Transcriptome Study of Rice Roots Status under High Alkaline Stress at Seedling Stage

Abstract

Alkaline stress is harmful to plant growth and development, it would induce endogenic ionic concentration and osmotic pressure, trigger relevant genes expression with transcription factor binding, signal transduction and hormone synthesis. In this study, we selected “Dongdao-4”, a salt-alkali stress tolerance rice cultivar, which was subjected to extreme high pH (pH = 11.5) alkaline stress at the trefoil stage for 7 days. Using the RNA-seq technology, we analyzed variations in genes expressed between the fourth and the seventh day of treatment. The number of differentially expressed genes (DEGs) was 3804, 2534, 207 and 3276 for fourth day-stress vs. fourth day-control, seventh day-stress vs. seventh day-control, seventh day-control vs. fourth day-control and seventh day-stress vs. fourth day-stress, respectively. Gene ontology (GO) results revealed that DEGs were mainly enriched in apoptotic process, electron carrier activity, receptor activity, molecular transducer activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results implied that DEGs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites. In particular, DEGs were distributed in genes related to the transcription factor, leucine rich repeats (LRRs) and hormones. We also report here for the first-time identification of 125 genes specifically expressed during the alkaline stress. Our results provided important information assisting with the exploration of the molecular mechanisms of rice plants subjected to high pH condition and can facilitate rice abiotic tolerance breeding.

Irrigation with Magnetized Water Alleviates the Harmful Effect of Saline–Alkaline Stress on Rice Seedlings

“…For example, Wang et al (2012), discovered that the NH 4 + transporter genes family ( OsAM T) was increased in rice roots to adapt to NH 4 + deficiency induced by saline–alkaline stress [ 41 ]. Lin et al (2020) conducted a transcriptome study of rice root’s status under saline–alkaline stress and found that the expression levels of OsAMT2;1 and OsAMT2;3 were up-regulated under high alkaline stress conditions [ 42 ]. Consistent with these results, the expression levels of OsAMT1;2 , OsAMT2;1 , OsAMT2;2 , OsAMT3;1 , OsAMT3;2 , and OsAMT3;3 in rice roots in our study were significantly up-regulated under a saline–alkaline stress environment, and the degree of the up-regulation was greater in plants when magnetized water was applied ( Figure 6 , Figure 7 and Figure 8 ).…”

Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax, Linum usitatissimum L.

“…RNA extraction and cDNA library construction methods were used as reported previously [ 65 ]. Three biological replicates were analyzed for each sample.…”

“…BWA and STAR were used for mapping analysis, and the differentially expressed genes (DEGs) were identified using the DESeq2 R package as in our previous reports [ 65 ]. The used criterion was a greater than two-folds change and a significant q value (false discovery rate-adjusted p value) of <0.01 to estimate differentially expressed genes [ 65 ]. The differentially expressed genes related to hormone metabolism, TFs activity, ionic transport, and epigenetic modification were compared to the annotation file and MapMan software [ 66 ].…”

“…The flax genome sequence Lusitatissimum_200_BGIv1.0.fa.gz and annotation file Lusitatissimum_200_v1.0.annotation_info.txt were downloaded from the website (https://data.jgi.doe.gov/refine-download/phytozome?organism=Lusitatissimum& expanded=Phytozome-200, accessed on 13 August 2021). BWA and STAR were used for mapping analysis, and the differentially expressed genes (DEGs) were identified using the DESeq2 R package as in our previous reports [65]. The used criterion was a greater than two-folds change and a significant q value (false discovery rate-adjusted p value) of <0.01 to estimate differentially expressed genes [65].…”

Genetic Dissection of Alkalinity Tolerance at the Seedling Stage in Rice (Oryza sativa) Using a High-Resolution Linkage Map

“…As both alkaline and saline stresses involve a high concentration of Na + salt around the rhizosphere and in shoots, it has been assumed that there might be overlapping tolerance mechanisms for both stresses. Several studies showed that alkaline stress is more detrimental to crops compared with saline stress due to high pH and nutrient deficiency in addition to salt stress caused by Na 2 CO 3 [ 9 , 27 , 28 ]. Apart from tolerance to ionic imbalance and osmotic stress, plants have evolved mechanisms for tolerating high pH and nutrient deficiency [ 29 , 30 ].…”