Transcriptome architecture reveals genetic networks of bolting regulation in spinach

Abolghasemi, Reza; Haghighi, Maryam; Etemadi, Nematollah; Wang, Shui; Soorni, Aboozar

doi:10.1186/s12870-021-02956-0

Cited by 17 publications

(10 citation statements)

References 72 publications

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“…Samples from 5 different seedlings were pooled together as one biological sample. Three biological replicates from each genotype were used for RNA extraction and the Real-Time PCR (qPCR) analysis according to the previous research [ 11 , 131 , 132 ]. In brief, total RNAs were extracted by the DENAzist column RNA isolation kit.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

et al. 2023

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Background Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. Results For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. Conclusion Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.

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Section: Methodsmentioning

confidence: 99%

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

et al. 2023

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“…Following the sequencing of the spinach genome, genome-wide association studies (GWAS) and RNA sequencing (RNA-seq) analyses were employed to pinpoint candidate genes responsible for governing crucial agronomic traits and other biological mechanisms ( 6 , 8 , 16–19 ). However, these analyses can yield extensive lists of genes associated with the traits, posing a challenge for the manual curation of gene functions.…”

Section: Introductionmentioning

confidence: 99%

Spinach genomes reveal migration history and candidate genes for important crop traits

Nguyen-Hoang,

Sandell,

Himmelbauer

et al. 2024

NAR Genomics and Bioinformatics

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Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.

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“…The interplay between FT and SOC1 is a critical regulatory mechanism that controls the timing of flowering in plants. Therefore, several environmental variables, in conjunction with endogenous genetic elements, influence the bolting and flowering of plants [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

GA signaling protein LsRGL1 interacts with the abscisic acid signaling-related gene LsWRKY70 to affect the bolting of leaf lettuce

Chen

Liu

Hao

et al. 2023

Horticulture Research

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A variety of endogenous hormone signals, developmental cues, and environmental stressors can trigger and promote leaf lettuce bolting. One such factor is gibberellin (GA), which has linked to bolting. However, the signaling pathways and the mechanisms that regulate the process have not been discussed in full detail. To clarify the potential role of GAs in leaf lettuce, significant enrichment of GA pathway genes was found by RNA-seq, among which the LsRGL1 gene was considered significant. Upon overexpression of LsRGL1, a noticeable inhibition of leaf lettuce bolting was observed, whereas its knockdown by RNA interference led to an increase in bolting. In situ hybridization analysis indicated a significant accumulation of LsRGL1 in the stem tip cells of overexpressing plants. The leaf lettuce plants stably expressing LsRGL1 were examined concerning differentially expressed genes through RNA-seq analysis, and the data indicated an enhanced enrichment of these genes in “plant hormone signal transduction” and “phenylpropanoid biosynthesis” pathways. Additionally, significant changes in LsWRKY70 gene expression were identified in COG functional classification. The results of the yeast one-hybrid, GUS, and BLI experiments showed that LsRGL1 proteins directly bind to the LsWRKY70 promoters. Silencing LsWRKY70 by VIGS can delay bolting, regulate the expression of endogenous hormones, ABA-linked genes, and flowering genes, as well as improve the nutritional quality of leaf lettuce. These results strongly associate the positive regulation of bolting with LsWRKY70 by identifying its vital functions in the GA-mediated signaling pathway. The data obtained in this research is invaluable for further experiments concerning the development and growth of leaf lettuce.

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Transcriptome architecture reveals genetic networks of bolting regulation in spinach

Cited by 17 publications

References 72 publications

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

Spinach genomes reveal migration history and candidate genes for important crop traits

GA signaling protein LsRGL1 interacts with the abscisic acid signaling-related gene LsWRKY70 to affect the bolting of leaf lettuce

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