RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress

Field experiments quantified factors affecting root growth and anchorage by transplanted ‘Tifgreen’ (Cynodon dactylon (L.) Pers. × Cynodon transvaalensis Burtt Davy) sod, a globally important warm-season C4 turfgrass. Vertical force required to detach recently transplanted sod from underlying soil was the measure of root anchoring strength. In early spring, date of sod harvest and transplantation was important to root growth and anchorage measured 30 days after transplantation. Delaying sod harvest/transplantation by about a month after the end of the winter shoot dormancy period increased root anchoring strength 200% and root dry mass 640% during the 30 days after sodding. The strong effect of early-spring sodding date on root anchorage was related to cumulative thermal time before sod harvesting. Root anchoring strength was directly proportional to the number, but not mass, of roots produced by transplanted sod. In late spring, anchoring of sod to very firm traffic-compacted clay was 87% greater than to loamy sand, measured 14 days after sodding. N-P-K fertilisation did not affect late-spring sod anchorage to loamy sand soil, measured 18 days after sodding, but did enhance shoot density and colour. Sod root penetration into a silt loam soil was unaffected by an initially dry surface layer when sufficient irrigation was used. Overall, root anchorage by transplanted Tifgreen sod was similar to, or greater than, values reported for cool-season C3 turfgrasses in similar circumstances.

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Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20102391 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2391 ◽

Cited By ~ 3

Author(s):

Jiayang Xu ◽

Qiansi Chen ◽

Pingping Liu ◽

Wei Jia ◽

Zheng Chen ◽

...

Keyword(s):

Salinity Stress ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Crop Yields ◽

Antioxidant Activities ◽

Expression Patterns ◽

Differentially Expressed ◽

Alkali Stress ◽

Rna Seq ◽

Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

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RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth

Genes ◽

10.3390/genes10030213 ◽

2019 ◽

Vol 10 (3) ◽

pp. 213

Author(s):

Yu Xu ◽

Junjie Zou ◽

Hongyan Zheng ◽

Miaoyun Xu ◽

Xuefeng Zong ◽

...

Keyword(s):

Cell Wall ◽

Root Growth ◽

Primary Root ◽

Glutathione Metabolism ◽

Auxin Signaling ◽

Antioxidant Enzyme Activities ◽

Rna Seq ◽

Root Tips ◽

Primary Roots ◽

Quercetin Treatment

Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.

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