Rice (
Oryza sativa L.) is the primary staple food crop for nearly half of the world’s population. Due to the drier and warmer climate trends, the amount of water used in agricultural irrigation is expected to increase
[1], but limited available freshwater resources are likely to cause more severe drought pressure on crops. The Global Drought Information System (GDIS) reveals that drought is becoming progressively more severe and intense on a global scale
[2]. Asia is the most important rice production area that is deeply influenced by drought stress. Agricultural zones in China are suffering from water shortages, with droughts occurring frequently. Since the 1990s, about 26 million hectares of arable land have been annually affected by drought, directly leading to a reduction in 70 million tons of food crops
[3]. Similarly, in the Mekong River Delta (MRD), salt stress has also caused great economic losses. From 2015 to 2016, MRD experienced severe saltwater intrusion, causing a total of 215,445 hectares of rice to be severely affected
[4]. Compared with the baseline period (2000), the sea level is expected to increase by 5 cm in 2050, and another 30,000 hectares of the agricultural area will be affected, which will cause serious economic losses
[5]. Moreover, the pH of the soil has an influence on rice. For instance, the pH of the soil is controlled by the leaching of cations, such as Ca, Mg, K and Na, far exceeding their loss in weathered minerals, leaving H
+ and Al
3+ for the main cation exchange
[6]. The most suitable soil condition for
Geng/
japonica is pH 4.0
[7], while for
Xian/
indica is at pH 5.0–5.5
[8]. The suitable pH can provide nutrients for plant growth, while an unsuitable pH can cause plant ion poisoning. Some salt-tolerant species can withstand higher soil pH environments up to 10
[9]. In recent years, some drought- and salt-tolerant rice varieties have been identified
[10]. For example, Torres et al. (2013) screened the yield of 988 rice materials from the International Rice Research Institute (IRRI) under drought stress and finally identified more than 65 drought-tolerant rice materials, including Kataktara Da2, Shada Shaita and Dular
[10][11][12]. There are also many well-known salt-tolerant varieties bred in south/east Asia, such as Kala Rata 1-24, Nona Bokra, Bhura Rata, SR 26B and Chin.13.
[13] Many important QTLs, such as
Deeper Rooting 1 (
DRO1), increased plant deep roots under drought stress and
SKC1 promoted Na
+/K
+ transport under salt stress
[14][15]. Among them, many important genes have been successfully cloned and their functions have been identified. The functional genes, such as
D,
OsHKT1;5, were related to drought and salt stress, respectively
[16]. Meanwhile, epigenetic (modifications) are instrumental in response to plant adversity stresses, involving histone modification, chromatin remodeling, non-coding RNAs and DNA methylation, and each play an important role in different epigenetic modifications. These modifications, which are single or in combination with each another, could affect gene expression and cause response to abiotic stress
[17][18]. For instance, the expression of drought-related genes is closely associated with the alteration of histone dynamics, such as
RD29A,
RD29B,
RD22, and
RAP2.4 [19]. In wild-type Arabidopsis, a putative small RNA target region was identified that negatively regulates Na
+-selective transporter gene
AtHKT1 expression
[19]. The mechanisms by which plants respond to drought and salt might be closely related
[20]; however, analyses of drought and salt co-response mechanisms are rare, and most of these have focused on the function of genes responsive to a single stress.