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Identification of russet-associated microRNAs in the exocarp of a Dangshansuli pear mutant (Pyrus bretschneideri Rehd.) by high-throughput sequencing

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Abstract

Russet skin is a very important trait that allows pear fruits to defend themselves against biotic and abiotic stresses. Small RNAs from a russet skin mutant ‘Xiusu’ derived from a ‘Dangshansuli’ pear were sequenced by high-throughput sequencing to reveal the role of miRNAs in the regulation of pear russet skin formation. A total of 12,158,547 and 12,053,678 high-quality reads were obtained for ‘Dangshansuli’ and ‘Xiusu’, respectively, with the majority between 19 and 25 nt in size. Forty-four and 45 known miRNAs were identified in the ‘Dangshansuli’ and ‘Xiusu’ libraries, respectively, and these miRNAs belonged to 31 miRNA families. The expression levels of 534 miRNAs varied drastically, ranging from 0 to 493,274 reads with a logarithm of fold changes between −9.33 and 12.71. In addition, 215 and 228 novel miRNAs with high-abundance were detected in ‘Dangshansuli’ and ‘Xiusu’, respectively. Many miRNAs, especially miR396, miR408, and the novel miRNAs, miR102, miR274, miR42, and miR442, were potentially involved in suberin biosynthesis and showed differential expression between the exocarp of ‘Dangshansuli’ and that of ‘Xiusu’. The relative expression levels of known and novel miRNAs as determined by quantitative PCR indicated that those miRNAs may contribute to the formation of mutant russet pear fruit skin.

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Acknowledgments

This project was supported by the National Natural Science Foundation of China (31101519) and the earmarked fund for the China Agriculture Research System (CARS-29-14). We thank American Journal Experts for helpful suggestions and revision of the paper.

Author contribution statement

HW and ZLW conceived and designed the study. HHN and YJY collected and prepared RNA samples for transcriptome analysis. JB, WZT, and LP performed RNA extraction and qPCR. LL and YZF contributed to bioinformatic analysis. HW and JB contributed to writing the manuscript and data analysis. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People’s Republic of China

    Wei Heng, Bing Jia, Hai-na Huang, Jin-yu Yang, Zi-teng Wang, Pu Liu, Li Liu, Zhen-feng Ye & Li-wu Zhu

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  1. Wei Heng
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  2. Bing Jia
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  3. Hai-na Huang
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  7. Li Liu
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  9. Li-wu Zhu
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Correspondence to Li-wu Zhu.

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Data archiving statement

The data sets supporting the results of this article (BioProject: PRJNA279180) are currently being submitted to the National Center for Biotechnology Information, and additional information will be added once available.

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Communicated by C. Dardick

Wei Heng and Bing Jia contributed equally to this work.

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Heng, W., Jia, B., Huang, Hn. et al. Identification of russet-associated microRNAs in the exocarp of a Dangshansuli pear mutant (Pyrus bretschneideri Rehd.) by high-throughput sequencing. Tree Genetics & Genomes 12, 107 (2016). https://doi.org/10.1007/s11295-016-1058-z

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  • DOI: https://doi.org/10.1007/s11295-016-1058-z

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