Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance

Abstract

Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiotic stress conditions. For this purpose, we sequenced the flag leaf transcriptome of a highly tolerant bread wheat germplasm (KRL 3–4) in order to extend our knowledge and better understanding of the molecular basis of sodicity tolerance. A total of 1,980 genes were differentially expressed in the flag leaf due to sodicity stress. Among these genes, 872 DEGs were upregulated and 1,108 were downregulated. Furthermore, annotation of DEGs revealed that a total of 1,384 genes were assigned to 2,267 GO terms corresponding to 502 (biological process), 638 (cellular component), and 1,127 (molecular function). GO annotation also revealed the involvement of genes related to several transcription factors; the important ones are expansins, peroxidase, glutathione-S-transferase, and metal ion transporters in response to sodicity. Additionally, from 127 KEGG pathways, only 40 were confidently enriched at a p-value <0.05 covering the five main KEGG categories of metabolism, i.e., environmental information processing, genetic information processing, organismal systems, and cellular processes. Most enriched pathways were prioritized using MapMan software and revealed that lipid metabolism, nutrient uptake, and protein homeostasis were paramount. We have also found 39 SNPs that mapped to the important sodicity stress-responsive genes associated with various pathways such as ROS scavenging, serine/threonine protein kinase, calcium signaling, and metal ion transporters. In a nutshell, only 19 important candidate genes contributing to sodicity tolerance in bread wheat were identified, and these genes might be helpful for better understanding and further improvement of sodicity tolerance in bread wheat.

Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR)

“…For example, the homologous genes of OsSPX1 in wheat, Traescs7a02g376200, Traescs7b02g277700, and Traescs7d02g372600, were all induced due to Pi starvation. It is also interesting that Traescs7a02g376200 and Traescs7d02g372600, as candidate genes for saline-alkali tolerance, were significantly upregulated after salinealkali treatment [46]. However, we know that OsSPX1 responds to Pi starvation and plays a positive regulatory role in cold tolerance.…”

The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum)

“…LLG1 plays a role in plant immunity (Shen et al 2017) and acts as a chaperone and coreceptor for FERONIA to regulate plant growth and development (Li et al 2015). Similarly, TraesCS2A03G0353700 was upregulated and encodes for SPX domain-containing protein 5 which was one of seven phosphate signalling regulatory proteins (SPX) that were upregulated in wheat flag leaf transcriptomes in response to sodicity stress (Prasad et al 2021). Also in this set is a helix-turn-helix (HTH) myb-type domain-containing transcription factor called NIGT1 (2023) or InterPro predictions are given where available.…”

Multivariate Genome-Wide Association Study of Concentrations of Seven Elements in Seeds Reveals Four New Loci in Russian Wheat Lines

“…Wheat is a cereal grain that plays an important role in the world's food industry. Wheat lines have been studied using many genomic approaches, such as genome sequencing and resequencing [1][2][3]), transcriptome analysis [4][5][6], and SNP arrays [7][8][9], that have given one an opportunity to investigate many wheat traits, such as element concentrations, immune response, and drought resistance.…”