Abstract
Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.
Highlights
Rice is the most important food crop in the world and is predominantly grown in South, Southeast, and East Asia
It is important to understand the molecular underpinnings of salt tolerance, which is controlled by multiple genes and involves several mechanisms [for reviews: (Chen et al, 2021a; Liu et al, 2021; Ponce et al, 2021)], including osmotic adjustment (Sripinyowanich et al, 2013; Nounjan et al, 2018) for review: (Rajasheker et al, 2019), ion homeostasis [for review: (Hussain et al, 2021)], reactive oxygen species (ROS) scavenging (Chutimanukul et al, 2019; Parveen et al, 2021), membrane repairs and photosynthesis adaptation (Udomchalothorn et al, 2017; Chutimanukul et al, 2018; Lekklar et al, 2019; Chaudhry et al, 2021)
Gene expression was measured by Tag-Seq at 0, 3, 6, 12, 24, and 48 h after the salt shock, producing 36 libraries
Summary
Rice is the most important food crop in the world and is predominantly grown in South, Southeast, and East Asia. Salinity is a limiting factor in rice production, in Southeast Asia, where many regions have experienced decreasing rice yields due to increased soil salinity (Pattanagul and Thitisaksakul, 2008) To solve this problem, it is important to understand the molecular underpinnings of salt tolerance, which is controlled by multiple genes and involves several mechanisms [for reviews: (Chen et al, 2021a; Liu et al, 2021; Ponce et al, 2021)], including osmotic adjustment (Sripinyowanich et al, 2013; Nounjan et al, 2018) for review: (Rajasheker et al, 2019), ion homeostasis [for review: (Hussain et al, 2021)], reactive oxygen species (ROS) scavenging (Chutimanukul et al, 2019; Parveen et al, 2021), membrane repairs and photosynthesis adaptation (Udomchalothorn et al, 2017; Chutimanukul et al, 2018; Lekklar et al, 2019; Chaudhry et al, 2021). With the development of sequencing techniques, the identification of candidate genes that are related to biological phenotypes was mainly based on comparing their gene expression levels among different experimental groups
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