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Genome-wide identification and characterization of miRNAs in the hypocotyl and cotyledon of cauliflower (Brassica oleracea L. var. botrytis) seedlings

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Abstract

MicroRNAs (miRNAs) are a class of small endogenous, non-coding RNAs that have key regulatory functions in plant growth, development, and other biological processes. Hypocotyl and cotyledon are the two major tissues of cauliflower (Brassica oleracea L. var. botrytis) seedlings. Tissue culture experiments have indicated that the regenerative abilities of these two tissues are significantly different. However, the characterization of miRNAs and their roles in regulating organ development in cauliflower remain unexplored. In the present study, two small RNA libraries were sequenced by Solexa sequencing technology. 99 known miRNAs belonging to 28 miRNA families were identified, in which 6 miRNA families were detected only in Brassicaceae. A total of 162 new miRNA sequences with single nucleotide substitutions corresponding to the known miRNAs, and 32 potentially novel miRNAs were also first discovered. Comparative analysis indicated that 42 of 99 known miRNAs and 17 of 32 novel miRNAs exhibited significantly differential expression between hypocotyl and cotyledon, and the differential expression of several miRNAs was further validated by stem-loop RT-PCR. In addition, 235 targets for 89 known miRNAs and 198 targets for 24 novel miRNAs were predicted, and their functions were further discussed. The expression patterns of several representative targets were also confirmed by qRT-PCR analysis. The results identified that the transcriptional expression patterns of miRNAs were negatively correlated with their targets. These findings gave new insights into the characteristics of miRNAs in cauliflower, and provided important clues to elucidate the roles of miRNAs in the tissue differentiation and development of cauliflower.

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Acknowledgments

We are grateful to the anonymous reviewers for their critical reading of the manuscript. We greatly thank Dr. Deling Sun at Tianjin Kernel Vegetable Research Institute, China for kindly providing the cauliflower seeds. This work was performed with financial support from The National Natural Science Foundation of China (No. 31100234) and The Natural Science Foundation from Tianjin (No. 10JCZDJC17900).

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The authors declare no competing interests.

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Authors and Affiliations

  1. College of Life Sciences, Nankai University, Tianjin, 300071, China

    Meijuan Geng, Chuan Jin, Qian Liu, Chengbin Chen, Wenqin Song & Chunguo Wang

  2. Department of Horticulture, Tianjin Agricultural University, Tianjin, 300384, China

    Hui Li

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  1. Meijuan Geng
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Correspondence to Chunguo Wang.

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M. Geng and H. Li contributed equally to this work.

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425_2013_1986_MOESM1_ESM.tif

Supplementary material 1 Fig. S1 The expression abundance of each predicted novel miRNA in the cotyledon and hypocotyl of cauliflower seedlings (TIFF 509 kb)

425_2013_1986_MOESM2_ESM.tif

Supplementary material 2 Fig. S2 The GO analysis of biological process of known miRNA targets in the hypocotyl of cauliflower seedlings. The sequences of each targets could be found in Table S7 (TIFF 3903 kb)

425_2013_1986_MOESM3_ESM.tif

Supplementary material 3 Fig. S3 The GO analysis of biological process of known miRNA targets in the cotyledon of cauliflower seedlings. The sequences of each targets could be found in Table S7 (TIFF 2635 kb)

425_2013_1986_MOESM4_ESM.tif

Supplementary material 4 Fig. S4 The regenerative capacity of the hypocotyl and cotyledon of cauliflower seedlings in vitro. a The 5-old-cauliflower seedlings; b the explant culture of hypocotyl for 5 days; c the explant culture of hypocotyl for 15 days; d the explant culture of hypocotyl for 25 days; e the explant culture of cotyledon with petiole for 5 days; f the explant culture of cotyledon without petiole for 5 days; g the explant culture of cotyledon with petiole for 35 days; h the explant culture of cotyledon without petiole for 35 days (TIFF 22099 kb)

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Geng, M., Li, H., Jin, C. et al. Genome-wide identification and characterization of miRNAs in the hypocotyl and cotyledon of cauliflower (Brassica oleracea L. var. botrytis) seedlings. Planta 239, 341–356 (2014). https://doi.org/10.1007/s00425-013-1986-x

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