Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses.
Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses.
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DOI：
10.1186/s12870-022-03477-0
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发表时间：
2022-03-08
影响因子：
5.3
通讯作者：
Kalavacharla VK
中科院分区：
文献类型：
--
作者：
Hayford RK;Serba DD;Xie S;Ayyappan V;Thimmapuram J;Saha MC;Wu CH;Kalavacharla VK
高质量原料的可持续生产一直是生物能源研究的热点。尽管经济上的重要性，高温和缺水是半干旱地区柳枝稷成功种植的限制因素。目前关于柳枝稷复合非生物胁迫耐受性的分子基础研究报道较少，特别是干旱和高温胁迫的复合耐受性。我们使用转录组学方法来阐明柳枝稷同时对干旱和高温的反应变化。我们在柳枝稷植物Alamo AP 13中通过在生长45天后停止供水进行单独的干旱处理。对于干旱和热效应的组合，在干旱开始72小时后施加热处理（35 °C/25 °C白天/夜晚）。在处理施加后0 h、72 h、96 h、120 h、144 h和168 h收集样品，提取总RNA，并进行RNA-Seq。在总共32，190个基因中，我们鉴定出3912个为干旱（DT）响应基因，2339个和4635个分别为热（HT）和干旱和热（DTHT）响应基因。在DT、HT和DTHT条件下分别有209、106和220个转录因子差异表达。基因本体注释将代谢过程确定为DTHT基因中富集的重要术语。在DTHT响应基因中鉴定的其他生物过程包括：对水的响应、光合作用、氧化还原过程和对胁迫的响应。对DT和DTHT反应基因的KEGG途径富集分析表明，TF和控制苯丙烷途径的基因对个体以及组合应激反应都很重要。例如，通过单一DT和DTHT应激的组合诱导来自苯丙素途径的羟基肉桂酰-CoA莽草酸/奎尼酸羟基肉桂酰转移酶（HCT）。通过RNA-Seq分析，我们已经确定了柳枝稷中响应DT和组合DTHT胁迫的独特和重叠基因。DT和HT联合胁迫可能会影响柳枝稷的光合机制和苯丙烷途径，从而对柳枝稷的木质素合成和生物量产生负面影响。通过单点突变或RNAi等技术，可以进一步证实特别是在DTHT胁迫反应中鉴定的基因的生物学功能。在线版本包含补充材料，可通过10.1186/s12870-022-03477-0获得。
Sustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously. We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3912, as drought (DT) responsive genes, 2339 and 4635 as, heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress. Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi. The online version contains supplementary material available at 10.1186/s12870-022-03477-0.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
CC型谷胱甘肽的过表达，OSGRX6影响水稻植物中的激素和氮状况。
影响因子：
5.6
作者：
El-Kereamy A;Bi YM;Mahmood K;Ranathunge K;Yaish MW;Nambara E;Rothstein SJ
通讯作者：
Rothstein SJ
影响因子：
11.6
作者：
Anderson, JP;Badruzsaufari, E;Kazan, K
通讯作者：
Kazan, K
影响因子：
2.1
作者：
Adler, Paul R.;Sanderson, Matt A.;Jung, Hans-Joachim G.
通讯作者：
Jung, Hans-Joachim G.
影响因子：
7.2
作者：
Dubos, Christian;Le Gourrierec, Jose;Lepiniec, Loic
通讯作者：
Lepiniec, Loic