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.
Highlights
Perennial plants from temperate regions complete an annual life cycle of growth and dormancy
Data was obtained from five time points during peach bud dormancy release, including two endodormant bud stages at 0 and 500 chill hours (CH), an ecodormant bud stage at 1000 CH, as well as two bud break stages, day 3 and day 7 after being moved into conditions to induce flowering (Zhu et al, 2020)
We identified 72,984 putative small RNA loci and defined a single major RNA sequence for each locus, which were used for all downstream analysis. 3,972 loci were identified as peach transfer RNA (tRNA), ribosomal RNA (rRNA), snRNA, microRNA, or ta-small interfering RNAs (siRNA) (Table 1)
Summary
Perennial plants from temperate regions complete an annual life cycle of growth and dormancy. To survive unfavorable environmental conditions in winter, plants enter dormancy, which protects their reproductive tissues from freezing temperatures. Plants experiencing warm winters are impacted if they do not experience sufficient CR to fully release from dormancy, which impacts reproduction (Luedeling et al, 2011; Bartolini et al, 2020). Earlier warm spells during winter or early spring may induce early flowering, subsequent frosts can damage newly emerged tissues (Viti et al, 2010; Martínez-Gómez et al, 2017). These losses make dormancy research important both economically for fruit and nut trees and ecologically for forest trees. The underlying mechanisms controlling dormancy transition and release in temperate trees and other perennial species are still unclear
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