Elsevier

Gene

Volume 674, 20 October 2018, Pages 161-169
Gene

Research paper
The chrysanthemum leaf and root transcript profiling in response to salinity stress

https://doi.org/10.1016/j.gene.2018.06.075Get rights and content

Highlights

  • Much more DTGs in root than those in leaf under salinity

  • DTGs are mainly in osmotic adjustment, ion transport, ROS scavenging and ABA signaling regulation

  • Ion transport in root and osmotic adjustment and Ca2+ transport in leaf dominated the salt stress response

  • WRKY and bHLH family provided the highest number of DTGs under salinity both in root and leaf

Abstract

RNA-Seq was applied to capture the transcriptome of the leaf and root of non-treated and salinity-treated chrysanthemum cv. ‘Jinba’ plants. A total of 206,868 unigenes of mean length 849 nt and of N50 length 1363 nt was identified; of these about 64% (> 132,000) could be functionally assigned. Depending on the severity of the salinity stress, differential transcription was observed for genes encoding proteins involved in osmotic adjustment, in ion transport, in reactive oxygen species scavenging and in the regulation of abscisic acid (ABA) signaling. The root stress response was dominated by the up-regulation of genes involved in ion transport, while that of the leaf reflected the plant's effort to make osmotic adjustments and to regulate Ca2+ transport. An array of known transcription factors (WRKY, AP2/ERF, MYB, bHLH and NAC) were differentially transcribed.

Introduction

Soil salinity has developed as a significant constraint to crop productivity worldwide (Munns and Tester, 2008; Veeranagamallaiah et al., 2007). The stress it imposes includes both an osmotic and an ionic component (Xiong et al., 2002), for which plants have evolved a variety of mechanisms to cope. Osmotic adjustment is typically accomplished by the accumulation of compatible solutes, such as glycine betaine, sugar alcohols and certain unusual amino acids (Greenway and Munns, 1980; Xu et al., 1996). Since most saline soils feature an excess of Na+ (Ji et al., 2013), restricting the influx of Na+, its sequestration into the vacuole and/or the maximization of its efflux from the cell both represent important features of salinity tolerance. Various transporter proteins mediate the import of Na+ into plant cells, among which the best known are the high affinity potassium transporters (HKTs) (Garciadeblás et al., 2003), along with the Na+/H+ antiporters NHX1 and SOS1 (Blumwald et al., 2000; Pardo et al., 2006). The product of the Arabidopsis thaliana gene HKT1 localizes to the stele, where it functions largely as a Na+ selective uniporter (Uozumi et al., 2000), while in wheat, the down-regulation of HKT1 results in an enhanced level of salinity tolerance (Laurie et al., 2002). The plasmamembrane Na+/H+ antiporter SOS1 is found in most higher plants (Tang et al., 2010); in A. thaliana, SOS1 transcript is concentrated in the root tip epidermis and the root/stem/leaf parenchyma xylem-symplast boundary; the function of its product is to export and to control the long distance transport of Na+ (Gao et al., 2016). In addition to ionic stress, salinity induces a measure of oxidative stress, reflecting the inhibition of the photosynthetic electron transport chain and the over-production of reactive oxygen species (ROS). The ability to neutralize ROS represents a prominent means of improving salinity tolerance (Nagamiya et al., 2007). The enzymes involved in ROS removal include superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) (Shigeoka et al., 2002; Moradi and Ismail, 2007). A universal response to abiotic (including salinity) stress is the generation of the phytohormone abscisic acid (ABA): ABA-mediated gene expression typically inhibits growth (Fujita et al., 2011). Finally, an array of transcription factors (TFs) are known to be integral in linking the various pathways which respond to salinity stress (Jiang and Deyholos, 2009; Kasuga et al., 1999; Mei et al., 2013; Zhou et al., 2009; Yu et al., 2016), thereby regulating the expression a suite of genes governing the salinity stress response (Deinlein et al., 2014).

The chrysanthemum (Chrysanthemum morifolium) cultivar ‘Jinba’ is not considered to be salinity tolerant (Gao et al., 2016). A study of the transcriptomic response of its leaf to salinity stress has been described recently, the salt treatment was different (100 mM for the first day, 200 mM for the second day and 400 mM for three days) (Wu et al., 2016), this analysis indicated that plant hormones, amino acid metabolism, photosynthesis and secondary metabolism of chrysanthemum were all changed under salt stress. Here, the RNA-Seq platform was applied to both the leaf and root of the same cultivar, imposing two levels of salinity stress; the purpose of the experiment was gain a fuller picture of the salinity response of the cultivar. In the longer term, this information could feed into ongoing efforts to enhance the salinity tolerance of chrysanthemum via transgenic means.

Section snippets

Plant materials and the assessment of salinity tolerance

Uniform cuttings of cv. ‘Jinba’ were obtained from the Chrysanthemum Germplasm Resource Preserving Center (Nanjing Agricultural University, China). After rooting in sand, the cuttings were transplanted into a 1:3 mixture of vermiculite and garden soil in a greenhouse delivering a 16 h photoperiod, a day/night temperature of 22 °C/18 °C and a relative humidity of 70–80%. Plants at the 8–10 leaf stage were transferred to a container (volume 20 L) filled with half strength Hoagland nutrient

RNA-Seq analysis and read mapping

A summary of the sequence reads is given in Table 2: the number of raw reads acquired per library ranged from 68.4–74.5 million. After filtering, the remaining 65–69 million reads (5.7–6.2 × 109 nt) featured a Q20 of >96.93%, an N% of <0.01% and a GC% of 42.9–49.5%. The reads resolved into 136,432–201,315 contigs; within each library the mean contig length varied from 244 to 339 nt. Average N50 lengths among the root and leaf transcriptome contigs were, respectively 295–414 and 598–631 nt.

The RNA-Seq derived transcriptome of cv. ‘Jinba’

More than 200,000 unigenes were identified from the sequencing of the eight libraries; of these, nearly two thirds could be assigned a putative function through reference to homologs from other species. The level of transcription of a large number of genes was affected by the imposition of salinity stress, offering many opportunities for exploring the mechanistic basis of the salinity response of chrysanthemum. A study of the transcriptomic response of its leaf to salinity stress described that

Conclusions

In summary, the application of the RNA-Seq platform has demonstrated that salinity stress altered the transcription level of a variety of genes associated with a number of regulatory networks, including osmotic adjustment, ion transport, scavenging system of the active oxygen species and ABA signaling regulation. Functional enrichment analyses for the candidate genes showed both common and tissue-specific patterns of transcriptome remodelling under salt treatments. The response to the stress of

Acknowledgments

This work was supported by funding from the National Science Fund for Distinguished Young Scholars (31425022) and the National Natural Science Foundation of China (31372100).

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