<scp>RNA</scp>‐Seq of <i>Agropyron mongolicum</i> Keng in response to drought stress

Ma, Yanhong; Yu, Xiaoxia; Zhuo, Yu; Sun, Fengcheng; Li, Xiaodong; Li, Xiaolei

doi:10.1111/grs.12176

Cited by 5 publications

(7 citation statements)

References 67 publications

(72 reference statements)

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“…In total, 262,427,357 high-quality sequencing reads were assembled into 76,601 contigs, and a total of 72,474 transcripts were generated by the program CD-HIT-EST (Tables 1 and S2 ). The average length of 803 bp and N50 of 1,377 bp are comparable to the results from other de novo transcriptome assemblies [ 24 – 29 ]. BLASTx results were obtained for 45.6% transcripts against S .…”

Section: Discussionsupporting

confidence: 79%

“…Abscisic acid is known as a major hormone playing crucial roles in abiotic stress responses by inducing stomatal closure and regulating gene expression [ 52 ]. Previous studies have shown that many genes involved in ABA biosynthesis and signaling were upregulated under water deficit [ 28 , 29 , 53 , 54 ]. A rate-limiting enzyme in ABA biosynthesis was induced and its expression level was gradually increased as dehydration prolonged in pear [ 4 ].…”

Section: Discussionmentioning

confidence: 99%

“…Several TFs have crucial roles in regulating downstream gene expression, and many TFs have been identified in transcriptome analysis under abiotic stresses [ 28 , 29 , 63 ]. The members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP TF families were differentially expressed as found in other studies [ 7 , 28 , 64 ].…”

Section: Discussionmentioning

confidence: 99%

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Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing

et al. 2021

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Water deficit limits plant growth and development, resulting in quality loss of horticultural crops. However, there is limited information on gene regulation and signaling pathways related to water deficit stress response at multiple time points. The objective of this research was to investigate global gene expression patterns under water deficit stress to provide an insight into how petunia (Petunia ×hybrida ‘Mitchell Diploid’) responded in the process of stress. Nine-week-old petunias were irrigated daily or placed under water stress by withholding water. Stressed plants reduced stomatal conductance after five days of water deficit, indicating they perceived stress and initiated stress response mechanisms. To analyze transcriptomic changes at the early stage of water deficit, leaf tissue samples were collected 1, 3, and 5 days after water was withheld for RNA sequencing. Under water deficit stress, 154, 3611, and 980 genes were upregulated and 41, 2806, and 253 genes were downregulated on day 1, 3, and 5, respectively. Gene Ontology analysis revealed that redox homeostasis processes through sulfur and glutathione metabolism pathways, and hormone signal transduction, especially abscisic acid and ethylene, were enriched under water deficit stress. Thirty-four transcription factor families were identified, including members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP families, and TFs in AP2/ERF family was the most abundant in petunia. Interestingly, only one member of GRFs was upregulated on day 1, while most of TFs were differentially expressed on day 3 and/or 5. The transcriptome data from this research will provide valuable molecular resources for understanding the early stages of water stress-responsive networks as well as engineering petunia with enhanced water stress tolerance.

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Section: Discussionsupporting

confidence: 79%

Section: Discussionmentioning

confidence: 99%

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Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing

et al. 2021

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“…However, the results reported here do indicate that genetic variation between the three genotypes has significant and measurable impacts on patterns of gene expression in response to water stress. The fact that such variation should exist is not surprising and there are numerous examples of gene-expression studies and QTL analyses for different aspects of drought tolerance in forage and other grasses (e.g., Alm et al, 2011 ; Merewitz et al, 2014 ; Baldoni et al, 2016 ; Jiang et al, 2017 ; Liang et al, 2017 ; Zhu et al, 2017 ; Cheruiyot et al, 2018 ; Hu et al, 2018 ; Ji et al, 2018 ; Kumar et al, 2018 ; Ling et al, 2018 ; Ma et al, 2018 ; Chaichi et al, 2019 ; Dinkins et al, 2019 ; Fradera-Sola et al, 2019 ). However, in the context of Brachiaria breeding, these genotypes were selected from a cultivar development program and the results suggest selectable variation with measurable impacts.…”

Section: Discussionmentioning

confidence: 99%

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes

et al. 2021

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Brachiaria (Trin.) Griseb. (syn. Urochloa P. Beauv.) is a C4 grass genus belonging to the Panicoideae. Native to Africa, these grasses are now widely grown as forages in tropical areas worldwide and are the subject of intensive breeding, particularly in South America. Tolerance to abiotic stresses such as aluminum and drought are major breeding objectives. In this study, we present the transcriptomic profiling of leaves and roots of three Brachiaria interspecific hybrid genotypes with the onset of water stress, Br12/3659-17 (gt-17), Br12/2360-9 (gt-9), and Br12/3868-18 (gt-18), previously characterized as having good, intermediate and poor tolerance to drought, respectively, in germplasm evaluation programs. RNA was extracted from leaf and root tissue of plants at estimated growing medium water contents (EWC) of 35, 15, and 5%. Differentially expressed genes (DEGs) were compared between different EWCs, 35/15, 15/5, and 35/5 using DESeq2. Overall, the proportions of DEGs enriched in all three genotypes varied in a genotype-dependent manner in relation to EWC comparison, with intermediate and sensitive gt-9 and gt-18 being more similar to each other than to drought tolerant gt-17. More specifically, GO terms relating to carbohydrate and cell wall metabolism in the leaves were enriched by up-regulated DEGs in gt-9 and gt-18, but by down-regulated DEGs in gt-17. Across all genotypes, analysis of DEG enzyme activities indicated an excess of down-regulated putative apoplastic peroxidases in the roots as water stress increased. This suggests that changes in root cell-wall architecture may be an important component of the response to water stress in Brachiaria.

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“…MwAP2/EREBP, isolated through RT-PCR and RACE techniques, demonstrated its involvement in drought-tolerance in A. mongolicum Keng [8]. Recently, Ma and associates have identified and evaluated drought-responsive RNAs through transcriptome analysis in A. mongolicum [9]. However, to date to the best of our knowledge, no experimentally or computationally identified drought-responsive miRNAs in A. mongolicum have been reported.…”

Section: Introductionmentioning

confidence: 99%

Functional Analysis of Three miRNAs in Agropyron mongolicum Keng under Drought Stress

et al. 2019

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Agropyron mongolicum Keng, a perennial diploid grass with high drought tolerance, belongs to the genus Agropyron, tribe Triticeae. It has made tremendous contributions toward reseeding natural pasture and seeding artificial grassland in China, especially in the arid and semi-arid area of northern China. As a wild relative of wheat, A. mongolicum is also a valuable resource for the genetic improvement of wheat crops. MicroRNAs are small non-coding RNA molecules ubiquitous in plants, which have been involved in responses to a wide variety of stresses including drought, salinity, chilling temperature. To date, little research has been done on drought-responsive miRNAs in A. mongolicum. In this study, two miRNA libraries of A. mongolicum under drought and normal conditions were constructed, and drought-responsive miRNAs were screened via Solexa high throughput sequencing and bioinformatic analysis. A total of 114 new miRNAs were identified in A. mongolicum including 53 conservative and 61 unconservative miRNAs, and 1393 target genes of 98 miRNAs were predicted. Seventeen miRNAs were found to be differentially expressed under drought stress, seven (amo-miR21, amo-miR62, amo-miR82, amo-miR5, amo-miR77, amo-miR44 and amo-miR17) of which were predicted to target on genes involved in drought tolerance. QRT-PCR analysis confirmed the expression changes of the seven drought related miRNAs in A. mongolicum. We then transformed the seven miRNAs into Arabidopsis thaliana plants, and three of them (amo-miR21, amo-miR5 and amo-miR62) were genetically stable. The three miRNAs demonstrated the same expression pattern in A. thaliana as that in A. mongolicum under drought stress. Findings from this study will better our understanding of the molecular mechanism of miRNAs in drought tolerance and promote molecular breeding of forage grass with improved adaption to drought.

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RNA‐Seq of Agropyron mongolicum Keng in response to drought stress

Cited by 5 publications

References 67 publications

Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing

Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes

Functional Analysis of Three miRNAs in Agropyron mongolicum Keng under Drought Stress

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