Parallel Bud Mutation Sequencing Reveals that Fruit Sugar and Acid Metabolism Potentially Influence Stress in Malus
Parallel Bud Mutation Sequencing Reveals that Fruit Sugar and Acid Metabolism Potentially Influence Stress in Malus
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平行芽突变测序揭示果实糖和酸代谢可能影响苹果的应激
DOI：
10.3390/ijms20235988
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发表时间：
2019-11
影响因子：
5.6
通讯作者：
Wang Kun
中科院分区：
文献类型：
--
作者：
Zhao Jirong;Shen Fei;Gao Yuan;Wang Dajiang;Wang Kun
苹果的糖分和酸度是苹果果实最重要的特性。花蕾品种可为苹果功能基因研究提供丰富的研究材料。本研究以糖酸风味差异较大的芽体材料“乔纳森”和“甜乔纳森”为材料，采用全基因组测序和RNA测序的方法，对果实发育过程中的全基因组变异和转录调控网络进行了研究。变异分析发现两个品种间存在4,198,955个SNPs、319,494个Indels和32,434个SNPs。结果表明，在两个品种果实发育过程中所表达的d44,399个基因中，共有4313个差异表达基因，功能分析表明胁迫反应和信号转导相关基因丰富。利用24047个表达值变化较大的基因，通过加权相关网络分析，构建了28个共表达模块。破译了14个与果实发育过程中糖或酸积累相关的共表达模块，揭示了与糖和酸代谢相关的HUB基因，如MdDSP4、MdINVE和MdSTP7。此外，对共表达模块内部网络的探索表明，糖与酸代谢或糖与胁迫之间存在密切关系。对17个差异表达的ATP结合盒转运蛋白基因进行了基于Motif的序列分析和酵母单杂交实验，鉴定并确认了一个转录因子MdBPC6，该转录因子调控着ATP结合盒转运蛋白基因，并可能参与苹果果实的发育或逆境反应。总而言之，所有的结果都证明了平行的芽突变测序和确定的HUB基因的使用，并推断了调控关系，提供了关于苹果果实糖和酸积累或胁迫反应的新信息。
Apple sugar and acid are the most important traits of apple fruit. Bud sport cultivars can provide abundant research materials for functional gene studies in apple. In this study, using bud sport materials with a rather different sugar and acid flavor, i.e., “Jonathan” and “Sweet Jonathan”, we profiled the whole genome variations and transcriptional regulatory network during fruit developmental stages using whole genome sequencing and RNA-sequencing. Variation analysis identified 4,198,955 SNPs, 319,494 InDels, and 32,434 SVs between the two cultivars. In total, 4313 differentially expressed genes among all of the d 44,399 genes expressed were identified between the two cultivars during fruit development, and functional analysis revealed stress response and signal transduction related genes were enriched. Using 24,047 genes with a more variable expression value, we constructed 28 co-expression modules by weighted correlation network analysis. Deciphering of 14 co-expression modules associated with sugar or acid accumulation during fruit development revealed the hub genes associated with sugar and acid metabolism, e.g., MdDSP4, MdINVE, and MdSTP7. Furthermore, exploration of the intra network of the co-expression module indicated the close relationship between sugar and acid metabolism or sugar and stress. Motif-based sequence analysis of the 17 differentially expressed ATP-binding cassette transporter genes and Yeast one-hybrid assay identified and confirmed a transcription factor, MdBPC6, regulating the ATP-binding cassette (ABC) transporter genes and potentially participating in the apple fruit development or stress response. Collectively, all of the results demonstrated the use of parallel bud mutation sequencing and identified hub genes, and inferred regulatory relationships providing new information about apple fruit sugar and acid accumulation or stress response.
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