Abstract
BackgroundBud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud dormancy are not yet clear. This work was aimed to explore the underlying molecular mechanism regulating bud dormancy in grape.ResultsWe have performed transcriptome and differential transcript expression analyses of “Shine Muscat” grape buds using the Illumina RNA-seq system. Comparisons of transcript expression levels among three stages of dormancy, paradormancy (PD) vs endodormancy (ED), summer buds (SB) vs ED and SB vs PD, resulted in the detection of 8949, 9780 and 3938 differentially expressed transcripts, respectively. Out of approximately 78 million high-quality generated reads, 6096 transcripts were differentially expressed (log2 ratio ≥ 1, FDR ≤ 0.001). Grape reference genome was used for alignment of sequence reads and to measure the expression level of transcripts. Furthermore, findings obtained were then compared using two different databases; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to annotate the transcript descriptions and to assign a pathway to each transcript. KEGG analysis revealed that secondary metabolites biosynthesis and plant hormone signaling was found most enriched out of the 127 total pathways. In the comparisons of the PD vs ED and SB vs ED stages of grape buds, the gibberellin (GA) and abscisic acid (ABA) pathways were found to be the most enriched. The ABA and GA pathways were further analyzed to observe the expression pattern of differentially expressed transcripts. Transcripts related to the PP2C family (ABA pathway) were found to be up-regulated in the PD vs ED comparison and down-regulated in the SB vs ED and SB vs PD comparisons. GID1 family transcripts (GA pathway) were up-regulated while DELLA family transcripts were down-regulated during the three dormancy stages. Differentially expressed transcripts (DEGs) related to redox activity were abundant in the GO biological process category. RT-qPCR assay results for 12 selected transcripts validated the data obtained by RNA-seq.ConclusionAt this stage, taking into account the results obtained so far, it is possible to put forward a hypothesis for the molecular mechanism underlying grape bud dormancy, which may pave the way for ultimate improvements in the grape industry.
Highlights
Bud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances
Analysis of RNA sequencing (RNA-seq) libraries In this study, three cDNA libraries constructed from grape buds during three different stages were sequenced and generated 79.6 million sequence reads
After elimination of low-quality reads and adaptor sequences, 78.5 million clean reads (98.5% of the generated data) were recorded, which were mapped to the reference genome of grape using hierarchical indexing for spliced alignment of transcripts (HISAT) [24]
Summary
Bud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; underlying mechanisms involved in grape bud dormancy are not yet clear. Grape (Vitis vinifera) is the most widely grown fruit crop globally. There are several developmental and metabolic processes that occur in the buds and twigs of grape plants during the winter period. These processes include enzyme synthesis, respiration, cell division, photosynthesis, growth stimulator production and growth inhibitor down-regulation. Dormancy is a controlling mechanism that enables woody perennials to adapt seasonal environmental changes and affects the following season’s vegetative growth and fruit production. Global warming has a substantial influence on winter chilling
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