Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor
Abstract
:1. Introduction
2. Results
2.1. Leaf Anatomy in SS and ST Lines under Control and Stress Conditions
2.2. Root Anatomy in SS and ST Lines under Stress Conditions
2.3. Ultra-Structural Changes in the Leaf Cuticle
2.4. Ultra-Structural Changes and Lignin Distribution Pattern in the Root
2.5. Accumulation of Ions in Different Organs in SS, SSN, ST and STN Plants
2.6. Identification of DEGs, KEGG, and GO Pathways
2.7. DEGs in SS and ST Genotypes under Control and Salt-Treatment
2.8. Validation of Selected DEGs by qRT-pCR
3. Discussion
3.1. Anatomical Modifications in Tolerant and Susceptible Sorghum Genotypes
3.2. Estimation of Na+ and K+ Ions in SS and ST Lines
3.3. Transcript Profiling
3.4. Validation of Genes via qRT-PCR
4. Material and Methods
4.1. Sample Preparation for Microscopy
4.2. Ion Analysis
4.3. Plant Material and RNA Isolation
4.4. Nextseq Paired End (PE) Library Preparation and RNA-Seq
4.5. Downstream Annotation and Bioinformatic Analysis
4.6. Downstream Annotation and Bioinformatic Analysis
4.7. DEG, KEGG and GO Enrichment and Pathway Analysis
4.8. GO Enrichment and Pathway Analysis
4.9. Validation of DEGs by qRT-PCR Analysis
4.10. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Biological Process | Cellular Components | Molecular Function | ||
---|---|---|---|---|
SS vs. SSN | Downregulated | 83 | 81 | 118 |
Exclusive SS | 6 | 6 | 7 | |
Exclusive SSN | 29 | 36 | 35 | |
Expressed in both | 6396 | 7340 | 7858 | |
False discovery rate (FDR) downregulated | 14 | 13 | 16 | |
FDR upregulated | 38 | 35 | 47 | |
Downregulated | 239 | 245 | 296 | |
ST vs. STN | Downregulated | 299 | 321 | 343 |
Exclusive ST | 29 | 32 | 36 | |
Exclusive STN | 2 | 2 | 2 | |
Expressed in both | 6213 | 7136 | 7632 | |
FDR downregulated | 32 | 32 | 39 | |
FDR upregulated | 4 | 6 | 10 | |
Downregulated | 89 | 96 | 120 |
S. No. | Name of Gene Selected for qRT-PCR | SSN/STN Up- and Down-Regulated/Function | References |
---|---|---|---|
1 | Glucan endo-1,3-beta glucosidase 3-like Upregulated) | It stimulates and initiates the plant defence mechanism. A glucan endo-1,3-beta-glucosidase precursor has been detected in rice under salt stress. It plays a role during abiotic stress. | [37,38] |
2 | BARWIN (Upregulated) | BARWIN has similarity with proteins encoded by the wound-induced genes of barley (win) and others. It is involved in a common defence mechanism in plants. | [39] |
3 | Peroxidase 42 (Upregulated) | Peroxidases play prominent roles in antioxidant response through removing hydrogen peroxide from the system. Its overexpression results in salt stress tolerance. | [40] |
4 | Chitinase 2 (Upregulated) | Overexpression of a chitinase 2 gene (LcCHI2) in maize and tobacco improved salt and alkaline stress tolerance through reducing Na+ accumulation and malon-dialdehyde content. | [41] |
5 | Heavy metal-associated isoprenylated plant protein 16 (HIPP16) (Upregulated) | In addition to involvement in heavy metal homeostasis and detoxification, they are associated with abiotic stresses such as drought, cold, and plant–pathogen interactions. | [42] |
6 | Receptor kinase-like protein XA 21 (Upregulated) | XA 21 is an immune sensor protein, which promotes survival during dehydration stress. Its overexpression has enhanced lignin deposition and cellulose in the xylem vessels and surrounding cells. | [43] |
7 | K+ transporter (Upregulated) | Acquisition of K+ during salt stress is crucial. Its tissue-specific regulation of Na+ and K+ transporters explains genotypic differences in salt stress tolerance. | [44] |
8 | Tubulin and alpha 2-tubulin (Upregulated) | Microtubules and their dynamics play key roles in the adaptation of plants and their tolerance to salt stress. | [45] |
9 | Lipid transfer protein (LTP) (Downregulated) | LTPs are regulated by upstream transcription factors or kinase orphosphatases. They are critical for imparting salt/abiotic stress tolerance. However, it is downregulated in the SSN line but not in STN. | [46,47] |
10 | Micro RNA (miRf11471-akr) (Downregulated) | They are involved in gene regulation at the post-transcriptional level and associated with salt/abiotic stress tolerance. It is downregulated in SSN but not in STN. | [48] |
11 | MYB 61 (v-Myb avian myeloblastosis viral oncogene homolog transcription factor) (Upregulated) | Several MYBs have been shown to be associated with salinity stress in diverse plant systems. | [49,50,51,52,53] |
12 | Bowman-Birk type trypsin inhibitor (Upregulated) | It is involved in salt stress tolerance in wheat and other plants via limiting the transport of Na+ from the root to the shoot. | [54] |
13 | Heavy metal-associated isoprenylated plant protein (HIPP) (Upregulated) | Besides involvement in heavy metal homeostasis and detoxification, they are associated with abiotic stresses such as drought, cold, and plant–pathogen interactions. | [42] |
14 | Glucan endo-1,3-beta glucosidase (Upregulated) | It stimulates and initiates the plant defence mechanism. It plays a role in cell division, flower formation, and a vital role during abiotic stress. | [37,38] |
15 | Tubulin beta-4 chain (Upregulated) | Microtubules and their dynamics play key roles in the adaptation of plants and tolerance to salt stress. | [45] |
16 | Fasciclin-like arabinogalactan protein 12 (Downregulated) | This gene is involved in developing xylem and cell wall formation during salt stress. Additionally, it controls ROS levels. It is downregulated in STN, but not in SSN. | [11,55] |
17 | HHO5 (HRS1 homolog, (transcription factor) (Upregulated) | NIGT1/HRS1/HHO transcription factors are associated with salt stress tolerance, though the precise function is obscure. | [56] |
18 | Peroxidase 2 (Upregulated) | It removes ROS-like hydrogen peroxide generated during salt stress. | [57] |
19 | Pyrophospha-tase/phospho-diesterase (Upregulated) | It improves salt stress tolerance. | [58] |
20 | Micro RNA (ncRNA) (un-characterized) (miR8709c) (Upregulated) | It is suspected to be associated with cis-trans inter-conversion of cytokinin zeatin. Its overexpression led to decreased FAD and enhanced FMN and riboflavin contents, but its precise function is not known. | [48] |
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Karumanchi, A.R.; Sivan, P.; Kummari, D.; Rajasheker, G.; Kumar, S.A.; Reddy, P.S.; Suravajhala, P.; Podha, S.; Kishor, P.B.K. Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor. Plants 2023, 12, 2400. https://doi.org/10.3390/plants12132400
Karumanchi AR, Sivan P, Kummari D, Rajasheker G, Kumar SA, Reddy PS, Suravajhala P, Podha S, Kishor PBK. Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor. Plants. 2023; 12(13):2400. https://doi.org/10.3390/plants12132400
Chicago/Turabian StyleKarumanchi, Appa Rao, Pramod Sivan, Divya Kummari, G. Rajasheker, S. Anil Kumar, Palakolanu Sudhakar Reddy, Prashanth Suravajhala, Sudhakar Podha, and P. B. Kavi Kishor. 2023. "Root and Leaf Anatomy, Ion Accumulation, and Transcriptome Pattern under Salt Stress Conditions in Contrasting Genotypes of Sorghum bicolor" Plants 12, no. 13: 2400. https://doi.org/10.3390/plants12132400