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The identification of small RNAs differentially expressed in apple buds reveals a potential role of the miR159-MYB regulatory module during dormancy

ABSTRACT: Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.

ORGANISM(S): Malus domestica

PROVIDER: GSE189658 | GEO | 2021/11/30

REPOSITORIES: GEO

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Project description:Winter survival and maintenance strategy is crucial in temperate woody plants. Here, we demonstrate novel aspects of the transcriptional regulations adopted by perennial tree species in winter/dormancy, employing a biochemical and whole transcriptome analysis. As expected, genes related to cold hardiness and defense are over-represented. Interestingly, carbohydrate biosynthesis and transport-related genes were very actively expressed in winter/dormancy. Further biochemical analyses verified the dormancy/winter transcription phenotype. Furthermore, dormancy/winter preferential expression of genes involved in the cell wall biosynthesis/modification, circadian rhythm, the indirect transcriptional regulation (RNA metabolism), and chromatin modification/remodeling were identified. Taken together, regulation of gene expression in the winter survival and maintenance may include not only controlled by promoter binding transcription factors but may also be regulated at the post-transcriptional and chromatin levels. In the first step towards the understanding of molecular mechanisms underlying the winter survival and maintenance of perennial trees, we examined the characteristics of transcription phenotype of the dormancy/winter stem compared to the active growth/summer stem by using a whole transcriptome analysis (GeneChip Poplar Genome Array; Affymetrix). Poplar Genome Array has a total of 61,251 probe sets, representing 57,423 poplar gene models, and allows us to interrogate a total of 41,558 unique gene models because of the probe set redundancy. Slight redundancy of the probe sets within a single chip gave us a unique opportunity to have internal comparisons of the particular genes. Very high reproducibility (R2 > 0.97) between the replicated samples was found. Further confirmation of the GeneChip data was made by semi-quantitative RT-PCR analysis using several genes showing the summer or winter biased expression. Based on these results, further analysis of winter stem transcriptome against summer stem was performed.

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The identification of small RNAs differentially expressed in apple buds reveals a potential role of the miR159-MYB regulatory module during dormancy

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