Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice.

Panita Chutimanukul,Kitiporn Plaimas,Puriphot Mahaprom,Meechai Siangliw,Teerapong Buaboocha,Theerayut Toojinda,Triono Bagus Saputro,Supachitra Chadchawan,Luca Comai

doi:10.3389/fpls.2021.704549

Abstract

Salinity stress tolerance is a complex polygenic trait involving multi-molecular pathways. This study aims to demonstrate an effective transcriptomic approach for identifying genes regulating salt tolerance in rice. The chromosome segment substitution lines (CSSLs) of “Khao Dawk Mali 105 (KDML105)” rice containing various regions of DH212 between markers RM1003 and RM3362 displayed differential salt tolerance at the booting stage. CSSL16 and its nearly isogenic parent, KDML105, were used for transcriptome analysis. Differentially expressed genes in the leaves of seedlings, flag leaves, and second leaves of CSSL16 and KDML105 under normal and salt stress conditions were subjected to analyses based on gene co-expression network (GCN), on two-state co-expression with clustering coefficient (CC), and on weighted gene co-expression network (WGCN). GCN identified 57 genes, while 30 and 59 genes were identified using CC and WGCN, respectively. With the three methods, some of the identified genes overlapped, bringing the maximum number of predicted salt tolerance genes to 92. Among the 92 genes, nine genes, OsNodulin, OsBTBZ1, OsPSB28, OsERD, OsSub34, peroxidase precursor genes, and three expressed protein genes, displayed SNPs between CSSL16 and KDML105. The nine genes were differentially expressed in CSSL16 and KDML105 under normal and salt stress conditions. OsBTBZ1 and OsERD were identified by the three methods. These results suggest that the transcriptomic approach described here effectively identified the genes regulating salt tolerance in rice and support the identification of appropriate QTL for salt tolerance improvement.

Highlights

Salinity is a major environmental stressor that affects rice production worldwide
The Ci levels of rice grown under normal conditions were not significantly different; contrarily, the Ci levels of both flag leaves and second leaves of rice lines grown under salt stress were significantly different with the second leaves of “CSSL16” recording the highest Ci level (Figures 3E,F)
Because the bt3 mutant displayed the highest growth inhibition and photosynthesis pigment reduction and the OsBTBZ1 gene was highly-induced under salt stress, we focused on its promoter

Summary

Introduction

Salinity is a major environmental stressor that affects rice production worldwide. Salt stress decreases crop yield and limits agricultural productivity (Munns, 2002), in nonirrigated farmlands by triggering two primary effects on plants, osmotic stress, and ion toxicity (Boyer, 1982). A combination of ion toxicity and osmotic stress inhibits growth and affects plant development or cause cell death (Hasegawa et al, 2000; Zhu, 2001, 2002). These factors affect enzyme activities, which lead to a reduction in photosynthetic rate, metabolism, growth, and development; pollen germination may be affected, lowering fertility. These effects contribute to the lower yield of crops exposed to salt stress (Abdullah et al, 2001)

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