Khalil-Ur-Rehman Muhammad, Sun Long, Li Chun-Xia, Faheem Muhammad, Wang Wu, Tao Jian-Min
Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
BMC Plant Biol. 2017 Jan 19;17(1):18. doi: 10.1186/s12870-016-0960-8.
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; 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.
We 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.
At 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.
芽休眠是多年生植物的一种重要生物学现象，使其能够在恶劣环境条件下生存。葡萄（Vitis vinifera）是全球种植最广泛的水果作物之一；然而，葡萄芽休眠的潜在机制尚不清楚。这项工作旨在探索调控葡萄芽休眠的潜在分子机制。
我们使用Illumina RNA-seq系统对“阳光玫瑰”葡萄芽进行了转录组和差异转录本表达分析。在休眠的三个阶段（侧芽休眠期（PD）与内休眠期（ED）、夏芽（SB）与ED以及SB与PD）之间比较转录本表达水平，分别检测到8949、9780和3938个差异表达转录本。在大约7800万个高质量生成的读段中，6096个转录本差异表达（log2比值≥1，FDR≤0.001）。使用葡萄参考基因组对序列读段进行比对，并测量转录本的表达水平。此外，然后使用两个不同的数据库（基因本体论（GO）和京都基因与基因组百科全书（KEGG））对所得结果进行比较，以注释转录本描述并为每个转录本指定一条途径。KEGG分析表明，在总共127条途径中，次生代谢物生物合成和植物激素信号传导途径最为丰富。在葡萄芽的PD与ED以及SB与ED阶段的比较中，发现赤霉素（GA）和脱落酸（ABA）途径最为丰富。进一步分析ABA和GA途径以观察差异表达转录本的表达模式。在PD与ED的比较中，发现与PP2C家族（ABA途径）相关的转录本上调，而在SB与ED以及SB与PD的比较中下调。在三个休眠阶段，GID1家族转录本（GA途径）上调，而DELLA家族转录本下调。在GO生物学过程类别中，与氧化还原活性相关的差异表达转录本（DEG）丰富。对12个选定转录本的RT-qPCR分析结果验证了RNA-seq获得的数据。
在现阶段，考虑到目前获得的结果，可以提出一个关于葡萄芽休眠潜在分子机制的假设，这可能为葡萄产业的最终改进铺平道路。
