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Transcriptomic analysis of maize kernel row number-associated miRNAs between a single segment substitution line and its receptor parent

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Abstract

To detect microRNAs (miRNAs) involved in determining kernel row number in maize, next generation deep sequencing was performed on an elite inbred line Zong3 (row number 14–16) of maize in China and a single segment substitution line (SSSL) SSL-10 (row number 8–10) derived from the same genetic background. In SSL-10, the single segment is inserted in chromosome 1 between molecular marker bnlg1953 and bnlg1811. Twenty-eight miRNAs belonging to 11 conserved miRNA families in maize showed expression differences >2-fold in the two lines, among which 14 members from four miRNA families were up-regulated and 14 members from 7 miRNA families were repressed in SSL-10. A genome wide degradome was sequenced to validate the miRNA target genes in solid experiment. In addition, novel miRNAs associated with ear development were predicted using a series of strict criteria, and 29 miRNAs representing eight families were predicted as novel miRNAs. Among the novel miRNAs, only one showed an expression difference >2-fold. The conserved and novel miRNAs with >2-fold expression differences were treated as candidate miRNAs involved in maize kernel row number determination. MiRNA-dependent gene expression regulation and physiological and morphological effects on ear development may explain why the SSSL changed kernel row number compared with its recurrent parent. Based on the interaction of miRNAs and their target genes, a possible miRNA-dependent pathway leading to the given DNA fragment inducing a change in kernel row number was proposed.

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Abbreviations

ABA:

Abscisic acid

ARFs:

Auxin response factors

DCL:

Dicer-like

MFEI:

Minimal folding free energy index

NF-Y:

Nuclear factor Y

NGS:

Next generation sequencing

QTL:

Quantitative trait loci

RT-PCR:

Reverse transcription

SM:

Spikelet meristems

SPL:

SQUAMOSA promoter-binding-like

SPM:

Spikelet pair meristems

SSR:

Quantitative trait loci

SSSL:

Single segment substitution line

TFs:

Transcription factors

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Acknowledgments

This work was supported by a grant from the National Nature Foundation of China (31370033).

Conflict of interest

The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

      Bin Wang, Yadong Xue, Dong Ding, Zhiyuan Fu & Jihua Tang

    2. College of Agronomy, Henan University of Science and Technology, Luoyang, 471023, China

      Bin Wang

    3. National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China

      Zuxin Zhang

    4. Department of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China

      Jihua Tang

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    1. Bin Wang
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    2. Yadong Xue
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    4. Dong Ding
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    Correspondence to Jihua Tang.

    Additional information

    Bin Wang and Yadong Xue have contributed equally to this work.

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    Wang, B., Xue, Y., Zhang, Z. et al. Transcriptomic analysis of maize kernel row number-associated miRNAs between a single segment substitution line and its receptor parent. Plant Growth Regul 78, 145–154 (2016). https://doi.org/10.1007/s10725-015-0081-7

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    • DOI: https://doi.org/10.1007/s10725-015-0081-7

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