Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Growing Condition:
2.3. RNA Extraction and Illumina Sequencing
2.4. RNA-Seq Data Processing and Differential Gene Expression Analysis
2.5. Transcript Annotation, Gene Ontology and KEGG Pathway Analysis
2.6. Quantitative PCR Analysis
2.7. Statistical Analysis
3. Results
3.1. Comparative Analyses of Transcriptome Profiles during Grain Development
3.2. Identification of Differentially Expressed Transcripts (DETs) during Grain Development
3.3. Validation of Transcriptome Data
3.4. Functional Analysis of DEGs
3.5. Highly Up- and Down-Regulated Transcripts
3.6. Stage-Specific Expression Analysis of Highly Up- and Down-Regulated Genes
4. Discussion
4.1. RNA-Seq Analysis of Hexaploid Wheat and Its Diploid Progenitors
4.1.1. Transcriptome Data: Global View
4.1.2. Functional Analysis of DEGs
4.1.3. Highly Up- and Down-Regulated Transcripts
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Genotypes | Genome | Variety Name/Accession No. |
---|---|---|
Triticum monococcum | AA | AN104 |
Aegilops speltoides | BB | PN84 |
Aegilops tauschii | DD | PN95 |
Triticum aestivum | AABBDD | PBW343 |
Wheat Genotype | Total Raw Reads (in millions) | Processed Reads (in millions) | Alignment (%) | Expressed Transcripts |
---|---|---|---|---|
AA: T.monococcum (AN104&PKM1) | 55.63 | 50.81 | 45.73 | 79328 |
BB: Ae. speltoides (PN84&PKM2) | 55.23 | 49.55 | 54.48 | 113733 |
DD: Ae. tauschii (PN95&PKM3) | 68.13 | 61.98 | 64.64 | 90640 |
AABBDD: T. aestivum (PBW343&PKM5) | 103.31 | 93.19 | 71.44 | 121295 |
Comparison | ABD vs. A Up Down | ABD vs. B Up Down | ABD vs. D Up Down | |||
---|---|---|---|---|---|---|
Number of DETs | 7993 | 22052 | 8405 | 16354 | 14657 | 24616 |
Comparison | Molecular Function DEGs Up Down | Enriched GO Terms (Up-Regulated) at FDR<0.05 | Enriched GO (Gene Ontology) Terms (Down-Regulated) at FDR<0.05 | |
---|---|---|---|---|
ABD vs. A | 4549 | 2526 | 127 | 76 |
ABD vs. B | 4099 | 2507 | 95 | 52 |
ABD vs. D | 8296 | 9577 | 132 | 131 |
Enriched GO Terms Activity | ABD vs. A Up Down | ABD vs. B Up Down | ABD vs. D Up Down | |||
---|---|---|---|---|---|---|
Nutrient reservoir (GO:0045735) | 36 | 30 | 35 | 0 | 60 | 0 |
Transcription factor protein binding(GO:0000968) | 50 | 0 | 27 | 0 | 63 | 61 |
Catalytic activity (GO:0003824) | 2121 | 1228 | 1969 | 1186 | 3613 | 4563 |
Signal transducer (GO:0004871) | 42 | 42 | 55 | 26 | 122 | 116 |
Molecular function regulator (GO:0098772) | 91 | 56 | 142 | 56 | 187 | 230 |
Molecular transducer (GO:0060089) | 43 | 41 | 56 | 27 | 119 | 118 |
Carbohydrate transporter (GO:1901476) | 14 | 12 | 16 | 9 | 35 | 0 |
ABD vs. A Up Down | ABD vs. B Up Down | ABD vs. D Up Down | ||||
---|---|---|---|---|---|---|
Total number of DEGs | 1628 | 2625 | 1441 | 1617 | 2810 | 3014 |
Total Pathways involved | 209 | 303 | 167 | 258 | 398 | 317 |
Pathways | ABD vs. A | ABD vs. B | ABD vs. D |
---|---|---|---|
Pehnylpropanoid biosynthesis | 247 | 208 | 304 |
Starch and sucrose metabolism | 202 | 160 | 248 |
Oxidative Phosphorylation | 139 | 97 | 166 |
Galactose metabolism | 120 | 99 | 202 |
Ubiquinone and other terpenoid-quinone biosynthesis | 36 | 34 | 63 |
Cutin, suberine, and wax biosynthesis, glycerolipid metabolism | 47 | 31 | 42 |
Purine metabolism | 28 | 308 | 677 |
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Kaushik, M.; Rai, S.; Venkadesan, S.; Sinha, S.K.; Mohan, S.; Mandal, P.K. Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors. Genes 2020, 11, 509. https://doi.org/10.3390/genes11050509
Kaushik M, Rai S, Venkadesan S, Sinha SK, Mohan S, Mandal PK. Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors. Genes. 2020; 11(5):509. https://doi.org/10.3390/genes11050509
Chicago/Turabian StyleKaushik, Megha, Shubham Rai, Sureshkumar Venkadesan, Subodh Kumar Sinha, Sumedha Mohan, and Pranab Kumar Mandal. 2020. "Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors" Genes 11, no. 5: 509. https://doi.org/10.3390/genes11050509