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Special Issue:
园艺-分子生物合辑Horticulture — Genetics · Breeding
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| Genome-wide identification and expression profiling of MYB transcription factor genes in radish (Raphanus sativus L.) |
Everlyne M’mbone MULEKE1*, WANG Yan1*, ZHANG Wan-ting1*, XU Liang1, YING Jia-li1, Bernard K. KARANJA1, ZHU Xian-wen2, FAN Lian-xue1, Zarwali AHMADZAI1, LIU Li-wang1 |
1 National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China
2 Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA |
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摘要
萝卜是一种重要的十字花科根菜类蔬菜作物，在其有色的根中有高水平的花青素累积。MYB转录因子(TFs)在植物发育和花青素代谢中起着重要作用，并且PAP1/2能促进花青素生物合成基因的表达。本研究在萝卜基因组中共鉴定出187个RsMYB基因，并将其分为32个亚家族；其中159个RsMYB基因被定位在9条染色体上。在4个不同颜色的萝卜品种肉质根发育阶段，14个RsMYB基因表现出差异的表达模式。一些RsMYB基因在成熟期有色根组织中高表达，这些基因包括RsMYB41，RsMYB117以及与PAP1/2同源的RsMYB132在‘NAU-YH’的红色根皮中高表达，RsMYB65和RsMYB159基因在‘NAU-YZH’的紫色根皮中高表达，表明这些RsMYB基因可能促进萝卜肉质根花青素积累。研究结果为进一步研究萝卜RsMYB基因功能特性提供有价值的信息，并有助于阐明萝卜花青素生物合成的分子机制。
Abstract Radish (Raphanus sativus L.), an important root vegetable crop of the Brassicaceae family, has a high level of anthocyanin accumulation in its pigment root tissues. It was reported that MYB transcription factors (TFs) play vital roles in plant development and anthocyanin metabolism, and the PAP1/2 could promote expression of anthocyanin biosynthesis genes. In this study, a total of 187 radish MYB genes (RsMYBs) were identified in the radish genome and clustered into 32 subfamilies. Among them, 159 RsMYBs were localized on nine radish chromosomes. Interestingly, 14 RsMYBs exhibited differential expression profiles in different taproot developmental stages among four differently colored radish lines. A number of RsMYBs were highly expressed in the pigmented root tissues at the maturity stage, several genes including RsMYB41, RsMYB117, and RsMYB132 being homologous to PAP1/2, showed high expression levels in the red skin of NAU-YH (red skin-white flesh) taproot, while RsMYB65 and RsMYB159 were highly expressed in the purple root skin of NAU-YZH (purple skin-red flesh), indicating that these RsMYBs might positively regulate the process of anthocyanin accumulation in radish taproot. These results would provide valuable information for further functional characterization of RsMYBs, and facilitate clarifying the molecular mechanism underlying anthocyanin biosynthesis in radish.
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Received: 01 March 2020
Accepted:
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| Fund: This work was in part supported by the National Key Research and Development Program of China (2017YFD0101806), the Open Funds of State Key Laboratory of Crop Genetics and Germplasm Enhancement, China (ZW201709), the Key Laboratory of Biology and Genetics Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, China (IVF201706) and the Jiangsu Agricultural Science and Technology Innovation Fund, China (CX(19)3045). |
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Corresponding Authors:
Correspondence LIU Li-wang, Tel: +86-25-84395563, Fax: +86-25-84395266, E-mail: nauliulw@njau.edu.cn
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| About author: Everlyne M’mbone MULEKE, E-mail: mmboneve@gmail.com; WANG Yan, E-mail: wangyanhs@njau.edu.cn; ZHANG Wan-ting, E-mail: 2018104061@njau.edu.cn; * These authors contributed equally to this study. |
Cite this article:
Everlyne M’mbone MULEKE, WANG Yan, ZHANG Wan-ting, XU Liang, YING Jia-li, Bernard K. KARANJA, ZHU Xian-wen, FAN Lian-xue, Zarwali AHMADZAI, LIU Li-wang.
2021.
Genome-wide identification and expression profiling of MYB transcription factor genes in radish (Raphanus sativus L.). Journal of Integrative Agriculture, 20(1): 120-131.
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Albert N W, Davies K M, Lewis D H, Zhang H, Montefiori M, Brendolise C, Schwinn K E. 2014. A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in Eudicots. The Plant Cell, 26, 962–980.
Bailey T L, Johnson J, Grant C E, Noble W S. 2015. The MEME suite. Nucleic Acids Research, 43, W39–W49.
Borevitz J O, Xia Y, Blount J, Dixon R A, Lamb C. 2000. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. The Plant Cell, 12, 2383–2393.
Cannon S B, Mitra A, Baumgarten A, Young N D, May G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology, 4, 10.
Cao Y, Han Y, Li D, Lin Y, Cai Y. 2016. MYB transcription factors in Chinese pear (Pyrus bretschneideri Rehd.): Genome-wide identification, classification, and expression profiling during fruit development. Frontiers in Plant Science, 7, 577.
Cao Z, Zhang S, Wang R, Zhang R, Hao Y. 2013. Genome wide analysis of the apple MYB transcription factor family allows the identification of MdoMYB121 gene conferring abiotic stress tolerance in plants. PLoS ONE, 8, e69955.
Chen F, Xing C, Huo S, Cao C, Yao Q, Fang P. 2016. Red pigment content and expression of genes related to anthocyanin MYB transcription factor family allows the identification of MdoMYB121 gene confering abiotic stress tolerance in plants biosynthesis in radishes (Raphanus sativus L.) with different colored flesh. Journal of Agricultural Science, 8, 126.
Cominelli E, Gusmaroli G, Allegra D, Galbiati M, Wade H K, Jenkins G I, Tonelli C. 2008. Expression analysis of anthocyanin regulatory genes in response to different light qualities in Arabidopsis thaliana. Journal of Plant Physiology, 165, 886–894.
Du H, Yang S, Liang Z, Feng B, Liu L, Huang Y, Tang Y. 2012. Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biology, 12, 106.
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. 2010. MYB transcription factors in Arabidopsis. Trends in Plant Science, 15, 573–581.
Feng K, Xu Z, Que F, Liu J, Wang F, Xiong A. 2018. An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica. Planta, 247, 301–315.
Gonzalez A, Zhao M, Leavitt J M, Lloyd A M. 2008. Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. The Plant Journal, 53, 814–827.
Gutiérrez R M P, Perez R L. 2004. Raphanus sativus (Radish): Their chemistry and biology. The Scientific World Journal, 4, 811–837.
Holton T A, Cornish E C. 1995. Genetics and biochemistry of anthocyanin biosynthesis. The Plant Cell, 7, 1071.
Hou X, Li S, Liu S, Hu C, Zhang J. 2014. Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange. PLoS ONE, 9, e112375.
Huang W, Wu H, Li D, Song J, Xiao Y, Liu C, Zhou J, Sui Z. 2018. Protective effects of blueberry anthocyanins against H2O2-induced oxidative injuries in human retinal pigment epithelial cells. Journal of Agricultural and Food Chemistry, 66, 1638–1648.
Jeong Y M, Kim N, Ahn B O, Oh M, Chung W H, Chung H. 2016. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the brassica genomes. Theoretical and Applied Genetics, 129, 1357–1372.
Jia L, Clegg M T, Jiang T. 2004. Evolutionary dynamics of the DNA-binding domains in putative R2R3-MYB genes identified from rice subspecies indica and japonica genomes. Plant Physiology, 134, 575–585.
Jiang C, Gu X, Peterson T. 2004. Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biology, 5, R46.
Katiyar A, Smita S, Lenka S K, Rajwanshi R, Chinnusamy V, Bansal K C. 2012. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics, 13, 544.
Kranz H D, Denekamp M, Greco R, Jin H, Leyva A, Meissner R C, Petroni K, Urzainqui A, Bevan M, Martin C, Smeekens S, Tonelli C, Paz-Ares J, Weisshaar B. 1998. Towards functional characterization of the members of the R2R3-MYB gene family from Arabidopsis thaliana. The Plant Journal, 16, 263–276.
Lai B, Cheng Y, Liu H, Wang Q, Wang Q, Wang C, Su R, Chen F, Wang H, Du L. 2020. Differential anthocyanin accumulation in radish taproot: importance of RsMYB1 gene structure. Plant Cell Reports, 39, 217–226.
Li Q, Zhang C, Li J, Wang L, Ren Z. 2012. Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus. PLoS ONE, 7, e47576.
Lim S H, Song J H, Kim D H, Kim J K, Lee J Y, Kim Y M, Ha S H. 2016. Activation of anthocyanin biosynthesis by expression of the radish R2R3-MYB transcription factor gene RsMYB1. Plant Cell Reports, 35, 641–653.
Lin-Wang K, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie T K, Espley R V, Hellens R P, Allan A C. 2010. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biology, 10, 50.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.
Luo X, Xu L, Wang Y, Dong J, Chen Y, Tang M, Fan L, Zhu Y, Liu L. 2020. An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin color in radish (Raphanus sativus L.). Plant Biotechnology Journal, 18, 274–286.
Matsui K, Umemura Y, Ohme-Takagi M. 2008. Atmybl2, a protein with a single MYB domain, acts as a negative regulator of anthocyanin biosynthesis in Arabidopsis. Plant Journal for Cell & Molecular Biology, 55, 954–967.
Matus J T, Aquea F, Arce-Johnson P. 2008. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biology, 8, 83.
Mitsui Y, Shimomura M, Komatsu K. 2015. The radish genome and comprehensive gene expression profile of tuberous root formation and development. Scientific Reports, 5, 10835.
Muleke E, Fan L, Wang Y, Xu L, Zhu X, Zhang W, Cao Y, Karanja B K, Liu L. 2017. Coordinated regulation of anthocyanin biosynthesis genes confers varied phenotypic and spatial-temporal anthocyanin accumulation in radish (Raphanus sativus L.). Frontiers in Plant Science, 8, 1243.
Muthamilarasan M, Khandelwal R, Yadav C B, Bonthala V S, Khan Y, Prasad M. 2014. Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.). PLoS ONE, 9, e109920.
Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L. 2001. The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. The Plant Cell, 13, 2099–2114.
Nhukarume L, Chikwambi Z, Muchuweti M, Chipurura B. 2010. Phenolic content and antioxidant capacities of Parinari curatelifolia, Strychnos spinosa and Adansonia digitata. Journal of Food Biochemistry, 34, 207–221.
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Nishimura Y. 1994. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell, 79, 639–648.
Ogatallz K, Kanei-Ishiil C, Sasaki M, Hatanaka H, Nagadoiz A, Enariz M, Nishimuraz Y, Ishii S, Sarai A. 1996. The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nature Structural Biology, 3, 178–187.
Park N I, Xu H, Li X, Jang I H, Park S, Ahn G H, Lim Y P, Kim S J, Park S U. 2011. Anthocyanin accumulation and expression of anthocyanin biosynthetic genes in radish (Raphanus sativus). Journal of Agricultural and Food Chemistry, 59, 6034–6039.
Ptashne M. 1988. How eukaryotic transcriptional activators work. Nature, 335, 683–689.
Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson A H. 2019. Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology, 20, 38.
Stracke R, Werber M, Weisshaar B. 2001. The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology, 4, 447–456.
Voorrips R E. 2001. MapChart: Software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93, 77–78.
Wang K L, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie T K, Espley R V, Hellens R P, Allan A C. 2010. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biology, 10, 50.
Wang Z, Tang J, Hu R, Wu P, Hou X L, Song X M, Xiong A S, 2015. Genome-wide analysis of the R2R3-MYB transcription factor genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals their stress and hormone responsive patterns. BMC Genomics, 16, 17.
Xie S, Song C, Wang X, Liu M, Zhang Z, Xi Z. 2015. Tissue-specific expression analysis of anthocyanin biosynthetic genes in white- and red-fleshed grape cultivars. Molecules, 20, 22767–22780.
Xie Y, Xu L, Wang Y, Fan L, Chen Y, Tang M, Luo X, Liu L. 2018. Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.). Horticulture Research, 5, 51.
Xu L, Wang Y, Zhai L, Xu Y, Wang L, Zhu X, Gong Y, Yu R, Limera C, Liu L. 2013. Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots. Journal of Experimental Botany, 64, 4271–4287.
Zhu H. F, Fitzsimmons K, Khandelwal A, Kranz R G. 2009. CPC, a single-repeat R3 MYB, is a negative regulator of anthocyanin biosynthesis in Arabidopsis. Molecular Plant, 2, 790–802.
Zuluaga D L, Gonzali S, Loreti E, Pucciariello C, Degl’Innocenti E, Guidi L, Alpi A, Perata P. 2008. Arabidopsis thaliana MYB75/PAP1 transcription factor induces anthocyanin production in transgenic tomato plants. Functional Plant Biology, 35, 606–618. |
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