Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes

Parvathi, M. S.; Nataraja, K.; Reddy, Y. A. Nanja; Naika, Mahantesha Bn; Gowda, Malali

doi:10.1007/s12041-019-1087-0

Cited by 49 publications

(14 citation statements)

References 40 publications

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“…The drought-associated enriched pathways primarily related to photosynthesis, response to water deprivation, translation, ribosome process and carbon metabolism. Previous studies have also found a similar pattern in the finger millet model system during abiotic stress [ 31 ]. In the proteomics data from this study, some key protein families were found which participate in the regulation of drought stress response.…”

Section: Discussionsupporting

confidence: 73%

Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Wang

et al. 2021

PLoS ONE

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Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

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Section: Discussionsupporting

confidence: 73%

Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Wang

et al. 2021

PLoS ONE

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“…Next-generation sequencing (NGS), particularly RNA-seq is a highly effective tool for generating high quality transcriptome sequence reads in several crops such as Eleusine coracana (Parvathi et al, 2019), oat (Avena sativa; (Kim et al, 2022), sugar cane (Saccharum officinarum; (Rosa-Santos et al, 2020) and Japanese carpet shell (Ruditapes philippinarum; (Nie et al, 2017). However, no transcriptome-based research has been published on finger millet in association with Al-tolerance.…”

Section: Discussionmentioning

confidence: 99%

“…In the present study, Altolerance based transcriptomic analysis generated 495 differentially expressed genes, of which 322 genes were significantly differentially expressed between Al-tolerant and Al-susceptible finger millet genotypes. These are a large number of genes although they are fewer than 6165 Al-stress responsive DEGs identified in sugarcane (Rosa-Santos et al, 2020), and 1790 drought responsive DEGs identified in finger millet (Parvathi et al, 2019) using RNA-seq. Due to the use of leaf tissue instead of root tissue for the transcriptome analyses, there may have been fewer significant DEGs identified in this study, indicating that leaves are less responsive to the effects of Al.…”

Section: Differentially Expressed Genesmentioning

confidence: 99%

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

et al. 2022

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Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.

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“…The data concluded that ascorbate-tartrate pathway could be a predominant player in oxalic acid biosynthesis, and this could be useful in studying the nutrients-antinutrients interactions in this crop. Parvathi et al [132] had analyzed the transcriptome dynamics in the leaf samples of finger millet exposed to drought stress. The study highlighted two candidate genes, CIPK31 and TAF6, that could be studied further to delineate their roles in conferring drought tolerance.…”

Section: Transcriptomicsmentioning

confidence: 99%

Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions

Vetriventhan

Azevedo

Upadhyaya

et al. 2020

Nucleus

117

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Current agricultural and food systems encourage research and development on major crops, neglecting regionally important minor crops. Small millets include a group of small-seeded cereal crops of the grass family Poaceae. This includes finger millet, foxtail millet, proso millet, barnyard millet, kodo millet, little millet, teff, fonio, job's tears, guinea millet, and browntop millet. Small millets are an excellent choice to supplement major staple foods for crop and dietary diversity because of their diverse adaptation on marginal lands, less water requirement, lesser susceptibility to stresses, and nutritional superiority compared to major cereal staples. Growing interest among consumers about healthy diets together with climate-resilient features of small millets underline the necessity of directing more research and development towards these crops. Except for finger millet and foxtail millet, and to some extent proso millet and teff, other small millets have received minimal research attention in terms of development of genetic and genomic resources and breeding for yield enhancement. Considerable breeding efforts were made in finger millet and foxtail millet in India and China, respectively, proso millet in the United States of America, and teff in Ethiopia. So far, five genomes, namely foxtail millet, finger millet, proso millet, teff, and Japanese barnyard millet, have been sequenced, and genome of foxtail millet is the smallest (423-510 Mb) while the largest one is finger millet (1.5 Gb). Recent advances in phenotyping and genomics technologies, together with available germplasm diversity, could be utilized in small millets improvement. This review provides a comprehensive insight into the importance of small millets, the global status of their germplasm, diversity, promising germplasm resources, and breeding approaches (conventional and genomic approaches) to accelerate climate-resilient and nutrient-dense small millets for sustainable agriculture, environment, and healthy food systems.

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Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes

Cited by 49 publications

References 40 publications

Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions

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