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.

全球气候变化的结果是，对作物生产率产生负面影响的某些压力因素，例如热，冷，干旱和盐碱化正变得越来越普遍。我们进行了荟萃分析，以鉴定涉及（1）一般非生物胁迫条件和（2）叶片组织中特定和独特的非生物胁迫因子（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，并使用我们先前发布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个样品。使用MapMan和PageMan进行基因集富集分析，而将DAVID（注释，可视化和集成发现数据库）用于代谢过程富集分析。考虑所有非生物胁迫时，我们鉴定了总共5122个差异表达基因（上调了3895个，下调了1227个）。茉莉酸相关的基因更常被干旱上调，而赤霉素的下调是干旱和高温的关键信号。相反，冷胁迫明显上调了涉及ABA（脱落酸），细胞分裂素和赤霉素的基因。基因（通过热诱导参与IAA（吲哚乙酸）反应的非光养性下胚轴）。关于次级代谢，正如预期的那样，MVA途径（甲羟戊酸途径），萜类化合物和生物碱通常在所有不同的胁迫下均被上调。然而，类黄酮，木质素和木脂素被热抑制（肉桂酰基辅酶A还原酶1和异戊烯基焦磷酸酶）。冷胁迫极大地调节了涉及类萜和生物碱的基因。关于转录因子，AP2-EREBP，MADS-box，WRKY22，MYB，homoebox基因成员受干旱胁迫显着调节，而冷胁迫则增强AP2-EREBPs，bZIP成员，MYB7，BELL 1和一个bHLH成员。C2C2-CO-LIKE，MADS-box和homeobox（HOMEOBOX3）大多受热抑制。基因集富集分析显示，泛素介导的蛋白质降解会因热而增强，从而意外地抑制了戊二醛毒素基因。冷应激主要上调MAP激酶（促分裂原激活的蛋白激酶）。这项工作的发现将有助于鉴定与与受不同非生物胁迫影响的定量农艺性状有关的主要基因有关的作物中保守的新分子标记。