid. Biochemical Journal, 441, 161–171.
Qi W, Sun F, Wang Q, Chen M, Huang Y, Feng YQ, Luo X, Yang J. 2011. Rice ethylene-response AP2/ERF factor OsEATB restricts internode elongation by down-regulating a gibberellin biosynthetic gene. Plant Physiology, 157, 216–228.
Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush G S, Kitano H, Matsuoka M. 2002. Green revolution: A mutant gibberellin-synthesis gene in rice. Nature, 416, 701–702.
Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Jeong D H, An G, Kitano H, Ashikari M, Matsuoka M. 2003. Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science, 299, 1896–1898.
Schwechheimer C. 2018. NEDD8-its role in the regulation of Cullin-RING ligases. Current Opinion in Plant Biology, 45, 112–119.
Shi F, Wang M, An Y. 2020. Overexpression of a B-type cytokinin response regulator (OsORR2) reduces plant height in rice. Plant Signaling & Behavior, 15, 1780405.
Song Y, You J, Xiong L. 2009. Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Plant Molecular Biology, 70, 297–309.
Spielmeyer W, Ellis M H, Chandler P M. 2002. Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences of the United States of America, 99, 9043–9048.
Tanabe S, Ashikari M, Fujioka S, Takatsuto S, Yoshida S, Yano M, Yoshimura A, Kitano H, Matsuoka M, Fujisawa Y, Kato H, Iwasaki Y. 2005. A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length. The Plant Cell, 17, 776–790.
Tang L, Xu H, Wang Y, Wang H, Li Z, Liu X, Shu Y, Li G, Liu W, Ying J, Tong X, Yao J, Xiao W, Tang S, Ni S, Zhang J. 2021. OsABF1 represses gibberellin biosynthesis to regulate plant height and seed germination in rice (Oryza sativa L.). International Journal of Molecular Sciences, 22, 12220.
Teng F, Zhai L, Liu R, Bai W, Wang L, Huo D, Tao Y, Zheng Y, Zhang Z. 2013. ZmGA3ox2, a candidate gene for a major QTL, qPH3.1, for plant height in maize. The Plant Journal, 73, 405–416.
Tian P, Liu J, Yan B, Zhou C, Wang H, Shen R. 2023. BRASSINOSTEROID–SIGNALING KINASE1–1, a positive regulator of brassinosteroid signalling, modulates plant architecture and grain size in rice. Journal of Experimental Botany, 74, 283–295.
Tian X, Xia X, Xu D, Liu Y, Xie L, Hassan M A, Song J, Li F, Wang D, Zhang Y, Hao Y, Li G, Chu C, He Z, Cao S. 2022. Rht24b, an ancient variation of TaGA2ox-A9, reduces plant height without yield penalty in wheat. New Phytologist, 233, 738–750.
Tiwari S B, Hagen G, Guilfoyle T. 2003. The roles of auxin response factor domains in auxin-responsive transcription. The Plant Cell, 15, 533–543.
Van De Velde K, Thomas S G, Heyse F, Kaspar R, Van Der Straeten D, Rohde A. 2021. N-terminal truncated RHT-1 proteins generated by translational reinitiation cause semi-dwarfing of wheat Green Revolution alleles. Molecular Plant, 14, 679–687.
Voorend W, Nelissen H, Vanholme R, De Vliegher A, Van Breusegem F, Boerjan W, Roldán-Ruiz I, Muylle H, Inzé D. 2016. Overexpression of GA20-OXIDASE1 impacts plant height, biomass allocation and saccharification efficiency in maize. Plant Biotechnology Journal, 14, 997–1007.
Wang B, Chu J, Yu T, Xu Q, Sun X, Yuan J, Xiong G, Wang G, Wang Y, Li J. 2015. Tryptophan-independent auxin biosynthesis contributes to early embryogenesis in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 112, 4821–4826.
Wang F, Yu Z, Zhang M, Wang M, Lu X, Liu X, Li Y, Zhang X, Tan BC, Li C, Ding Z. 2022. ZmTE1 promotes plant height by regulating intercalary meristem formation and internode cell elongation in maize. Plant Biotechnology Journal, 20, 526–537.
Winkler R G, Helentjaris T. 1995. The maize Dwarf3 gene encodes a cytochrome P450-mediated early step in gibberellin biosynthesis. The Plant Cell, 7, 1307–1317.
Wu J, Kong X, Wan J, Liu X, Zhang X, Guo X, Zhou R, Zhao G, Jing R, Fu X, Jia J. 2011. Dominant and pleiotropic effects of a GAI gene in wheat results from a lack of interaction between DELLA and GID1. Plant Physiology, 157, 2120–2130.
Würschum T, Langer S M, Longin C F H, Tucker M R, Leiser W L. 2017. A modern Green Revolution gene for reduced height in wheat. The Plant Journal, 92, 892–903.
Xie P, Peng Z, Chen Y, Li H, Du M, Tan Y, Zhang X, Lu Z, Cui CP, Liu C H, He F, Zhang L. 2021. Neddylation of PTEN regulates its nuclear import and promotes tumor development. Cell Research, 31, 291–311.
Xue C, Zhi H, Fang X, Liu X, Tang S, Chai Y, Zhao B, Jia G, Diao X. 2016. Characterization and fine mapping of SiDWARF2 (D2) in foxtail millet. Crop Science, 56, 95.
Yan Z, Zhao J, Peng P, Chihara R K, Li J. 2009. BIN2 functions redundantly with other Arabidopsis GSK3-like kinases to regulate brassinosteroid signaling. Plant Physiology, 150, 710–721.
Yang D, Yao J, Mei C, Tong X, Zeng L, Li Q, Xiao L, Sun T, Li J, Deng X, Lee CM, Thomashow M F, Yang Y, He Z, He S. 2012. Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proceedings of the National Academy of Sciences of the United States of America, 109, E1192–E1200.
Yang Z, Zhang H, Li X, Shen H, Gao J, Hou S, Zhang B, Mayes S, Bennett M, Ma J, Wu C, Sui Y, Han Y, Wang X. 2020. A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system. Nature Plants, 6, 1167–1178.
Yu H, Zhang Y, Moss B L, Bargmann B O, Wang R, Prigge M, Nemhauser J L, Estelle M. 2015. Untethering the TIR1 auxin receptor from the SCF complex increases its stability and inhibits auxin response. Nature Plants, 1, 14030.
Zhang A M, Li Z H, Zhou Q R, Zhao J W, Zhao Y, Zhao M T, Ma S Y, Fan Y H, Huang Z L, Zhang W J. 2025. An integrated physiology and proteomics analysis reveals the response of wheat grain to low temperature stress during booting. Journal of Integrative Agriculture, 24, 114–131.
Zhang B, Wang X, Zhao Z, Wang R, Huang X, Zhu Y, Yuan L, Wang Y, Xu X, Burlingame A L, Gao Y, Sun Y, Tang W. 2016. OsBRI1 activates BR signaling by preventing binding between the TPR and kinase domains of OsBSK3 via phosphorylation. Plant Physiology, 170, 1149–1161.
Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, et al. 2012. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 30, 549–554.
Zhang L, Liu P, Wu J, Qiao L, Zhao G, Jia J, Gao L, Wang J. 2020. Identification of a novel ERF gene, TaERF8, associated with plant height and yield in wheat. BMC Plant Biology, 20, 263.
Zhang R, Jia G, Diao X. 2023. geneHapR: An R package for gene haplotypic statistics and visualization. BMC Bioinformatics, 24, 199.
Zhao M, Tang S, Zhang H, He M, Liu J, Zhi H, Sui Y, Liu X, Jia G, Zhao Z, Yan J, Zhang B, Zhou Y, Chu J, Wang X, Zhao B, Tang W, Li J, Wu C, Liu X, Diao X. 2020. DROOPY LEAF1 controls leaf architecture by orchestrating early brassinosteroid signaling. Proceedings of the National Academy of Sciences of the United States of America, 117, 21766–21774.
Zhao M, Zhi H, Zhang X, Jia G, Diao X. 2019. Retrotransposon-mediated DELLA transcriptional reprograming underlies semi-dominant dwarfism in foxtail millet. The Crop Journal, 7, 458–468.
Zhao Z, Tang S, Li W, Yang X, Wang R, Diao X, Tang W. 2021a. Overexpression of a BRASSINAZOLE RESISTANT 1 homolog attenuates drought tolerance by suppressing the expression of PLETHORA-LIKE 1 in Setaria italica. The Crop Journal, 9, 1208–1213.
Zhao Z, Tang S, Zhang Y, Yue J, Xu J, Tang W, Sun Y, Wang R, Diao X, Zhang B. 2021b. Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet. BMC Plant Biology, 21, 291.
Zhou H, Wang X, Huo C, Wang H, An Z, Sun D, Liu J, Tang W, Zhang B. 2019. A quantitative proteomics study of early heat-regulated proteins by two-dimensional difference gel electrophoresis identified OsUBP21 as a negative regulator of heat stress responses in rice. Proteomics, 19, e1900153.
|