|
|
|
|
|
| Genome-wide identification, phylogeny and expression analysis of the SBP-box gene family in maize (Zea mays) |
| ZHANG Wei, LI Bei, YU Bin |
1、Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong
Agricultural University, Wuhan 430070, P.R.China
2、National Key Laboratory of Crop Genetic Improvement/Biomass and Bioenergy Research Centre/College of Life Sciences and
Technology, Huazhong Agricultural University, Wuhan 430070, P.R.China |
|
|
|
摘要 The SQUAMOSA promoter binding protein (SBP)-box genes encode a kind of plant-specific transcription factors (TFs) and play important roles in the regulation of plant development. In this study, a genome-wide characterization of this family was conducted in maize (Zea mays). Thirty-one SBP-box genes were identified to be distributed in nine chromosomes and 16 of them were complementary to the mature ZmmiR156 sequences. All the Z. mays SBP (ZmSBP) genes were classified into two clusters with eight subgroups according to the phylogenetic analysis of proteins, which were consistent with the pattern of exon-intron structures. The phylogenetic tree of the ZmSBP, Oryza sativa SBP-like (OsSPL) and Arabidopsis thaliana SBP-like (AtSPL) genes were constructed and all the SBP-box genes were divided into eight groups, which was the same as the classification of ZmSBP genes. The comparision of the expression profiles of all SBP-box genes in these three species indicated that most orthologous genes had similar expression patterns. The results from this study provided a basic understanding of the ZmSBP genes and might facilitate future researches for elucidating the SBP-box genes function in maize.
Abstract The SQUAMOSA promoter binding protein (SBP)-box genes encode a kind of plant-specific transcription factors (TFs) and play important roles in the regulation of plant development. In this study, a genome-wide characterization of this family was conducted in maize (Zea mays). Thirty-one SBP-box genes were identified to be distributed in nine chromosomes and 16 of them were complementary to the mature ZmmiR156 sequences. All the Z. mays SBP (ZmSBP) genes were classified into two clusters with eight subgroups according to the phylogenetic analysis of proteins, which were consistent with the pattern of exon-intron structures. The phylogenetic tree of the ZmSBP, Oryza sativa SBP-like (OsSPL) and Arabidopsis thaliana SBP-like (AtSPL) genes were constructed and all the SBP-box genes were divided into eight groups, which was the same as the classification of ZmSBP genes. The comparision of the expression profiles of all SBP-box genes in these three species indicated that most orthologous genes had similar expression patterns. The results from this study provided a basic understanding of the ZmSBP genes and might facilitate future researches for elucidating the SBP-box genes function in maize.
|
|
Received: 02 November 2014
Accepted:
|
| Fund: We wish to express our warm thanks to the support by the National Natural Science Foundation of China (31200911, 31101576), the China Postdoctoral Science Foundation (20100471197, 201104475) and the Research Fund for the Doctoral Program of Higher Education of China (20110146120040). |
|
Corresponding Authors:
YU Bin, Tel: +86-27-87281765,E-mail: bin.yu@mail.hzau.edu.cn
E-mail: bin.yu@mail.hzau.edu.cn
|
Cite this article:
ZHANG Wei, LI Bei, YU Bin.
2016.
Genome-wide identification, phylogeny and expression analysis of the SBP-box gene family in maize (Zea mays). Journal of Integrative Agriculture, 15(1): 29-41.
|
| Cardon G, Höhmann S, Klein J, Nettesheim K, SaedlerH, Huijser P. 1999. Molecular characterisation of theArabidopsis SBP-box genes. Gene, 237, 91-104Cardon G H, Höhmann S, Nettesheim K, Saedler H, HuijserP. 1997. Functional analysis of the Arabidopsis thalianaSBP-box gene SPL3: A novel gene involved in the floraltransition. The Plant Journal, 12, 367-377Chen G H, Huang W F. 2008. Progress in pharmacologicaleffects of compositions of Astragalus membranaceus.Chinese Journal of New Drugs, 17, 1482-1485 (in Chinese)Chuck G, Whipple C, Jackson D, Hake S. 2010. The maizeSBP-box transcription factor encoded by tasselsheath4regulates bract development and the establishment ofmeristem boundaries. Development, 137, 1243-1250Gandikota M, Birkenbihl R P, Höhmann S, Cardon G H, SaedlerH, Huijser P. 2007. The miRNA156/157 recognitionelement in the 3’ UTR of the Arabidopsis SBP box geneSPL3 prevents early flowering by translational inhibition inseedlings. The Plant Journal, 49, 683-693Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, JacksonD, Kellogg E, Lawrence C, McCouch S, Mockler T, MooseS, Paterson A, Peterson T, Rokshar D, Souza GM, SpringerN, Stein N, Timmermans M, Wang G L, Grotewold E. 2009.A recommendation for naming transcription factor proteinsin the grasses. Plant Physiology, 149, 4-6Haas B J, Delcher A L, Wortman J R, Salzberg S L. 2004.DAGchainer: a tool for mining segmental genomeduplications and synteny. Bioinformatics, 20, 3643-3646Hou H, Li J, Gao M, Singer S D, Wang H, Mao L, Fei Z, WangX. 2013. Genomic organization, phylogenetic comparisonand differential expression of the SBP-box family genes ingrape. PLOS ONE, 8, e59358.Hultquist J F, Dorweiler J E. 2008. Feminized tassels of maizemop1 and ts1 mutants exhibit altered levels of miR156 andspecific SBP-box genes. Planta, 229, 99-113Ishii T, Numaguchi K, Miura K, Yoshida K, Thanh P T, HtunTM, Yamasaki M, Komeda N, Matsumoto T, TerauchiR, Ishikawa R, Ashikari M. 2013. OsLG1 regulates aclosed panicle trait in domesticated rice. Nature Genetics,45, 462-465Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, ZengD, Lu Z, Zhu X, Qian Q, Li J. 2010. Regulation of OsSPL14by OsmiR156 defines ideal plant architecture in rice. NatureGenetics, 42, 541-544Jung J H, Seo P J, Kang S K, Park C M. 2011. miR172 signalsare incorporated into the miR156 signaling pathway at theSPL3/4/5 genes in Arabidopsis developmental transitions.Plant Molecular Biology, 76, 35-45Klein J, Saedler H, Huijser P. 1996. A new family of DNAbinding proteins includes putative transcriptional regulatorsof the Antirrhinum majus floral meristem identity geneSQUAMOSA. Molecular and General Genetics, 250, 7-16Kropat J, Tottey S, Birkenbihl R P, Depège N, HuijserP, Merchant S. 2005. A regulator of nutritional coppersignaling in Chlamydomonas is an SBP domain protein thatrecognizes the GTAC core of copper response element.Proceedings of the National Academy of Sciences of theUnited States of America, 102, 18730-18735Lännenpää M, Jänönen I, Hölttä-Vuori M, GardemeisterM, Porali I, Sopanen T. 2004. A new SBP-box geneBpSPL1 in silver birch (Betula pendula). Plant Physiology,120, 491-500Li J, Hou H, Li X, Xiang J, Yin X, Gao H, Zheng Y, Bassett CL, Wang X. 2013. Genome-wide identification and analysisof the SBP-box family genes in apple (Malus×domesticaBorkh.). Plant Physiology Biochemistry, 70, 100-114Lu S, Yang C, Chiang V L.2011. Conservation and diversityof microRNA-associated copper-regulatory networks inPopulus trichocarpa. Journal of Integrative Plant Biology,53, 879-891Lu Z, Yu H, Xiong G, Wang J, Jiao Y, Liu G, Jing Y, MengX, Hu X, Qian Q, Fu X, Wang Y, Li J. 2013. Genome-widebinding analysis of the transcription activator IDEAL PLANT ARCHITECTURE1 reveals a complex network regulatingrice plant architecture. The Plant Cell, 25, 3743-3759Manning K, Tör M, Poole M, Hong Y, Thompson A J, KingG J, Giovannoni J J, Seymour G B. 2006. A naturallyoccurring epigenetic mutation in a gene encoding an SBPboxtranscription factor inhibits tomato fruit ripening. NatureGenetics, 38, 948-952Miura K, Ikeda M, Matsubara A, Song X J, Ito M, AsanoK, Matsuoka M, Kitano H, Ashikari M. 2010. OsSPL14promotes panicle branching and higher grain productivityin rice. Nature Genetics, 42, 545-549Moreno M A, Harper L C, Krueger R W, Dellaporta S L, FreelingM. 1997. liguleless1 encodes a nuclear-localized proteinrequired for induction of ligules and auricles during maizeleaf organogenesis. Genes & Development, 11, 616-628Riese M, Höhmann S, Saedler H, Münster T, Huijser P. 2007.Comparative analysis of the SBP-box gene families inP. patens and seed plants. Gene, 401, 28-37Salinas M, Xing S, Höhmann S, Berndtgen R, Huijser P. 2012.Genomic organization, phylogenetic comparison anddifferential expression of the SBP-box family of transcriptionfactors in tomato. Planta, 235, 1171-1184Schnable P S, Ware D, Fulton R S, Stein J C, Wei F, PasternakS, Liang C, Zhang J, Fulton L, Graves T A, Minx P, ReilyA D, Courtney L, Kruchowski S S, Tomlinson C, StrongC, Delehaunty K, Fronick C, Courtney B, Rock S M, et al.2009. The B73 maize genome: Complexity, diversity, anddynamics. Science, 326, 1112-1115Schwarz S, Grande AV, Bujdoso N, Saedler H, Huijser P. 2008.The microRNA regulated SBP-box genes SPL9 and SPL15control shoot maturation in Arabidopsis. Plant MolecularBiology, 67, 183-195Sekhon R S, Lin H, Childs K L, Hansey C N, Buell C R, de LeonN, Kaeppler S M. 2011. Genome-wide atlas of transcriptionduring maize development. The Plant Journal, 66, 553-563Shikata M, Koyama T, Mitsuda N, Ohme-Takagi M. 2009.Arabidopsis SBP-box genes SPL10, SPL11 and SPL2control morphological change in association with shootmaturation in the reproductive phase. Plant and CellPhysiology, 50, 2133-2145Stone J M, Liang X, Nekl E R, Stiers J J. 2005. ArabidopsisAtSPL14, a plant-specific SBP-domain transcriptionfactor, participates in plant development and sensitivity tofumonisin B1. The Plant Journal, 41,744-754Tamura K, Peterson D, Peterson N, Stecher G, Nei M, KumarS. 2011. MEGA5: Molecular evolutionary genetics analysisusing maximum likelihood, evolutionary distance, andmaximum parsimony methods. Molecular Biology andEvolution, 28, 2731-2739R Development Core Team. 2009. R: A Language andEnvironment for Statistical Computing. R Foundation forStatistical Computing, Vienna, Austria.Unte U S, Sorensen A M, Pesaresi P, Gandikota M, LeisterD, Saedler H, Huijser P. 2003. SPL8, an SBP-box genethat affects pollen sac development in Arabidopsis. ThePlant Cell, 15, 1009-1019Wang H, Nussbaum-Wagler T, Li B, Zhao Q, VigourouxY, Faller M, Bomblies K, Lukens L, Doebley J F. 2005. Theorigin of the naked grains of maize. Nature, 436, 714-719Wang J W, Schwab R, Czech B, Mica E, Weigel D. 2008. Dualeffects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsisthaliana. The Plant Cell, 20, 1231-1243Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, XuC, Xiao J, Zhang Q. 2010. A dynamic gene expression atlascovering the entire life cycle of rice. The Plant Journal, 61,752-766Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, ZhuH, Dong G, Qian Q, Zhang G, Fu X. 2012. Control ofgrain size, shape and quality by OsSPL16 in rice. NatureGenetics, 44, 950-954Wu G, Poethig R S. 2006. Temporal regulation of shootdevelopment in Arabidopsis thaliana by miR156 and itstarget SPL3. Development, 133, 3539-3547Xie K, Wu C, Xiong L. 2006. Genomic organization, differentialexpression, and interaction of SQUAMOSA promoterbinding-like transcription factors and microRNA156 in rice.Plant Physiology, 142, 280-293Xing S, Salinas M, Höhmann S, Berndtgen R, Huijser P. 2010.miR156-targeted and nontargeted SBP-box transcriptionfactors act in concert to secure male fertility in Arabidopsis.The Plant Cell, 22, 3935-3950Xu G, Guo C, Shan H, Kong H. 2012. Divergence of duplicategenes in exon-intron structure. Proceedings of the NationalAcademy of Sciences of the United States of America, 109,1187-1192Yamasaki H, Hayashi M, Fukazawa M, Kobayashi Y, ShikanaiT. 2009. SQUAMOSA promoter binding protein-like7 is acentral regulator for copper homeostasis in Arabidopsis.The Plant Cell, 21, 347-361Yamasaki K, Kigawa T, Inoue M, Tateno M, YamasakiT, Yabuki T, Aoki M, Seki E, Matsuda T, NunokawaE, Ishizuka Y, Terada T, Shirouzu M, Osanai T, TanakaA, Seki M, Shinozaki K, Yokoyama S. 2004. A novel zincbindingmotif revealed by solution structures of DNA-bindingdomains of Arabidopsis SBP-family transcription factors.Journal Molecular Biology, 337, 49-63Yilmaz A, Nishiyama Jr M Y, Fuentes B G, Souza G M, JaniesD, Gray J, Grotewold E. 2009. GRASSIUS: A platform forcomparative regulatory genomics across the grasses. PlantPhysiology, 149, 171-180Zhang Y, Schwarz S, Saedler H, Huijser P. 2007. SPL8, a localregulator in a subset of gibberellin-mediated developmentalprocesses in Arabidopsis. Plant Molecular Biology, 63,429-439 |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
