Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline–Alkaline Tolerance between Indica and Japonica Rice at the Seedling Stage

Abstract

Saline–alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline–alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline–alkaline-tolerant), to identify the main pathways and important factors related to saline–alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline–alkaline conditions, implying that a series of cascade changes from these genes promotes saline–alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline–alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline–alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline–alkaline stress tolerance.

Progress in Rice Breeding Based on Genomic Research

“…Transcriptome studies analyzing the ten most resistant and ten most susceptible individuals demonstrated that overexpression of the WAK91 gene improves rice resistance to rice blast, and through the 3000 Rice Genome Project and publicly available genomic data, it was determined that the resistance genes in the WAK91 SNP mutant appeared to be ancestrally inherited, and it was concluded that the WAK91 gene is a candidate for improved resistance to the leaf blight gene [55]. Under salt-alkali stress conditions, a comparative analysis of the transcriptomes of a salt-alkali-tolerant subspecies (RPY Geng) and a relatively sensitive subspecies (Luohui 9) of rice revealed the specific upregulation of multiple genes associated with salt-alkali tolerance in RPY Geng [56]. To understand how rice responds to various abiotic stresses, the transcriptome of IAC1131 rice related to interactions with these stresses was analyzed after various ABA pretreatments [57].…”

Identification of Ossnrk1a−1 Regulated Genes Associated with Rice Immunity and Seed Set

“…The former consists of pathogenic microorganisms (fungi, bacteria, and nematodes), insects, and herbivores, as well as nutrient deficiency, extreme temperature, salinity, drought, floods, etc. To survive, plants have evolved sophisticated coping mechanisms to perceive stressful stimuli and activate the necessary cellular responses, including the activation of various kinase cascades [ 1 ], transcriptional reprogramming [ 2 ], reactive oxygen species (ROS) production [ 3 ], and the accumulation of defense-related hormones [ 4 ].…”

Effect of ABA Pre-Treatment on Rice Plant Transcriptome Response to Multiple Abiotic Stress

“…IAC1131 is a drought-tolerant upland rice cultivar that has been previously shown to be more drought tolerant [16,17], and more tolerant to combined drought, salt, and temperature stress, than Nipponbare, which is a lowland rice that is sensitive to drought and heat stress [3]. Previous studies investigating plant stress responses at the transcriptome level are typically focused on one stress at a time; examples include the transcriptomic characterisation of salt tolerance in germinating rice [18], drought tolerance in rice [19], and salinity-alkalinity tolerance in rice seedlings [20]. In contrast, in this analysis, we analysed the rice transcriptome to explore how rice regulates responses to multiple abiotic stresses imposed simultaneously with or without prior ABA application.…”