Research Article: Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar

Date Published: March 15, 2019

Publisher: Public Library of Science

Author(s): Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad Reza Ghaffari, Farhad Nazarian Firouzabadi, Zahra-Sadat Shobbar, Mukesh Jain.


Salt stress is one of the major adverse environmental factors limiting crop productivity. Considering Iran as one of the bread wheat origins, we sequenced root transcriptome of an Iranian salt tolerant cultivar, Arg, under salt stress to extend our knowledge of the molecular basis of salinity tolerance in Triticum aestivum. RNA sequencing resulted in more than 113 million reads and about 104013 genes were obtained, among which 26171 novel transcripts were identified. A comparison of abundances showed that 5128 genes were differentially expressed due to salt stress. The differentially expressed genes (DEGs) were annotated with Gene Ontology terms, and the key pathways were identified using Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping. The DEGs could be classified into 227 KEGG pathways among which transporters, phenylpropanoid biosynthesis, transcription factors, glycosyltransferases, glutathione metabolism and plant hormone signal transduction represented the most significant pathways. Furthermore, the expression pattern of nine genes involved in salt stress response was compared between the salt tolerant (Arg) and susceptible (Moghan3) cultivars. A panel of novel genes and transcripts is found in this research to be differentially expressed under salinity in Arg cultivar and a model is proposed for salt stress response in this salt tolerant cultivar of wheat employing the DEGs. The achieved results can be beneficial for better understanding and improvement of salt tolerance in wheat.

Partial Text

Soil salinity is a major environmental factor which limits the growth and development of plants, resulting in decrease in crop productivity and quality[1, 2]. It is estimated that salt stress affects approximately 20% of the irrigated land worldwide and will lead to the loss of 50% of cultivable land by the middle of the twenty-first century[3].

This study presents a comprehensive overview of the transcriptome changes of an Iranian salt tolerant bread wheat cultivar, Arg, under salt stress, which can help understanding the molecular basis of salinity tolerance in T. aestivum. A model is proposed for salt stress response in Arg cultivar employing the DEGs (Fig 7) (S15 Table and. S9 Fig). Based on the achieved results, salinity-induced osmotic and ionic stress might be sensed by mechanosensitive ion channels (e.g. Ta.Msc) and membrane Na+/H+ antiporter (Ta.SOS1), respectively. After sensing the stress, signaling cascades are triggered[6]. To this end, Ca+2 has been reported to serve as a secondary messenger, so an increase in cytosolic Ca+2 concentrations is expected[98]. In this study, the genes coding for Ca2+ transporters such as Ta.ANN4, Ta.ACA7 and Ta.NCL2 were appeared to be up-regulated, which may adjust the Ca+2 cytosolic concentrations. Ta.GLR, which encodes a non-selective cation channel were also induced in Arg under salt stress, and is supposed to be involved in Ca2+ transport. The genes coding for CaM, CIPK and CPK were also up-regulated, which are involved in Ca+2 signaling pathway [41, 42, 46]. The genes coding for transcription factors such as MYB, NAC, bHLH, WRKY, bZIPs and AP2/ERF were observed among the DEGs. Some of these genes have been proved to be involved in salt stress response based on the information about their orthologues in Arabidopsis (S1 Table). These transcription factors can regulate the expression of the genes engaged in dealing with osmotic, ionic and oxidative stresses arising from salinity[6]. The genes coding for Aquaporins (Ta.TP4-1-like and Ta.NIP1-1-like), LEA proteins (Ta.Wrab18, Ta.LEA1, Ta.LEA3, Ta.LEA-D34-Like and Ta.LEA14-A) and dehydrins (Ta.DHN3, Ta.DHN4, Ta.DHN7 and Ta.DHN9), P5CS (involved in proline synthesis) (Ta.P5CS) with increased expression and proline oxidase (Ta.ProDH) (involved in proline degradation) with decreased expression can alleviate the osmotic stress. In order to deal with the ionic stress, plasma membrane Na+/H+ antiporter SOS1, K+ transporters (such as Ta.HAK25) and ABC transporters (such as Ta.ABAC15) were significantly up-regulated under salt stress. The gene coding for SOS2-like protein kinase PKS12 is likely to control the activity of the Na+/H+ antiporter SOS1. Although the transcript level of Na+/H+ antiporter NHX1 was not increased under salinity in this study, but the protein encoded by up-regulated Ta.HXK1 is able to phosphorylate Ta-NHX1, leading to higher compartmentalization of Na+ into vacuole. In addition, the genes coding for catalases (Ta.CAT), glutaredoxins (Ta.GRXC1) and Gluthatione-S- transferases (Ta.GST) appear to deal with oxidative stress (Fig 7). We hope the attained results could be useful toward achieving salt tolerant cultivars through molecular breeding or genetic engineering.




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