Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.)

BMC Plant Biology

Research Article

Xianwen Zhu¹  Ronghua Wang²  Yiqin Gong²  Cecilia Limera²  Liwang Liu²  Yan Wang²  Liang Xu²  Wei Zhang²  Rugang Yu³ 

[1] Department of Plant Sciences, North Dakota State University, 58108, Fargo, ND, USA;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, 210095, Nanjing, P.R. China;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, 210095, Nanjing, P.R. China;School of Life Sciences, Huaibei Normal University, 235000, Huaibei, Anhui, P.R. China;

关键词: Raphanus sativus;    Taproot;    Thickening;    microRNA;    Solexa sequencing;   

DOI  :  10.1186/s12870-015-0427-3

 received in 2014-09-21, accepted in 2015-01-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundRadish (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.ResultsThree 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Yu et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.