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Title:: Bioinformatics Analysis of Soybean miR164Family

Author(s):: TENG Lu; YU Yue-hua; HE Ru-yue; CHEN Quan-jia; NI Zhi-yong; (College of Agriculture, Xinjiang Agricultural University, Urumqi 831300，China)

Keywords:: Soybean; MiR164family; Bioinformatics; Promoter analysis

PACS:: -

DOI:: 10.11861/j.issn.1000-9841.2018.05.0704

Abstract:: MicroRNA164is a highly conserved miRNA family, widely involved in plant cell and physiological processes. The purpose of this study was to investigate the important role of miR164gene family in soybean growth and stress response by bioinformatics, and to provide a theoretical basis for molecular breeding and variety improvement in soybean. Using Plant MicroRNA Database，PLACE and NCBI Database, Clustal X2.0，MEGA5.0 and DNAMAN to analyze the sequence, chromosome location, target gene regulation function, promoter element, secondary structure and the phylogenetic tree was analyzed by bioinformatics. In the miRBase, 11 gma-miR164gene homologous sequences were searched and distributed on 7 chromosomes. There were 3 sequences in Chr3, two in Chr10 and two in Chr19, and one in Chr02，Chr09，Chr18 and Chr20. 11 members of gma-miR164gene family predicted 6 target genes, all of which were NAC transcription factors. The mature sequence of gma-miR164gene family was highly conserved, and its precursor sequence can form a stable secondary stem ring structure. The analysis of cis-regulatory elements in promoter showed that the four elements of ABRE, DRE, MYB and MYC were found in gma-miR164gene. The family promoter sequences were unevenly distributed, in which the number of MYB and MYC elements was the majority. This study provides a data basis and theoretical basis for exploring the regulatory role of miR164family in stress response.

References:

［1］Liu H, Yu H, Tang G, et al. Small but powerful: Function of microRNAs in plant development［J］. Plant Cell Reports, 2018, 37(3):515-528.

［2］D′Ario M, Griffithsjones S, Kim M. Small RNAs: Big impact on plant development［J］. Trends in Plant Science, 2017, 22(12):1056-1068.

［3］Kumar V, Khare T, Shriram V, et al. Plant small RNAs: The essential epigenetic regulators of gene expression for salt-stress responses and tolerance［J］. Plant Cell Reports, 2018,37(1):61-75.

［4］Ohbayashi I, Sugiyama M. Plant nucleolar stress response, a new face in the nac-dependent cellular stress responses［J］. Frontiers in Plant Science, 2017, 8: 2247.

［5］Afa S, Sajad M, Nazaruddin N, et al. MicroRNA and transcription factor: Key players in plant regulatory network［J］. Frontiers in Plant Science, 2017, 8: 565.

［6］Kim H J, Nam H G, Lim P O. Regulatory network of NAC transcription factors in leaf senescence［J］. Current Opinion in Plant Biology, 2016, 33: 48-56.

［7］杨春文. 番茄miR164对花器官形成和果实发育的调控研究［D］. 重庆: 重庆大学, 2012:1-62. (Yang C W. Studies on the regulation of miR164on flower organ formation and fruit development in tomato［D］. Chongqing: Chongqing University, 2012:1-62. )

［8］Wei H, Yordanov Y S, Georgieva T, et al. Nitrogen deprivation promotes populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks［J］. New Phytologist, 2013, 200(2):483-497.

［9］李春贺,阴祖军,刘玉栋,等.盐胁迫条件下不同耐盐棉花miRNA差异表达研究［J］.山东农业科学,2009(7): 12-17. (Li C H, Ying Z J, Liu Y D, et al. Study on miRNA differential expression of different salt tolerant cotton under salt stress［J］. Shandong Agricultural Science, 2009(7):12-17. )

［10］牟桂萍, 纪春艳, 许东林, 等. 植物miR164家族研究进展［J］.生命科学, 2013, 25(5): 525-531. (Mu G P, Ji C Y, Xu D L, et al. Research progress of plant miR164family［J］. Chinese Bulletin of Life Sciences, 2013, 25(5):525-531.)

［11］Kim J H, Woo H R, Kim J, et al. Trifurcate feed-forward regulation of age-dependent cell death involving miR164in Arabidopsis［J］. Science, 2009, 323(5917):1053-1057.

［12］Wu X M, Liu M Y, Ge X X, et al. Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange［J］. Planta, 2011, 233(3):495-505.

［13］Bazzini A A, Almasia N I, Manacorda C A, et al. Virus infection elevates transcriptional activity of miR164apromoter in plants［J］. BMC Plant Biology, 2009, 9(1):1-12.

［14］Li Y J, Fu Y, Ji L S, et al. Characterization and expression analysis of the Arabidopsis miR169 family［J］. Plant Science, 2010, 178(3):271-280.

［15］Zhao B, Ge L, Liang R, et al. Members of miR-169 amily are induced by high salinity and transiently inhibit the NF-YA transcription factor［J］. BMC Molecular Biology, 2009, 10(1):1-10.

［16］罗中钦. 大豆逆境胁迫相关microRNA的发掘与验证［D］. 北京: 中国农业科学院, 2012.（Luo Z Q. Discovery and validation of microRNA related to stress in Soybean［D］. Beijing: Chinese Academy of Agricultural Sciences, 2012.）

［17］Sun Z, Wang Y, Mou F, et al. Genome-wide small RNA analysis of soybean reveals auxin-responsive microRNAs that are differentially expressed in response to salt stress in root apex［J］. Frontiers in Plant Science, 2016, 6:1273.

［18］许硕. 野生大豆盐胁迫相关microRNA的功能分析［D］. 北京: 中国农业科学院, 2011.（Xu S.Functional analysis of microRNA related to salt stress in wild soybean［D］. Beijing: Chinese Academy of Agricultural Sciences, 2011.）

［19］Zhao B, Liang R, Ge L, et al. Identification of drought-induced microRNAs in rice［J］. Biochemical & Biophysical Research Communications, 2007, 354(2): 585-590.

［20］Zhou X, Wang G, Su T K, et al. Identification of cold-inducible microRNAs in plants by transcriptome analysis［J］. Biochemica et Biophysica Acta, 2008, 1779 (11): 780-788．

［21］Llave C, Xie Z, Kasschau K D, et al. Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA［J］. Science, 2002, 297(5589): 2053-2056.

［22］Nikovics K, Blein T, Peaucelle A, et al. The balance between the miR164aand CUC2genes controls leaf margin serration in Arabidopsis［J］. Plant Cell, 2006, 18(11): 2929-2945.

Bioinformatics Analysis of Soybean miR164Family(PDF)

《大豆科学》[ISSN:1000-9841/CN:23-1227/S]

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