title: Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.).
abstract: BACKGROUND
  Radish (Raphanus sativus L.) is an economically important root vegetable crop, and the taproot-thickening process is the most critical period for the final productivity and quality formation. MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory function in plant growth and development. However, the characterization of miRNAs and their roles in regulating radish taproot growth and thickening remain largely unexplored. A Solexa high-throughput sequencing technology was used to identify key miRNAs involved in taproot thickening in radish.
  
  
  RESULTS
  Three small RNA libraries from 'NAU-YH' taproot collected at pre-cortex splitting stage, cortex splitting stage and expanding stage were constructed. In all, 175 known and 107 potential novel miRNAs were discovered, from which 85 known and 13 novel miRNAs were found to be significantly differentially expressed during taproot thickening. Furthermore, totally 191 target genes were identified for the differentially expressed miRNAs. These target genes were annotated as transcription factors and other functional proteins, which were involved in various biological functions including plant growth and development, metabolism, cell organization and biogenesis, signal sensing and transduction, and plant defense response. RT-qPCR analysis validated miRNA expression patterns for five miRNAs and their corresponding target genes.
  
  
  CONCLUSIONS
  The small RNA populations of radish taproot at different thickening stages were firstly identified by Solexa sequencing. Totally 98 differentially expressed miRNAs identified from three taproot libraries might play important regulatory roles in taproot thickening. Their targets encoding transcription factors and other functional proteins including NF-YA2, ILR1, bHLH74, XTH16, CEL41 and EXPA9 were involved in radish taproot thickening. These results could provide new insights into the regulatory roles of miRNAs during the taproot thickening and facilitate genetic improvement of taproot in radish.
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2012204019@njau.edu.cn.|School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, P.R. China. 2012204019@njau.edu.cn.
authors: Rugang
authors: R
authors: Yu
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2011204020@njau.edu.cn.
authors: Yan
authors: Y
authors: Wang
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. nauxuliang@njau.edu.cn.
authors: Liang
authors: L
authors: Xu
authors: Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. zhuxianwen8866@163.com.
authors: Xianwen
authors: X
authors: Zhu
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2014204013@njau.edu.cn.
authors: Wei
authors: W
authors: Zhang
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2014204022@njau.edu.cn.
authors: Ronghua
authors: R
authors: Wang
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. jwcgyq@njau.edu.cn.
authors: Yiqin
authors: Y
authors: Gong
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. cnlimera@gmail.com.
authors: Cecilia
authors: C
authors: Limera
authors: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. nauliulw@njau.edu.cn.
authors: Liwang
authors: L
authors: Liu
mesh_terms: D035683:MicroRNAs / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics*; D031224:Raphanus / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs
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