Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes

Abstract

Background Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique. Results A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL , OsNAAT , OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29. Conclusions The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k + , ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent. Electronic supplementary material The online version of this article (10.1186/s12284-019-0273-2) contains supplementary material, which is available to authorized users.

Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

“…There were OsHOX22 and OsHOX24 from homeobox familyin Chr3:M-QTL1 and Chr4:M-QTL3, respectively, which were both up-regulated in the seedlings (Table S6, Fig.6). OsHOX24 was the most up-regulated gene under 150 mM NaCl in the salt tolerant genotype (FL478); while it was highly down-regulated in the salt sensitive genotype (IR29) [31]. Also, the role of OsHOX24 has been already found to regulate the abiotic stress responses through ne tuning the expression of stress-responsive genes in rice [47].…”

“…The DEGs were identi ed under salinity stress compared to control conditions in the salinity tolerant genotypes. A total of 1714 DEGs were observed in the roots of FL478 as a salinity tolerant genotype, among which, 927 and 787 were up-and down-regulated in the salinity conditions [31]. DEGs from multiple RNA-seq datasets were combined and the DEGs were classi ed into root, shoot, seedling, and leaves to have a deeper understanding about the salt responsive genes in the salinity tolerant rice genotypes.…”

“…Brie y, the young seedlings of FL478 (Salt tolerant) and IR29 (Salt sensitive) were treated with 150 mM NaCl and the root samples were collected 24 h after inception of the salt stress. Along with, normal samples (at the same conditions but without salinity treatment) were also collected as control samples [31]. The puri ed RNA was used to construct the cDNA library; the quali ed libraries were subsequently sequenced using IlluminaHiSeq™ 2500 sequencer.…”

Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

“…In our previous study, the DEGs were recognized under salinity stress compared to control conditions in the salinity tolerant genotypes. A total of 1714 DEGs were observed in roots of FL478 as a salinity tolerant genotype, among which, 927 were up-and 787 down-regulated under salinity conditions [31].…”

“…There were OsHOX22 and OsHOX24 from homeobox familyin Chr3:M-QTL1 and Chr4:M-QTL3, respectively, both up-regulated in seedlings (Table S6, Fig.6). OsHOX24 were the most up-regulated gene under 150 mM NaCl in the salt tolerant genotype (FL478); while it was highly down-regulated in the salt sensitive genotype (IR29) [31]. Also, the role of OsHOX24 was already detected as regulation of abiotic stress responses through fine tuning the expression of stress-responsive genes in rice [47].…”