Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach

Jiali Yu; Dennis Bennett; Christopher Dardick; Tetyana Zhebentyayeva; Albert G Abbott; Zongrang Liu; Margaret E Staton

doi:10.3389/fmolb.2021.612881

Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach

Front Mol Biosci. 2021 Apr 9:8:612881. doi: 10.3389/fmolb.2021.612881. eCollection 2021.

Authors

Jiali Yu¹, Dennis Bennett², Christopher Dardick², Tetyana Zhebentyayeva³, Albert G Abbott⁴, Zongrang Liu², Margaret E Staton^{1

5}

Affiliations

¹ Genome Science and Technology Program, University of Tennessee, Knoxville, TN, United States.
² Appalachian Fruit Research Station, United States Department of Agriculture-Agriculture Research Service, Kearneysville, WV, United States.
³ Department of Ecosystem Science and Management, Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States.
⁴ Forest Health Research and Education Center, University of Kentucky, Lexington, KY, United States.
⁵ Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, United States.

Abstract

Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression. From endodormancy to ecodormancy, ppe-miR6285 was significantly upregulated while its target gene, an ASPARAGINE-RICH PROTEIN involved in the regulation of abscisic acid signaling, was downregulated. At ecodormancy, ppe-miR2275, a homolog of meiosis-specific miR2275 across angiosperms, was significantly upregulated, supporting microsporogenesis in anthers at a late stage of dormancy. The expression of 785 lncRNAs, unlike the overall expression pattern in the small RNAs, demonstrated distinctive expression signatures across all dormancy and flowering stages. We predicted that a subset of lncRNAs were targets of microRNAs and found 18 lncRNA/microRNA target pairs with both differentially expressed across time points. The genome-wide differential expression and network analysis of non-coding RNAs and mRNAs from the same tissues provide new candidate loci for dormancy regulation and suggest complex noncoding RNA interactions control transcriptional regulation across these key developmental time points.

Keywords: Prunus persica; dormancy; lncRNA; microRNA; siRNA.