A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator.
A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator.
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比较转录组学和eQTL方法将SlWD 40鉴定为番茄果实成熟调节剂。
DOI：
10.1093/plphys/kiac200
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发表时间：
2022-08-29
期刊：
影响因子：
7.4
通讯作者：
Fernie, Alisdair R.
中科院分区：
文献类型：
--
作者：
Zhu, Feng;Jadhav, Sagar Sudam;Tohge, Takayuki;Salem, Mohamed A.;Li, Je Min;Giovannoni, James J.;Cheng, Yunjiang;Alseekh, Saleh;Fernie, Alisdair R.
虽然通过成熟突变体的定位克隆和成熟相关转录因子（TFs）的克隆，已经确定了对番茄成熟过程有强烈影响的多个重要基因，但最近的研究表明，我们不太可能完全表征支撑这一过程的基因调控网络。本研究结合比较转录组学和表达qtl，确定了16个参与番茄果实成熟的候选基因，并通过病毒诱导的基因沉默分析对其进行了验证。为了进一步证实该方法的准确性，我们选择了一个潜在的成熟调控因子SlWD40 （WD-40 repeats）进行深入分析。共表达网络分析表明，主要调控因子如RIN（成熟抑制因子）和NOR（不成熟因子）以及重要的TFs包括FUL1 （FRUITFUL1）、SlNAC4 （NAM、ATAF1、2和cuc24）和AP2a（激活增强子结合蛋白2 α）与SlWD40强烈共表达。此外，与野生型相比，SlWD40过表达系和RNAi系分别表现出明显的加速和延迟成熟表型。此外，这些转基因的转录组分析显示，SlWD40- rnai系中乙烯生物合成基因、植物烯合成酶、果胶裂解酶和支链氨基转移酶2的表达模式与rin和nor的表达模式相似，进一步表明SlWD40可能与rin和nor一起发挥重要的成熟调节作用。这些结果在当前成熟模型的背景下进行了讨论，并在比较基因组学和转录组学作为分离基因型差异的因果基因的有效途径方面进行了讨论。基于比较转录组学和eQTL的可靠方法对成熟调节剂的鉴定是有价值的。
Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes. A reliable approach based on comparative transcriptomics and eQTL is valuable for ripening regulator identification.
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