Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing

Fengjiao Zhang; Wen Dong; Lulu Huang; Aiping Song; Haibin Wang; Weimin Fang; Fadi Chen; Nianjun Teng

doi:10.1371/journal.pone.0124371

Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing

PLoS One. 2015 Apr 24;10(4):e0124371. doi: 10.1371/journal.pone.0124371. eCollection 2015.

Authors

Fengjiao Zhang¹, Wen Dong², Lulu Huang³, Aiping Song³, Haibin Wang³, Weimin Fang³, Fadi Chen³, Nianjun Teng¹

Affiliations

¹ College of Horticulture, Nanjing Agricultural University, Nanjing, China; Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China.
² China Rural Technology Development Center, Beijing, China.
³ College of Horticulture, Nanjing Agricultural University, Nanjing, China.

Abstract

Background: MicroRNAs (miRNAs) are important regulators in plant development. They post-transcriptionally regulate gene expression during various biological and metabolic processes by binding to the 3'-untranslated region of target mRNAs to facilitate mRNA degradation or inhibit translation. Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental flowers with increasing demand each year. However, embryo abortion is the main reason for chrysanthemum cross breeding failure. To date, there have been no experiments examining the expression of miRNAs associated with chrysanthemum embryo development. Therefore, we sequenced three small RNA libraries to identify miRNAs and their functions. Our results will provide molecular insights into chrysanthemum embryo abortion.

Results: Three small RNA libraries were built from normal chrysanthemum ovules at 12 days after pollination (DAP), and normal and abnormal chrysanthemum ovules at 18 DAP. We validated 228 miRNAs with significant changes in expression frequency during embryonic development. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. In addition, a total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. Moreover, 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes. Gene ontology (GO) annotation also revealed that high-ranking miRNA target genes related to cellular processes and metabolic processes were involved in transcription regulation and the embryo developmental process.

Conclusions: The present study generated three miRNA libraries and gained information on miRNAs and their targets in the chrysanthemum embryo. These results enrich the growing database of new miRNAs and lay the foundation for the further understanding of miRNA biological function in the regulation of chrysanthemum embryo abortion.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Chrysanthemum / embryology*
Chrysanthemum / genetics*
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Gene Library
Gene Ontology
High-Throughput Nucleotide Sequencing
Hybridization, Genetic / genetics
MicroRNAs / genetics*
Molecular Sequence Data
RNA, Plant / genetics*
Sequence Analysis, RNA

Substances

MicroRNAs
RNA, Plant

Grants and funding

This study was supported by the National Natural Science Foundation of China (31171983, 31471901), the Programs for New Century Excellent Talents in Universities, Ministry of Education of China (NCET-11-0669), the Fundamental Research Funds for the Central Universities (KYZ201308), and the fourth phase of Jiangsu ''333'' project to NJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.