*Article* **Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (***Sesamum indicum* **L.)**

**Komivi Dossa 1,\*, Marie A. Mmadi <sup>1</sup> , Rong Zhou <sup>1</sup> , Tianyuan Zhang <sup>2</sup> , Ruqi Su <sup>1</sup> , Yujuan Zhang <sup>1</sup> , Linhai Wang <sup>1</sup> , Jun You <sup>1</sup> and Xiurong Zhang 1,\***


Received: 8 July 2019; Accepted: 10 August 2019; Published: 13 August 2019

**Abstract:** Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

**Keywords:** stress marker genes; sesame; gene co-expression; abiotic stress tolerance; hub genes; meta-analysis

## **1. Introduction**

Climate change causes the rising of sea levels, a decrease of available land for farming, and increased frequencies of severe droughts, intense precipitation events, elevated temperatures, as well as salt and heavy metals contamination of soils. Crop productivity and survival is tightly linked to its environment, which is being altered due to climate change [1], impairing crop yields and leading to enhanced risks of famine worldwide [2]. Being a sessile organism, plants have evolved an enormous capacity to adapt to environmental changes including heat, drought, salinity, osmotic pressure, waterlogging, etc., by modulating their physiology, growth and development. Until recently, numerous researches have focused on plant responses to individual abiotic stress [3–8]. Although these studies have potential applications in crop improvement for abiotic stress tolerance, crops growing in natural habitats are often exposed to multiple environmental stresses occurring simultaneously or at different development stages, which inflicts a more severe reduction in yields as compared to a single stress [9,10]. Hence, development of crops able to tolerate a wide range of abiotic stresses with high

productivity is imperative in order to meet various socio-economic and agro-economic challenges in the current climate change scenario [11,12]. However, the interactive improvement of multiple abiotic stress tolerances is a challenge [13], since increasing tolerance to one stress may be at the expense of tolerance to another [9,14]. Therefore, there is a need to investigate the metabolic pathways and regulatory networks of multiple abiotic stress acclimations in plants and obtain candidate genes for manipulation to improve tolerance to multiple abiotic stresses.

In recent years, it has become evident that a common battery of responses can be triggered by various stresses. For example in yeasts, it has been discovered that a set of genes are constantly activated upon exposure to various abiotic stresses and represent the core environmental stress responsive genes [15–19]. Similarly, the core environmental stress responsive genes were unraveled in plants, first in *Arabidopsis thaliana* through the AtGenExpress abiotic stress experiment [20–22] and later confirmed in various plant species, such as rice, soybean, banana, *Brachypodium distachyon* or barley [13,23–27], indicating the conservation of a core genome modulating various abiotic stresses responses between species. Thus, it is critical to compare and analyze different kinds of abiotic stress responses to find the common genes and understand how they regulate plant's adaptations to the multiple environmental stresses. This information will guide in strategies to enhance crop tolerance to multiple abiotic stresses.

Consumers become more and more health conscious, with a sharper focus on health-promoting diets. Oils and fats are an important part of a balanced and healthy diet. Among the most nutritious and healthy vegetable oils, sesame (*Sesamum indicum* L.) oil occupies a pro-eminent position because of the low level of saturated fatty acids (less than 15%) and the presence of strong antioxidants, reported to have health-promoting effects such as lowering cholesterol levels and hypertension [28,29], neuroprotective effects against hypoxia or brain damage [30] and reducing the incidence of certain cancers [31,32]. Therefore, demands for and world trade in sesame seeds have increased rapidly during the last two decades [33]. Although the global sesame planting area is extending, particularly in Africa, the productivity and yield are still very low, resulting in a huge gap between seed demand and supply [34]. In fact, sesame is cultivated in harsh environments and its growth and development are greatly affected by the adverse conditions [35]. Drought, waterlogging, heat and salt stresses represent the leading abiotic factors impairing sesame yield and productivity [36] and several of these environmental stressors often occur in combination at different growth stages. For example, in the arid and semi-arid areas of Africa, America and Asia, extreme heat and drought stresses co-occur and challenge sesame crop. In East and South Asia, waterlogging and salinity stress devastate sesame field. Over the past five years, tremendous efforts have been made to decipher the molecular basis of abiotic stress response and tolerance in sesame [6–8,37,38]. However, none of these studies has performed a meta-analysis of diverse transcriptome data to elucidate the similarities and differences among stress response pathways, and importantly, decode the core abiotic stress-responsive genes (CARG) in sesame.

Within the CARG, understanding how specific transcriptional changes are linked to stress adaptations and identifying central hubs controlling this interaction remain the main challenge. Weighted Gene Co-expression Network Analysis (WGCNA) is one of the widely used computational tools to detect co-expression modules in transcriptome data and identify hub genes playing preponderant functions based on a network construction [39]. Using WGCNA analysis of the RNA-Seq data, Shahan et al. [40] identified key regulators of flower and fruit development in strawberry. WGCNA has also been utilized to detect coexpression modules and major players for multiple biotic and abiotic stresses responses in various plant species, including Arabidopsis, rice, maize, soybean and poplar [41–45].

In this study, we conducted a meta-analysis of 72 RNA-Seq data from drought, salt, osmotic and waterlogging stresses aiming at identifying the CARGs modulating sesame responses to multiple abiotic stresses. By applying WGCNA, we revealed for the first time the co-expressed functional modules within these CARGs and highlighted the major genes to target for sesame improvement towards tolerance to multiple abiotic stresses.
