The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine (Vitis vinifera subsp. sylvestris)

Daldoul, Samia; Hanzouli, Faouzia; Hamdi, Zohra; Chenenaoui, Synda; Wetzel, Thierry; Nick, Peter; Mliki, Ahmed; Gargouri, Mahmoud

doi:10.3389/fpls.2022.1077710

Cited by 11 publications

(5 citation statements)

References 93 publications

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“…Notably, when the 24 h of stress was compared against the 2 h of stress (R5–R4), it exhibited the highest number of up- and down-regulated transcripts. Likewise, transcriptomic analysis of salt-tolerant wild grapevine Tebaba roots throughout salinity depicted similar results commensurate with the accumulation of polyphenol content and enhancement of antioxidant enzymatic activities [ 34 ]. The longer the time under salinity (in the range of 24–48 h), the higher the changes at the molecular, metabolic, and physiological levels.…”

Section: Discussionmentioning

confidence: 86%

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock ‘Ruggeri’ throughout Salinity

Gajjar,

Ismail,

Islam

et al. 2024

Plants

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Salinity is one of the substantial threats to plant productivity and could be escorted by other stresses such as heat and drought. It impairs critical biological processes, such as photosynthesis, energy, and water/nutrient acquisition, ultimately leading to cell death when stress intensity becomes uncured. Therefore, plants deploy several proper processes to overcome such hostile circumstances. Grapevine is one of the most important crops worldwide that is relatively salt-tolerant and preferentially cultivated in hot and semi-arid areas. One of the most applicable strategies for sustainable viticulture is using salt-tolerant rootstock such as Ruggeri (RUG). The rootstock showed efficient capacity of photosynthesis, ROS detoxification, and carbohydrate accumulation under salinity. The current study utilized the transcriptome profiling approach to identify the molecular events of RUG throughout a regime of salt stress followed by a recovery procedure. The data showed progressive changes in the transcriptome profiling throughout salinity, underpinning the involvement of a large number of genes in transcriptional reprogramming during stress. Our results established a considerable enrichment of the biological process GO-terms related to salinity adaptation, such as signaling, hormones, photosynthesis, carbohydrates, and ROS homeostasis. Among the battery of molecular/cellular responses launched upon salinity, ROS homeostasis plays the central role of salt adaptation.

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Section: Discussionmentioning

confidence: 86%

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock ‘Ruggeri’ throughout Salinity

Gajjar,

Ismail,

Islam

et al. 2024

Plants

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“…Soluble sugar metabolism contributes to salt tolerance [13,14]. Starch and sucrose metabolism is involved in the salt stress response in plants [13,14,42,43].…”

Section: Discussionmentioning

confidence: 99%

“…Soluble sugar metabolism contributes to salt tolerance [13,14]. Starch and sucrose metabolism is involved in the salt stress response in plants [13,14,42,43]. For example, Chen et al [43] found that DEGs associated with phenylpropanoid biosynthesis and starch and sucrose metabolism were involved in the salt stress response in maize.…”

Section: Discussionmentioning

confidence: 99%

“…The study of tree transcriptomes enables us to obtain new insights into the genetic basis for the formation of tree traits [7,8,10]. The study of salt stress response in plants has become a hot topic, and transcriptomic analysis has identified metabolic pathways associated with salt stress, including plant hormone signal transduction [12], lignin synthesis [13], starch, and the sucrose metabolism pathway [14,15].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Analysis of the Salt-Treated Actinidia deliciosa (A. Chev.) C. F. Liang and A. R. Ferguson Plantlets

Zhuo

Zhao

et al. 2023

CIMB

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The area of saline land in the world is quite large, and there is broad room for its development and usage. ‘Xuxiang’ is an Actinidia deliciosa variety that is tolerant to salt and can be planted in an area of light-saline land, and has good comprehensive characteristics and high economic value. However, the molecular mechanism of salt tolerance is unknown at present. To understand the molecular mechanism of salt tolerance, the leaves of A. deliciosa ‘Xuxiang’ were used as explants to establish a sterile tissue culture system, and plantlets were obtained using this system. One percent concentration (w/v) of sodium chloride (NaCl) was employed to treat the young plantlets cultured in Murashige and Skoog (MS) medium, then RNA-seq was used for transcriptome analysis. The results showed that the genes related to salt stress in the phenylpropanoid biosynthesis pathway and the anabolism of trehalose and maltose pathways were up-regulated; however, those genes in the plant hormone signal transduction and metabolic pathways of starch, sucrose, glucose, and fructose were down-regulated after salt treatment. The expression levels of ten genes that were up-regulated and down-regulated in these pathways were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. The salt tolerance of A. deliciosa might be related to the expression level changes in the genes in the pathways of plant hormone signal transduction, phenylpropanoid biosynthesis, and starch, sucrose, glucose, and fructose metabolism. The increased expression levels of the genes encoding alpha-trehalose-phosphate synthase, trehalose-phosphatase, alpha-amylase, beta-amylase, feruloyl-CoA 6-hydroxylase, ferulate 5-hydroxylase, and coniferyl-alcohol glucosyl transferase might be vital to the salt stress response of the young A. deliciosa plants.

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“…Before running MAKER, RNA-seq reads from diverse tissues in grapevine and protein sequences from related species were used to provide initial support for gene models. To do so, RNA-seq samples from previous studies [37][38][39][40][41][42] were downloaded from the NCBI Sequence Read Archive (SRA) using fasterq-dump v2.10.7 from the sra-toolkit [43] (see Supplementary Table S2 for the SRA IDs of the specific files used). Trimmomatic v0.39 [26] was used to trim adapters from Illumina RNAseq reads with the flags: --phred33 and ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10.…”

Section: Dakapo Genome Annotationmentioning

confidence: 99%

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

Ritter,

Cochetel,

Minio

et al. 2024

Preprint

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Background Teinturier grapevine varieties were first described in the 16th century and have persisted due to their deep pigmentation. Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. Findings For Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp with an N50 scaffold length of 25.6 Mbp and a BUSCO score of 98.0%. A combination approach of de novo annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. The diploid genome has an N50 scaffold length of 24.9 Mbp and a BUSCO score of 98.7%, and both haplotype-specific genomes are of similar quality. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. Conclusions The Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.

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The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine (Vitis vinifera subsp. sylvestris)

Cited by 11 publications

References 93 publications

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock ‘Ruggeri’ throughout Salinity

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock ‘Ruggeri’ throughout Salinity

Transcriptome Analysis of the Salt-Treated Actinidia deliciosa (A. Chev.) C. F. Liang and A. R. Ferguson Plantlets

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

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