Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

Abstract Background: Heat and drought are the serious threats to crop growth and development. As the sixth cereal crop in the world, pearl millet can be used not only for food and forage but also as bioenergy. Pearl millet has high tolerance under heat and drought. Given this, it is considered as an ideal crop for plant stress tolerance studying and can be used to excavate heat-resistant genes. Results: In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet for 48 hours under heat and drought stress. By taking an overview of previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2,792 transcription factors (TFs) and 1,223 transcriptional regulators (TRs). There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. By RNA sequencing, we identified 6,920 genes and 6,484 genes differentially expressed under heat stress and drought stress, respectively. Comparing DEGs under heat tolerance with DEGs under drought stress, we found that even in the same pathway, pearl millet would choose a different protein response. Conclusions: This information will provide new insights to study pearl millet at molecular and genetic level to understand the mechanisms involved in drought and heat stress tolerance.

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Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

10.21203/rs.3.rs-23605/v1 ◽

2020 ◽

Author(s):

Albert Maibam ◽

Sunil Nigombam ◽

Harinder Vishwakarma ◽

Showkat Ahmad Lone ◽

Kishor Gaikwad ◽

...

Keyword(s):

Heat Stress ◽

Pearl Millet ◽

Stress Responses ◽

Simple Sequence Repeats ◽

Pennisetum Glaucum ◽

Average Length ◽

Gc Content ◽

Functional Markers ◽

Sequencing Data ◽

Simple Sequence

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

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Assessment of pearl millet genotypes for drought stress tolerance at early and late seedling stages

Acta Physiologiae Plantarum ◽

10.1007/s11738-019-2831-z ◽

2019 ◽

Vol 41 (3) ◽

Author(s):

Radha Shivhare ◽

Charu Lata

Keyword(s):

Drought Stress ◽

Stress Tolerance ◽

Pearl Millet ◽

Drought Stress Tolerance

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Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize

Genes & Genomics ◽

10.1007/s13258-020-00962-4 ◽

2020 ◽

Vol 42 (8) ◽

pp. 937-955 ◽

Cited By ~ 2

Author(s):

Guo Liu ◽

Tinashe Zenda ◽

Songtao Liu ◽

Xuan Wang ◽

Hongyu Jin ◽

...

Keyword(s):

Drought Stress ◽

Stress Tolerance ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Drought Stress Tolerance

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Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress

PLoS ONE ◽

10.1371/journal.pone.0241966 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241966

Author(s):

Jessica Schmidt ◽

Melissa Garcia ◽

Chris Brien ◽

Priyanka Kalambettu ◽

Trevor Garnett ◽

...

Keyword(s):

Heat Stress ◽

Stress Tolerance ◽

Candidate Genes ◽

Abiotic Stress Tolerance ◽

Enrichment Analysis ◽

Genotyping By Sequencing ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Heat Stress Tolerance ◽

Drought And Heat Stress

Drought and heat stress constrain wheat (Triticum aestivum L.) yields globally. To identify putative mechanisms and candidate genes associated with combined drought and heat stress tolerance, we developed bread wheat near-isogenic lines (NILs) targeting a quantitative trait locus (QTL) on chromosome 6B which was previously associated with combined drought and heat stress tolerance in a diverse panel of wheats. Genotyping-by-sequencing was used to identify additional regions that segregated in allelic pairs between the recurrent and the introduced exotic parent, genome-wide. NILs were phenotyped in a gravimetric platform with precision irrigation and exposed to either drought or to combined drought and heat stress from three days after anthesis. An increase in grain weight in NILs carrying the exotic allele at 6B locus was associated with thicker, greener leaves, higher photosynthetic capacity and increased water use index after re-watering. RNA sequencing of developing grains at early and later stages of treatment revealed 75 genes that were differentially expressed between NILs across both treatments and timepoints. Differentially expressed genes coincided with the targeted QTL on chromosome 6B and regions of genetic segregation on chromosomes 1B and 7A. Pathway enrichment analysis showed the involvement of these genes in cell and gene regulation, metabolism of amino acids and transport of carbohydrates. The majority of these genes have not been characterized previously under drought or heat stress and they might serve as candidate genes for improved abiotic stress tolerance.

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Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress

Biotechnology for Biofuels ◽

10.1186/s13068-020-01810-z ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Peilin Chen ◽

Jing Chen ◽

Min Sun ◽

Haidong Yan ◽

Guangyan Feng ◽

...

Keyword(s):

Drought Stress ◽

Panicum Virgatum ◽

Differentially Expressed ◽

Drought Response ◽

Sequencing Data ◽

Short Term ◽

Microrna Sequencing ◽

Drought Resistant ◽

Effects Of Drought ◽

Physiological Tests

Abstract Background Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear. Result We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes. Conclusions This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding.

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The Foliar Application of Rice Phyllosphere Bacteria induces Drought-Stress Tolerance in Oryza sativa (L.)

Plants ◽

10.3390/plants10020387 ◽

2021 ◽

Vol 10 (2) ◽

pp. 387

Author(s):

Arun Kumar Devarajan ◽

Gomathy Muthukrishanan ◽

Jaak Truu ◽

Marika Truu ◽

Ivika Ostonen ◽

...

Keyword(s):

Drought Stress ◽

Stress Tolerance ◽

Foliar Application ◽

Oryza Sativa L ◽

Plant Stress ◽

Rice Cultivar ◽

Single Strain ◽

Rice Leaves ◽

Stress Related Genes ◽

Induced Tolerance

This study assessed the potential of Bacillus endophyticus PB3, Bacillus altitudinis PB46, and Bacillus megaterium PB50 to induce drought tolerance in a susceptible rice cultivar. The leaves of the potted rice plants subjected to physical drought stress for 10 days during the flowering stage were inoculated with single-strain suspensions. Control pots of irrigated and drought-stressed plants were included in the experiment for comparison. In all treatments, the plant stress-related physiochemical and biochemical changes were examined and the expression of six stress-responsive genes in rice leaves was evaluated. The colonization potential on the surface of the rice leaves and stomata of the most successful strain in terms of induced tolerance was confirmed in the gnotobiotic experiment. The plants sprayed with B. megaterium PB50 showed an elevated stress tolerance based on their higher relative water content and increased contents of total sugars, proteins, proline, phenolics, potassium, calcium, abscisic acid, and indole acetic acid, as well as a high expression of stress-related genes (LEA, RAB16B, HSP70, SNAC1, and bZIP23). Moreover, this strain improved yield parameters compared to other treatments and also confirmed its leaf surface colonization. Overall, this study indicates that the foliar application of B. megaterium PB50 can induce tolerance to drought stress in rice.

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Pyrophosphate modulates plant stress responses via SUMOylation

eLife ◽

10.7554/elife.44213 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 1

Author(s):

M Görkem Patir-Nebioglu ◽

Zaida Andrés ◽

Melanie Krebs ◽

Fabian Fink ◽

Katarzyna Drzewicka ◽

...

Keyword(s):

Heat Stress ◽

Stress Tolerance ◽

Stress Responses ◽

Plant Stress ◽

Mechanistic Explanation ◽

Stress Sensitivity ◽

Electrochemical Gradient ◽

Beneficial Effects ◽

Plant Stress Responses ◽

Low Levels

Pyrophosphate (PPi), a byproduct of macromolecule biosynthesis is maintained at low levels by soluble inorganic pyrophosphatases (sPPase) found in all eukaryotes. In plants, H+-pumping pyrophosphatases (H+-PPase) convert the substantial energy present in PPi into an electrochemical gradient. We show here, that both cold- and heat stress sensitivity of fugu5 mutants lacking the major H+-PPase isoform AVP1 is correlated with reduced SUMOylation. In addition, we show that increased PPi concentrations interfere with SUMOylation in yeast and we provide evidence that SUMO activating E1-enzymes are inhibited by micromolar concentrations of PPi in a non-competitive manner. Taken together, our results do not only provide a mechanistic explanation for the beneficial effects of AVP1 overexpression in plants but they also highlight PPi as an important integrator of metabolism and stress tolerance.

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