Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy; and Department of Biology, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.
Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze ed. 4 Palermo, 90128, Italy.
Funct Plant Biol. 2020 Dec;48(1):54-71. doi: 10.1071/FP20028.
As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.
由于全球气候变化，某些对作物生产力有负面影响的应激因素，如热、冷、干旱和盐度等，变得越来越普遍。我们进行了一项荟萃分析，以确定参与（1）一般非生物胁迫条件和（2）叶片组织中特定和独特非生物胁迫因子（干旱、盐度、极端温度）的植物物种中保守的基因。我们收集了原始数据，并使用我们之前发表的生物信息学管道重新分析了八项 RNA-Seq 研究。总共分析了 68 个样本。使用 MapMan 和 PageMan 进行了基因集富集分析，而 DAVID（注释、可视化和综合发现数据库）用于代谢过程富集分析。当考虑所有非生物胁迫时，我们总共鉴定了 5122 个差异表达基因（3895 个上调，1227 个下调）。茉莉酸相关基因在干旱时更常上调，而赤霉素下调是干旱和热的关键信号。相比之下，冷胁迫明显上调了参与 ABA（脱落酸）、细胞分裂素和赤霉素的基因。一个参与 IAA（吲哚乙酸）反应的基因（非光下胚轴）被热诱导。关于次生代谢，如预期的那样，MVA 途径（甲羟戊酸途径）、萜类化合物和生物碱通常受到所有不同胁迫的上调。然而，类黄酮、木质素和木质素更受热抑制（肉桂酰辅酶 A 还原酶 1 和异戊烯基焦磷酸酶）。冷胁迫剧烈调节萜类化合物和生物碱相关基因。关于转录因子，AP2-EREBP、MADS-box、WRKY22、MYB、同源盒基因成员显著受干旱胁迫调节，而冷胁迫增强了 AP2-EREBP、bZIP 成员、MYB7、BELL1 和一个 bHLH 成员。C2C2-CO-LIKE、MADS-box 和一个同源盒（HOMEOBOX3）在响应热时大多被抑制。基因集富集分析表明，热增强了泛素介导的蛋白质降解，这出人意料地抑制了谷氧还蛋白基因。冷胁迫主要上调 MAP 激酶（丝裂原激活蛋白激酶）。这项工作的结果将允许识别与受不同非生物胁迫影响的主要数量农艺性状相关的作物中保守的新分子标记。
