Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (09): 1273-1281.doi: 10.3724/SP.J.1006.2016.01273


Global Identification and Comparison of MicroRNA in Wild and Cultivated Adzuki Bean

MA Yan-Ming1,CHEN Chun-Hai2,YANG Kai1,LI Yi-Song1,ZHAO Bo1,LI Jiang2,LI Yong-Qiang1,WAN Ping1,*   

  1. 1 Beijing University of Agriculture /Beijing Key Laboratory of New Technology in Agricultural Application, Beijing 102206, China; 2BGI-Shenzhen, Shenzhen 518083, China
  • Received:2016-01-27 Revised:2016-05-04 Online:2016-09-12 Published:2016-05-09
  • Contact: 万平, E-mail: pingwan3@163.com, Tel: 010-80799134 E-mail:574088090@qq.com
  • Supported by:

    This study was supported byNational Natural Science Foundation of China (31371694)


MicroRNAs (miRNAs) are a class of small regulatory RNAs with thefunction as crucial regulators that repress the expression of their target genes at the transcriptional or post-transcriptional level. Global identification of miRNA is important for the functional study. Adzuki bean (Vigna angularis) genome sequencing has beenfinished recently, but lack of a systematical analysis of miRNA. In this study, we performed deep miRNA sequencing in wild (CW108) and cultivated (JN6) adzuki beans. Our investigation not only identified the miRNAs that shared by these two species, but also found miRNAs that specifically existed in individual accession. Through comparison of the miRNA expression and their target gene predictions between the wild and cultivated adzuki beans, we found that the miRNA was diverged between them, which may be associated with plant-pathogen interaction pathway. Our study provided a valuable resource for functional analysis in adzuki bean.

Key words: miRNA, Wild adzuki bean(Vignaangularis), Cultivated adzuki bean(Vignaangularisvar. nipponensis)

[1]LeeRC, FeinbaumR L,AmbrosV. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75:843–854
[2]Carrington JC,Ambros V. Role of microRNAs in plant and animal development. Science, 2003, 301:336–338
[3]AmbrosV, The functions of animal microRNAs. Nature, 2004, 431:350–355
[4]Jones-Rhoades M W, BartelDP,BartelB. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol, 2006, 57:19–53
[5]Zhang B, WangQ, Pan X. MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol, 2007, 210:279–289
[6]Fahlgren N,Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC.High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One, 2007, 2(2):e219
[7]AbroukM,Zhang R, Murat F, LiA, Pont C, Mao L, Salse J.Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication.Plant Cell, 2012, 24: 1776–1792
[8]Axtell M J, Bowman J L. Evolution of plant microRNAs and their targets. Trends Plant Sci, 2008, 13:343–349
[9]Felippes F F, Schneeberger K, DezulianT, Huson D H,Weigel D. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA,2008, 14:2455–2459
[10]MaherC, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res, 2006, 16:510–519
[11]Meunier J,LemoineF, SoumillonM, LiechtiA, WeierM, GuschanskiK,Hu H, KhaitovichP, KaessmannH. Birth and expression evolution of mammalian microRNA genes. Genome Res, 2013, 23:34–45
[12]ZhouZ, Wang Z, Li W, Fang C, Shen Y, Li C, Wu Y, Tian Z. Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome. Plant J, 2013, 76:332–344
[13]Liu L, Bestel S, Shi J, Song Y, Chen X. Paleolithic human exploitation of plant foods during the last glacial maximum in North China. Proc Natl Acad Sci USA, 2013, 110:5380–5385
[14]Amarowicz R, Estrella I, HernandezT, TroszynskaA.Antioxidant activity of extract of adzuki bean and its fractions. J Food Lipids, 2008, 15: 119–136
[15]Kitano-Okada T, Kitano-Okada T, Ito A, Ai K, Nakamura Y, Han K H.Anti-obesity role of adzuki bean extract containing polyphenols: in vivo and in vitro effects. J Sci Food Agric, 2012, 92:2644–2651
[16]ItohT, FuruichY. Lowering serum cholesterol level by feeding a 40% ethanol-eluted fraction from HP-20 resin treated with hot water extract of adzuki beans (Vignaangularis) to rats fed a high-fat cholesterol diet. Nutrition, 2009, 25: 318–321
[17]Sato S, Yamate J, Hori Y, Hatai A, Nozawa M, SagaiM. Protective effect of polyphenol-containing azuki bean (Vignaangularis) seed coats on the renal cortex in streptozotocin-induced diabetic rats. JNutrBiochem, 2005,16: 547–553
[18]Yang K, Tian Z, Chen C, Luo L, Zhao B, Wang Z, Yu L, Li Y, Sun Y, Li W, Chen Y, Li Y, Zhang Y, Ai D, Zhao J, Shang C, Ma Y, Wu B, Wang M, Gao L, Sun D, Zhang P, Guo F Wang W, Li Y, Wang J, Varshney RK, Wang J, LingHQ, Wan P.Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proc Natl Acad Sci USA, 2015, 112: 13213–13218
[19]Wu HJ, MaY K, Chen T, WangM, Wang X J. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucl Acids Res, 2012, 40:W22–28
[20]Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121:207–221
[21]Lopez JP, Fiori LM, Gross JA, Labonte B, Yerko V, Mechawar N, Turecki G. Regulatory role of miRNAs in polyamine gene expression in the prefrontal cortex of depressed suicide completers. Int J Neuropsychopharmacol, 2014, 17: 23–32
[22]Wang X, El Naqa I M. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 2008, 24: 325–332
[23]ZhouL, Chen J, Li Z, Li X, Hu X, Huang Y, Zhao X, Liang C, Wang Y, Sun L, Shi M, Xu X, Shen F, Chen M, Han Z, Peng Z, Zhai Q, Chen J, Zhang Z, Yang R, Ye J, Guan Z, Yang H, Gui Y, Wang J, Cai Z, Zhang X.Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS One, 2010, 5:e15224
[24]Audic S, ClaverieJM. The significance of digital gene expression profiles. Genome Res, 1997, 7:986–995
[25]Kanehisa M, ArakiM, GotoS, HattoriM, HirakawaM, ItohM, KatayamaT,Kawashima S, TokimatsuT, YamanishiY. KEGG for linking genomes to life and the environment. Nucl Acids Res, 2008, 36:D480–484
[26]Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. The birth and death of microRNA genes in Drosophila. Nat Genet, 2008, 40: 351–355
[27]Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee SH, Wang W, Tian Z.Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol, 2015, 33: 408–414
[28]LiYH, Zhou G, Ma J, Jiang W, Jin LG, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang SS, Zuo Q, Shi XH, Li YF, Zhang WK, Hu Y, Kong G, Hong HL, Tan B, Song J, Liu ZX, Wang Y, Ruan H, Yeung CK, Liu J, Wang H, Zhang LJ, Guan RX, Wang KJ, Li WB, Chen SY, Chang RZ, Jiang Z, Jackson SA, Li R, Qiu LJ. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol, 2014, 32: 1045–1052

[1] Qi-Yue WANG, Shu-Jun MENG, Ke ZHANG, Zhan-Hui ZHANG, Ji-Hua TANG, Dong DING. Investigation of Maize miRNA Involved in Developing-ear Heterosis [J]. Acta Agronomica Sinica, 2018, 44(6): 796-813.
[2] ZHAO Xu-Bo,LI Ai-Li,MAO Long*. Progress on Gene Regulatory Mechanisms by Small RNAs during Plant Polyploidization [J]. Acta Agron Sin, 2013, 39(08): 1331-1338.
[3] LUO Mao,PENG Hua,SONG Rui,GAO Jian,PAN Guang-Tang,ZHANG Zhi-Ming. Functional Analysis of miRNA Resistant to Banded Leaf-Sheath Blight in Maize [J]. Acta Agron Sin, 2013, 39(05): 837-844.
[4] WU Shao-Hua,ZHANG Hong-Yu,XUE Jing-Jing,XU Pei-Zhou,WU Xian-Jun. DNA Methylation Site Analysis of Haploid, Diploid and Hybrids in Twin-Seedling Rice [J]. Acta Agron Sin, 2013, 39(01): 50-59.
Full text



No Suggested Reading articles found!