Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress
Graphical abstract
Introduction
Flooding stress, which is major caused by excessive rainfall and increasing due to climate changes, become one of the main abiotic stresses containing waterlogging and submergence forms and affecting plant growth and physiology (Herzog et al., 2016; Sasidharan et al., 2017). Increase in number of flood events worldwide has reduced the agricultural outcome from crops no matter cereals or legumes. Cereals such as wheat (Triticum aestivum L.) (Setter and Waters, 2003), barley (Hordeum vulgare L.) (Celedonio et al., 2016; Masoni et al., 2016), and maize (Zea mays L.) (Arora et al., 2017b), and oat (Avena sativa L.) (Arduini et al., 2019) had been reported to be damaged by flooding stress and it also dealt in legumes like soybean (Glycine max L. Merr.) (Valliyodan et al., 2016) and some cool-season legumes containing faba bean (Vicia faba L. var. minor), pea (Pisum sativum L.), and white lupin (Lupinus albus L.) (Pampana et al., 2016). Flooding causes yield losses by reducing root and shoot growth, biomass accumulation, nodulation, nitrogen fixation, nutrient uptake, photosynthesis, and stomatal conductance, and it causes plant death through increased disease incidence (Valliyodan et al., 2016). In a water excess environment, one of the preliminary physiological alterations is flood-induced anaerobic respiratory pathways. During flood, there is absence of oxygen and roots rely on anaerobic respiration to produce limited energy to maintain the metabolic activities (Bailey-Serres and Voesenek, 2008). Therefore, adaptation to flooding stress is critical for plant survival.
Grasslands, occupying more than 25% of land area, are crucial global resources for grazing and environmental enhancement (Shantz, 1954; Jones and Izolda, 2005; Afkhami et al., 2014; Afkhami et al., 2015and). Forage grasses are one of the most important constructive components of grasslands (Barnes et al., 1995). Dactylis glomerata L. (commonly called ‘orchardgrass’, ‘cock's-foot’ or ‘cat grass’), belonging to Pooideae in the Poaceae family, is an important cool-season forage grass globally. D. glomerata adapts to well-drained soil conditions; however, some cultivars and wild accessions differ in submergence tolerance. Studies have suggested that stress response is controlled by a range of gene regulatory mechanisms that act collectively. Although these studies characterized some genes involved in submergence (Sairam et al., 2009a; Christianson et al., 2010a; Le Provost et al., 2012), The regulatory mechanisms and the signaling networks are yet to be addressed. Moreover, the molecular mechanism of D. glomerata response to flooding stress is still unknown.
RNA-sequencing (RNA-Seq) based on Next-generation sequencing (NGS) has been employed as a powerful high-throughput method to explore the gene expression variation, regulatory networks, and some technology development in various species (Huang et al., 2015; Yan et al., 2018, 2019; Zhou et al., 2018, 2019). RNA-Seq was used to analyze the transcriptome of Taxodium ‘Zhongshansa’ in response to short-term waterlogging (Qi et al., 2014), and the study concluded that ROS detoxification and energy maintenance were the primary coping mechanisms responsible for its remarkable waterlogging tolerance. A recent study on the floating-leaved aquatic plant Nymphoides peltata utilized RNA-Seq to analyze the response to flooding stress (Wu et al., 2017). They revealed that antioxidant process and glycolysis were induced under flooding environment, whereas photosynthesis and alanine metabolism rarely occurred in other flood-tolerant plants. In addition, transcriptome profiling of maize root by RNA-Seq revealed the important pathways that control adaptive mechanisms under waterlogged stress (Arora et al., 2017a). However, the transcriptional alterations in D. glomerata under flooding stress have not been reported.
In this study, two D. glomerata cultivars, submergence tolerant ‘Dianbei’ and sensitive ‘Anba’ whose submergence resistance was detected through some physiological indices (Supplemental file 1, 2 and 3), were selected to explore the submergence stress responses at transcriptional level using RNA-Seq. The objectives of this study are to document the initial alternation profile of transcriptome at genome-wide level; explore the critical genes or pathways involved in regulating D. glomerata tolerance to submergence; and facilitate further investigation of the underlying mechanisms of flooding tolerance in forage grass.
Section snippets
Submergence tolerance identification of ‘Dianbei’ and ‘Anba’
Through the measurement data of physiology (Supplemental file 1, 2 and 3), it was showed that the content of chlorophyll in ‘Anba’ decreased significantly especial for chlorophyll b and chlorophll (a+b) as treatment time prolonging while it was stable relatively in ‘Dianbei’. Under submergence, antioxidant enzymes (SOD, POD and CAT) in D. glomerata took increasing at 3 d and went down at 7 d and ‘Dianbei’ put up the highest increasing at 3 d comparing to other materials. Besides, the CAT
Expression profile analysis of two different submergence tolerant cultivars
The transcriptome profiling of waterlogging response in cotton (Gossypium hirsutum L.) and soybean using RNA-Seq technology identified unigenes (Wei et al., 2016; Christianson et al., 2010b). In D. glomerata, unigenes associated with high temperature response were investigated and many DEGs were detected by NGS (Huang et al., 2015). Despite the reports on the transcriptome of Oryza sativa (Mustroph et al., 2013), Zea mays (Zou et al., 2010), Brassica napus (Zou et al., 2015), Cucumis sativus (
Conclusion
In summary, this study generated the first large-scale transcriptome dataset in D. glomerata in response to submergence stress. Totally, 307 million raw reads and 299 million clean reads were generated, and the assembled 50,045 unique genes were identified, from which, 2456 DEGs were found to respond to submergence stress. And 1395 genes only expressed differently in tolerant material ‘Dianbei’ and 18 genes expressed differently between ‘Dianbei’ and ‘Anba’ all the time. In this paper, we
Plant growth and water treatment
Seven cultivars of Dactylis glomerata L. (Poaceae) with different submergence resistance which have been measured by our team (the data is unpublished) were selected. Seeds of seven materials were sown in plastic pots (13 cm diameter, 11 cm deep) respectively with about 30 seeds in each pot and each material was set 6 pots for experiment using a mix of sand and peat soil (1:1, v/v) watered with Hoagland solution (0.5 × ) once a week in the laboratory under natural sunlight, relative humidity of
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
This study was supported by the National Natural Science Foundation of China (31771866), China; the Sichuan Province Breeding Research Grant and Modern Agricultural Industry System Sichuan Forage Innovation Team, China; Technology integration and industry demonstration of forage silage distribution center (Industrial poverty alleviation of academy of agricultural sciences in Guizhou 2018No.1), China; Chongqing Herbivorous Livestock Industrial Technology System Forage and Feed Nutrition
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These authors contributed equally to this work.