scholarly journals Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245487
Author(s):  
Chris Gottschalk ◽  
Songwen Zhang ◽  
Phil Schwallier ◽  
Sean Rogers ◽  
Martin J. Bukovac ◽  
...  
Keyword(s):  
Vegetative Growth ◽  
Sequence Data ◽  
Expression Profiles ◽  
Fruit Trees ◽  
Floral Initiation ◽  
Flowering Genes ◽  
Repressive Effect ◽  
Genetic Mechanisms ◽  
Transcriptional Landscape ◽  
Fruit Load

Many apple cultivars are subject to biennial fluctuations in flowering and fruiting. It is believed that this phenomenon is caused by a repressive effect of developing fruit on the initiation of flowers in the apex of proximal bourse shoots. However, the genetic pathways of floral initiation are incompletely described in apple, and the biological nature of floral repression by fruit is currently unknown. In this study, we characterized the transcriptional landscape of bourse shoot apices in the biennial cultivar, ’Honeycrisp’, during the period of floral initiation, in trees bearing a high fruit load and in trees without fruit. Trees with high fruit load produced almost exclusively vegetative growth in the subsequent year, whereas the trees without fruit produced flowers on the majority of the potential flowering nodes. Using RNA-based sequence data, we documented gene expression at high resolution, identifying >11,000 transcripts that had not been previously annotated, and characterized expression profiles associated with vegetative growth and flowering. We also conducted a census of genes related to known flowering genes, organized the phylogenetic and syntenic relationships of these genes, and compared expression among homeologs. Several genes closely related to AP1, FT, FUL, LFY, and SPLs were more strongly expressed in apices from non-bearing, floral-determined trees, consistent with their presumed floral-promotive roles. In contrast, a homolog of TFL1 exhibited strong and persistent up-regulation only in apices from bearing, vegetative-determined trees, suggesting a role in floral repression. Additionally, we identified four GIBBERELLIC ACID (GA) 2 OXIDASE genes that were expressed to relatively high levels in apices from bearing trees. These results define the flowering-related transcriptional landscape in apple, and strongly support previous studies implicating both gibberellins and TFL1 as key components in repression of flowering by fruit.

scholarly journals Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 439
Author(s):  
Avinash Chandra Rai ◽  
Eyal Halon ◽  
Hanita Zemach ◽  
Tali Zviran ◽  
Isaac Sisai ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Mangifera Indica ◽  
Ectopic Expression ◽  
Fruit Trees ◽  
Floral Organ ◽  
Cytosolic Ph ◽  
Early Increase ◽  
Encoding Genes ◽  
Fruitlet Abscission

In mango (Mangifera indica L.), fruitlet abscission limits productivity. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide acts as a key component controlling abscission events in Arabidopsis. IDA-like peptides may assume similar roles in fruit trees. In this study, we isolated two mango IDA-like encoding-genes, MiIDA1 and MiIDA2. We used mango fruitlet-bearing explants and fruitlet-bearing trees, in which fruitlets abscission was induced using ethephon. We monitored the expression profiles of the two MiIDA-like genes in control and treated fruitlet abscission zones (AZs). In both systems, qRT-PCR showed that, within 24 h, both MiIDA-like genes were induced by ethephon, and that changes in their expression profiles were associated with upregulation of different ethylene signaling-related and cell-wall modifying genes. Furthermore, ectopic expression of both genes in Arabidopsis promoted floral-organ abscission, and was accompanied by an early increase in the cytosolic pH of floral AZ cells—a phenomenon known to be linked with abscission, and by activation of cell separation in vestigial AZs. Finally, overexpression of both genes in an Atida mutant restored its abscission ability. Our results suggest roles for MiIDA1 and MiIDA2 in affecting mango fruitlet abscission. Based on our results, we propose new possible modes of action for IDA-like proteins in regulating organ abscission.

scholarly journals Vegetative and Reproductive Response to Fruit Load in Two Jojoba (Simmondsia chinensis) Cultivars

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 889
Author(s):  
Aviad Perry ◽  
Noemi Tel-Zur ◽  
Arnon Dag
Keyword(s):  
Vegetative Growth ◽  
Accumulation Rate ◽  
Dry Weight ◽  
High Yield ◽  
Lower Amount ◽  
Simmondsia Chinensis ◽  
Alternate Bearing ◽  
Fruit Removal ◽  
Growing Period ◽  
Fruit Load

Jojoba (Simmondsia chinensis) is a wax crop cultivated mainly in arid and semi-arid regions. This crop has been described as an alternate-bearing plant, meaning that it has a high-yield year (“on-year”) followed by a low-yield year (“off-year”). We investigated the effect of fruit load on jojoba’s vegetative and reproductive development. For two consecutive years, we experimented with two high-yielding cultivars—Benzioni and Hazerim—which had opposite fruit loads, i.e., one was under an on-year load, while the other was under an off-year load simultaneously. We found that removing the developing fruit from the shoot during an off-year promotes further vegetative growth in the same year, whereas in an on-year, this action has no effect. Moreover, after fruit removal in an on-year, there was a delay in vegetative growth renewal in the consecutive year, suggesting that the beginning of the growing period is dependent on the previous year’s yield load. We found that seed development in the 2018 season started a month earlier than in the 2017 season in both cultivars, regardless of fruit load. This early development was associated with higher wax content in the seeds. Hence, the wax accumulation rate, as a percentage of dry weight, was affected by year and not by fruit load. However, on-year seeds stopped growing earlier than off-year seeds, resulting in smaller seeds and an overall lower amount of wax per seed.

Robust Metabolic Transcriptional Components in 34,494 Patient-Derived Samples and Cell Lines

2021 ◽  
Author(s):  
Vincent Christiaan Leeuwenburgh ◽  
Carlos G. Urzúa-Traslaviña ◽  
Arkajyoti Bhattacharya ◽  
Marthe T.C. Walvoort ◽  
Mathilde Jalving ◽  
...  
Keyword(s):  
Cell Lines ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Metabolic Processes ◽  
Gene Sets ◽  
Transcriptional Changes ◽  
Cancer Tissues ◽  
Tumor Biopsies ◽  
Transcriptional Landscape

Abstract Background: Patient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus Independent Component Analyses (c-ICA) can capture statistically independent transcriptional footprints, of both subtle and more pronounced metabolic processes. Methods: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs were determined in all samples to create a metabolic transcriptional landscape. Results: A set of 555 mTCs were identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal ( www.themetaboliclandscapeofcancer.com ). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

scholarly journals EPEN-10. UNRAVELLING THE TUMOR IMMUNE MICROENVIRONMENT OF POSTERIOR FOSSA A EPENDYMOMAS ON RNA AND PROTEIN EXPRESSION LEVELS

2021 ◽  
Vol 23 (Supplement_1) ◽  
pp. i15-i15
Author(s):  
Fenna F. Feenstra ◽  
Friso Calkoen ◽  
Johan M Kros ◽  
Lennart Kester ◽  
Mariëtte Kranendonk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Expression ◽  
Posterior Fossa ◽  
Antigen Processing ◽  
Sequence Data ◽  
Expression Profiles ◽  
Immune Microenvironment ◽  
Expression Levels ◽  
Tumor Immune Microenvironment ◽  
Immune Related Genes

Abstract Background Ependymomas account for 8–10% of pediatric brain tumors, and the standard therapy of surgery and radiation has not changed for the past two decades. Characterization of the tumor immune microenvironment (TIME) is of great importance in order to find better therapies. However, the TIME of ependymomas is still not defined. In this retrospective observational study we aimed to unravel the TIME of ependymomas at mRNA and protein expression levels. Methods Ependymoma samples from two locations were selected: Posterior Fossa (PF-A, n=8), and supratentorial (ST, n=5). Targeted gene expression profile using the PanCancer immune profile panel of NanoString technology was performed. Data were analyzed using the nSolver software. In addition, 8 samples were subjected to RNA bulk sequencing, and the sequenced data were connected to the expression data of the same samples. To validate some of the findings, immunohistochemistry was performed. Results Unsupervised hierarchical clustering showed that PF-A ependymomas can be divided into two groups based on the expression of their immune-related genes. PF-A that showed high immune-expression clustered closely to the ST ependymomas. Significant expressions of genes related to “antigen-processing” and “adhesion” pathways were found in the immune-active groups. On the contrary, the PF-A that had low expressions of immune-related genes showed a high expression of BMI1 that has a prognostic and therapeutic value. Connecting gene expression to bulk sequence data validated the findings. In addition, immunohistochemical analysis confirmed that protein expression for some of the findings. Conclusion The TIME varies in ependymomas based on the location of the tumor. Moreover, the immune-related expression profiles indicated that PF-A ependymomas can be divided into two groups: immune-active and immune-not active PF-A. The prognostic and therapeutic values of the immune activity of PF-A should be further studied.

scholarly journals Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

2018 ◽  
Author(s):  
Jun Zheng ◽  
Erliang Zeng ◽  
Yicong Du ◽  
Cheng He ◽  
Ying Hu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Sequence Data ◽  
Expression Profiles ◽  
Regulatory Role ◽  
Chromatin Modifications ◽  
Small Nuclear Rnas ◽  
Genome Copy Number ◽  
Rna Expression Profiling ◽  
Genomic Regions

AbstractSmall RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.

Sign in / Sign up

Export Citation Format

Share Document