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Journal of Integrative Agriculture
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RNA-binding protein ZmFRKH1 promotes maize flowering by modulating the stability of multiple flowering regulator RNAs

Yao Cao1, 2*, Qinglin Li1*, Babatope Samuel Ajayo1, Wanyi Nie1, Qiang Liao1, Yin Liu1, Lei Gao1, Xiujun Fan1, Yangping Li1, Yubi Huang1, 2#, Yufeng Hu1#

1 State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Chengdu 611130, China

2 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China

 Highlights 

 Knockout of the ZmFRKH1 gene leads to delayed flowering in maize.

 ZmFRKH1 protein interacts and modulates the stability of multiple flowering regulator RNAs.

• A SNP in the promoter was selectively fixed during maize domestication for early flowering.

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摘要  

适宜的花期对玉米(Zea mays ssp. mays产量至关重要。本研究一个玉米自然群体两年三点的抽雄期(DTA)和吐丝期DTS进行了全基因组关联分析(GWASDTADTS关联结果共同定位到一个主效位点 S9_120534257,其对应的候选基因 ZmFRKH1 编码一个KH结构域(K-homologous domainRNA结合蛋白。敲除ZmFRKH1显著迟玉米开花。进一步分析发现,ZmFRKH1蛋白结合多个开花调控因子的mRNA并影响其稳定性。等位变异分析发现 ZmFRKH1启动子区的一个单核苷酸多态性(SNP)位点显著影响启动子活性及玉米。驯化特征分析表明,此SNP在大刍草玉米驯化过程中被选择固定,其早花单倍型促进了玉米从热带向温带地区适应性的演化。本研究玉米花期调控分子设计育种提供了新的优异基因资源。



Abstract  

Optimal flowering time is crucial for maximizing maize (Zea mays ssp. mays) yield.  Here, we performed a genome-wide association analysis (GWAS) on days to anthesis (DTA) and days to silk (DTS) in a maize natural variation population across three environments over two years.  A major quantitative trait locus, S9_120534257, was consistently identified in two phenotypic datasets for DTA and DTS, with the candidate gene ZmFRKH1 encoding a K-homologous (KH) domain RNA-binding protein.  Knockout of ZmFRKH1 gene significantly delayed maize flowering. Further analysis revealed that ZmFRKH1 protein binds to the mRNAs of multiple flowering regulators, influencing their stability.  Allelic variation analysis identified a single nucleotide polymorphism (SNP) in the ZmFRKH1 promoter, which significantly impacts the promoter activity and has significant effect on flowering time.  Analysis of domestication signatures showed this SNP was selectively fixed during the teosinte-to-maize domestication process, with the early-flowering haplotype contributing to the adaptation of maize from tropical to temperate regions.  These findings provide a novel gene resource for optimizing maize flowering time through molecular breeding.

Keywords:  maize       flowering regulation       RNA binding protein       natural variation  
Online: 03 June 2025  
Fund: 

This research was supported by grants from the National Natural Science Foundation of China (32372168), National Key Research and Development Program of China (2021YFF1000304), and the Open Research Fund of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (SKL-ZD202201).

About author:  #Correspondence Yubi Huang, E-mail: yubihuang@sohu.com; Yufeng Hu, E-mail: huyufeng@sicau.edu.cn *These authors contributed equally to this work.

Cite this article: 

Yao Cao, Qinglin Li, Babatope Samuel Ajayo, Wanyi Nie, Qiang Liao, Yin Liu, Lei Gao, Xiujun Fan, Yangping Li, Yubi Huang, Yufeng Hu. 2025. RNA-binding protein ZmFRKH1 promotes maize flowering by modulating the stability of multiple flowering regulator RNAs. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.06.008

Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y, Ichinoki H, Notaguchi M, Goto K, Araki T. 2005. FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science309, 1052–1056.

Ajayo B S, Li Y, Wang Y, Dai C, Gao L, Liu H, Yu G, Zhang J, Huang Y, Hu Y. 2022. The novel ZmTCP7 transcription factor targets AGPase-encoding gene ZmBt2 to regulate storage starch accumulation in maize. Frontiers in Plant Science13, 943050.

Amara U, Hu J, Cai J, Kang H. 2023. FLK is an mRNA m6A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis. Molecular Plant, 16, 919-929.

Buckler E S, Holland J B, Bradbury P J, Acharya C B, Brown P J, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz J C. 2009. The genetic architecture of maize flowering time. Science, 325, 714–718.

Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, Wang B, Xu D, Yang B, Xie C, Fan L, Gao S, Xu X, Zhang G, Li Y, Jiao Y, Doebley J F, Ross-Ibarra J, Lorant A, Buffalo V, et al. 2018. Construction of the third-generation Zea mays haplotype map. Gigascience7, 112.

Colasanti J, Yuan Z, Sundaresan V. 1998. The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell93, 593–603.

Danilevskaya O N, Meng X, Hou Z, Ananiev E V, Simmons C R. 2008. A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiology146, 250–264.

Domagalska M A, Schomburg F M, Amasino R M, Vierstra R D, Nagy F, Davis S J. 2007. Attenuation of brassinosteroid signaling enhances FLC expression and delays flowering. Development134, 2841–2850.

Goretti D, Silvestre M, Collani S, Langenecker T, Mendez C, Madueno F, Schmid M. 2020. TERMINAL FLOWER1 functions as a mobile transcriptional cofactor in the shoot apical meristem. Plant Physiology, 182, 2081–2095.

Guo Y, Wu Q, Xie Z, Yu B, Zeng R, Min Q, Huang J. 2020. OsFPFL4 is involved in the root and flower development by affecting auxin levels and ROS accumulation in rice (Oryza sativa). Rice, 13, 2.

Guo L, Wang X, Zhao M, Huang C, Li C, Li D, Yang C J, York A M, Xue W, Xu G, Liang Y, Chen Q, Doebley J F, Tian F. 2018. Stepwise cis-regulatory changes in ZCN8 contribute to maize flowering-time adaptation. Current Biology, 28, 3005–3015.

Hu Y F, Li Y P, Zhang J, Liu H, Chen Z, Huang Y. 2011. PzsS3a, a novel endosperm specific promoter from maize (Zea mays L.) induced by ABA. Biotechnology Letters33, 1465–1471.

Huang C, Sun H, Xu D, Chen Q, Liang Y, Wang X, Xu G, Tian J, Wang C, Li D, Wu L, Yang X, Jin W, Doebley J F, Tian F. 2018. ZmCCT9 enhances maize adaptation to higher latitudes. Proceedings of the National Academy of Sciences of the United States of America115, e334–341.

Jiang J, Wang T, Wu Z, Wang J, Zhang C, Wang H, Wang Z X, Wang X. 2015. The intrinsically disordered protein BKI1 is essential for inhibiting BRI1 signaling in plants. Molecular Plant8, 1675–1678.

Jiang Y, Guo S, Wang D, Tu L, Liu P, Guo X, Wang A, Zhu Y, Lu X, Chen Z, Wu X. 2024. Integrated GWAS, linkage, and transcriptome analysis to identify genetic loci and candidate genes for photoperiod sensitivity in maize. Frontiers in Plant Science15, 1441288.

LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell121, 713–724.

Lapucci A, Donnini M, Papucci L, Witort E, Tempestini A, Bevilacqua A, Nicolin A, Brewer G, Schiavone N, Capaccioli S. 2002. AUF1 Is a bcl-2 A + U-rich element-binding protein involved in bcl-2 mRNA destabilization during apoptosis. The Journal of Biological Chemistry277, 16139–16146.

Lazakis C M, Coneva V, Colasanti J. 2011. ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize. Journal of Experimental Botany62, 4833–4842.

Li Y X, Li C, Bradbury P J, Liu X, Lu F, Romay C M, Glaubitz J C, Wu X, Peng B, Shi Y, Song Y, Zhang D, Buckler E S, Zhang Z, Li Y, Wang T. 2016. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. The Plant journal86, 391–402.

Liang Y, Liu Q, Wang X, Huang C, Xu G, Hey S, Lin H Y, Li C, Xu D, Wu L, Wang C, Wu W, Xia J, Han X, Lu S, Lai J, Song W, Schnable P S, Tian F. 2019. ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation. The New Phytologist221, 2335–2347.

Maple R, Zhu P, Hepworth J, Wang J W, Dean C. 2024. Flowering time: From physiology, through genetics to mechanism. Plant Physiology195, 190–212.

Martignago D, da Silveira Falavigna V, Lombardi A, Gao H, Korwin Kurkowski P K, Galbiati M, Tonelli C, Coupland G, Conti L. 2023. The bZIP transcription factor AREB3 mediates FT signalling and fforal transition at the Arabidopsis shoot apical meristem. PLoS Genetics, 19, e1010766.

Meng X, Muszynski M G, Danilevskaya O N. 2011. The FT-like ZCN8 gene functions as a floral activator and is involved in photoperiod sensitivity in maize. The Plant Cell23, 942–960.

Muszynski M G, Dam T, Li B, Shirbroun D M, Hou Z, Bruggemann E, Archibald R, Ananiev E V, Danilevskaya O N. 2006. delayed flowering1 encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize. Plant Physiology142, 1523–1536.

Nagarajan V K, Kukulich P M, von Hagel B, Green P J. 2019. RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4. Nucleic Acids Research47, 9216–9230.

Niu X M, Xu Y C, Li Z W, Bian Y T, Hou X H, Chen J F, Zou Y P, Jiang J, Wu Q, Ge S, Balasubramanian S, Guo Y L. 2019. Transposable elements drive rapid phenotypic variation in Capsella rubellaProceedings of the National Academy of Sciences of the United States of America116, 6908–6913.

Qi W, Zhu T, Tian Z, Li C, Zhang W, Song R. 2016. High-efficiency CRISPR/Cas9 multiplex gene editing using the glycine tRNA-processing system-based strategy in maize. BMC Biotechnology16, 58.

Qu J, Xu S, Gou X, Zhang H, Cheng Q, Wang X, Ma C, Xue J. 2023. Time-resolved multiomics analysis of the genetic regulation of maize kernel moisture. The Crop Journal, 11, 247-257.

Ripoll J J, Rodríguez-Cazorla E, González-Reig S, Andújar A, Alonso-Cantabrana H, Perez-Amador M A, Carbonell J, Martínez-Laborda A, Vera A. 2009. Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C. Developmental Biology333, 251–262.

Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler K A, Meeley R, Ananiev E V, Svitashev S, Bruggemann E, Li B, Hainey C F, Radovic S, Zaina G, Rafalski J A, Tingey S V, Miao G H, Phillips R L, Tuberosa R. 2007. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proceedings of the National Academy of Sciences of the United States of America104, 11376–11381.

Shi H, Medway C, Brown K, Kalsheker N, Morgan K. 2011. Using Fisher’s method with PLINK ‘LD clumped’ output to compare SNP effects across Genome-wide Association Study (GWAS) datasets. International Journal of Molecular Epidemiology and Genetics2, 30-35.

Teper-Bamnolker P, Samach A. 2005. The flowering integrator FT regulates SEPALLATA3 and FRUITFULL accumulation in Arabidopsis leaves. The Plant Cell17, 2661–2675.

Tomecki R, Drazkowska K, Dziembowski A. 2010. Mechanisms of RNA degradation by the eukaryotic exosome. Chembiochem11, 938–945.

Umezawa T, Yoshida R, Maruyama K, Yamaguchi-Shinozaki K, Shinozaki K. 2004. SRK2C, a SNF1-related protein kinase 2, improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thalianaProceedings of the National Academy of Sciences of the United States of America101, 17306–17311.

Vahedi SM, Ardestani SS. 2024. FSTest: an efficient tool for cross-population fixation index estimation on variant call format files. Journal of Genetics103, 38258299.

Wang H, Liu J, Zhao W, Terzaghi W, Deng L, Liu H, Zheng Q, Fan S, Hua W, Zheng M. 2023. DELAYED GREENING 409 encodes a dual-localized pentatricopeptide repeat protein required for chloroplast and mitochondrial development. Plant Physiology192, 2768–2784.

Wang X, Chory J. 2006. Brassinosteroids regulate dissociation of BKI1, a negative regulator of BRI1 signaling, from the plasma membrane. Science313, 1118–1122.

Wang Y, Li L, Ye T, Lu Y, Chen X, Wu Y. 2013. The inhibitory effect of ABA on floral transition is mediated by ABI5 in ArabidopsisJournal of Experimental Botany64, 675–684.

Wright S I, Bi I V, Schroeder S G, Yamasaki M, Doebley J F, McMullen M D, Gaut B S. 2005. The effects of artificial selection on the maize genome. Science, 308, 1310–1314.

Xiao Q, Zhang C, Li H, Wei B, Wang Y, Huang H, Li Y, Yu G, Liu H, Zhang J, Liu Y, Hu Y, Huang Y. 2017. Identification and functional analysis of the ICK gene family in maize. Scientific reports, 7, 43818

Yang J, Liu Z, Liu Y, Fan X, Gao L, Li Y, Hu Y, Hu K, Huang Y. 2024. Genome-wide association study identifies quantitative trait loci and candidate genes involved in deep-sowing tolerance in maize (Zea mays L.). Plants13, 1533.

Yin L, Zhang H, Tang Z, Xu J, Yin D, Zhang Z, Yuan X, Zhu M, Zhao S, Li X, Liu X. 2021. rMVP: A memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study. Genomics Proteomics Bioinformatics, 19, 619–628.

Yoo S D, Cho Y H, Sheen J. 2007. Arabidopsis mesophyll protoplasts: A versatile cell system for transient gene expression analysis. Nature Protocols2, 1565–1572.

Zhang D, Zhang H, Hu Z, Chu S, Yu K, Lv L, Yang Y, Zhang X, Chen X, Kan G, Tang Y, An YC, Yu D. 2019. Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication. PLoS Genetics, 15, e1008267.

Zhang R, Jia G, Diao X. 2023. geneHapR: an R package for gene haplotypic statistics and visualization. BMC Bioinformatics, 24, 199.

Zhu Y, Klasfeld S, Jeong CW, Jin R, Goto K, Yamaguchi N, Wagner D. 2020. TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. Nature Communications, 11, 5118.

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