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Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids

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Abstract

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. We used high-throughput sequencing to compare miRNA expression profiles between Brassica hexaploid and its parents. A total of 613, 784 and 742 known miRNAs were identified in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. We detected 618 miRNAs were differentially expressed (log2Ratio ≥ 1, P ≤ 0.05) between Brassica hexaploid and its parents, and 425 miRNAs were non-additively expressed in Brassica hexaploid, which suggest a trend of non-additive miRNA regulation following hybridization and polyploidization. Remarkably, majority of the non-additively expressed miRNAs in the Brassica hexaploid are repressed, and there was a bias toward repression of B. rapa miRNAs, which is consistent with the progenitor-biased gene repression in the synthetic allopolyploids. In addition, we identified 653 novel mature miRNAs in Brassica hexaploid and its parents. Finally, we found that almost all the non-additive accumulation of siRNA clusters exhibited a low-parent pattern in Brassica hexaploid. Non-additive small RNA regulation is involved in a range of biological pathways, probably providing a driving force for variation and adaptation in allopolyploids.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31370258, 31100876, 31070204) and National Found for Fostering Talents of Basic Sciences (J1103513).

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Yanyue Shen, Qin Zhao, Wenliang Wang, Yi Gao & Jianbo Wang

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Jun Zou & Jinling Meng

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  1. Yanyue Shen
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  2. Qin Zhao
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  4. Wenliang Wang
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  7. Jianbo Wang
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Correspondence to Jianbo Wang.

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11103_2014_185_MOESM1_ESM.tif

Supplementary material 1 GO classifications of coherent target genes of up-regulated and down-regulated miRNAs in Brassica hexaploid and B. rapa. The results are summarized in three main categories: cellular component, molecular function, and biological process by GO analysis (TIFF 17969 kb)

11103_2014_185_MOESM2_ESM.tif

Supplementary material 2 GO classifications of coherent target genes of up-regulated and down-regulated miRNAs in Brassica hexaploid and B. carinata. The results are summarized in three main categories: cellular component, molecular function, and biological process by GO analysis (TIFF 18123 kb)

11103_2014_185_MOESM3_ESM.tif

Supplementary material 3 GO classifications of target genes of additive and non-additive miRNAs in Brassica hexaploid. The results are summarized in three main categories: cellular component, molecular function, and biological process by GO analysis (TIFF 17,757 kb)

11103_2014_185_MOESM4_ESM.tif

Supplementary material 4 GO classifications of genes that highly correlated with non-additive siRNA clusters in Brassica hexaploid. The results are summarized in three main categories: cellular component, molecular function, and biological process by GO analysis (TIFF 6771 kb)

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Shen, Y., Zhao, Q., Zou, J. et al. Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids. Plant Mol Biol 85, 287–299 (2014). https://doi.org/10.1007/s11103-014-0185-x

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