Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca

Kang, Chunying; Darwish, Omar; Geretz, Aviva; Shahan, Rachel; Alkharouf, Nadim W.; Liu, Zhongchi

doi:10.1105/tpc.113.111732

Cited by 280 publications

(358 citation statements)

References 59 publications

Supporting

Mentioning

342

Contrasting

Order By: Relevance

“…A total of 22,046 genes, approximately two-thirds of the annotated genes in the tomato genome (Tomato Genome Consortium, 2012), were expressed in at least one sample (RPM $ 2; Supplemental Table S3), and more than half of the expressed genes (13,855) were present in all samples. There was little variation in the total number of genes represented in each tissue type, similar to other fruit transcriptomic studies (Kang et al, 2013).…”

Section: Rna-seq Analysis Of Microdissected Ovary and Fruit Tissuessupporting

confidence: 84%

“…Another gene set, cluster 5, indicates a spatial focus of hormone-related gene expression and suggests the coregulation of genes involved in controlling the levels of auxin in seed tissues. Up-regulation of GH3 family genes, putatively involved in auxin conjugation, in seeds relative to ovules has also been described in strawberry (Fragaria vesca; Kang et al, 2013) and may represent a mechanism for reducing active auxin concentration following fruit set.…”

Section: Gene Sets Associated With Seed Developmentmentioning

confidence: 99%

See 1 more Smart Citation

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

Pattison

Csukasi²,

Zheng³

et al. 2015

Plant Physiol.

131

142

View full text Add to dashboard Cite

Fruit formation and early development involve a range of physiological and morphological transformations of the various constituent tissues of the ovary. These developmental changes vary considerably according to tissue type, but molecular analyses at an organ-wide level inevitably obscure many tissue-specific phenomena. We used laser-capture microdissection coupled to high-throughput RNA sequencing to analyze the transcriptome of ovaries and fruit tissues of the wild tomato species Solanum pimpinellifolium. This laser-capture microdissection-high-throughput RNA sequencing approach allowed quantitative global profiling of gene expression at previously unobtainable levels of spatial resolution, revealing numerous contrasting transcriptome profiles and uncovering rare and cell type-specific transcripts. Coexpressed gene clusters linked specific tissues and stages to major transcriptional changes underlying the ovary-to-fruit transition and provided evidence of regulatory modules related to cell division, photosynthesis, and auxin transport in internal fruit tissues, together with parallel specialization of the pericarp transcriptome in stress responses and secondary metabolism. Analysis of transcription factor expression and regulatory motifs indicated putative gene regulatory modules that may regulate the development of different tissues and hormonal processes. Major alterations in the expression of hormone metabolic and signaling components illustrate the complex hormonal control underpinning fruit formation, with intricate spatiotemporal variations suggesting separate regulatory programs.

show abstract

Section: Rna-seq Analysis Of Microdissected Ovary and Fruit Tissuessupporting

confidence: 84%

Section: Gene Sets Associated With Seed Developmentmentioning

confidence: 99%

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

Pattison

Csukasi²,

Zheng³

et al. 2015

Plant Physiol.

131

142

View full text Add to dashboard Cite

show abstract

“…Therefore, we studied the mRNA levels of GA biosynthetic gene homologs Kang et al, 2013). We found opposite changes in the expression of several genes in Fv SOC1-OX and Fv SOC1-RNAi lines in the SD strawberry background.…”

Section: Fv Soc1 Activates Ga Biosynthesismentioning

confidence: 99%

TheFragaria vescaHomolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 Represses Flowering and Promotes Vegetative Growth

et al. 2013

View full text Add to dashboard Cite

In the annual long-day plant Arabidopsis thaliana, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) integrates endogenous and environmental signals to promote flowering. We analyzed the function and regulation of the SOC1 homolog (Fragaria vesca [Fv] SOC1) in the perennial short-day plant woodland strawberry (Fragaria vesca). We found that Fv SOC1 overexpression represses flower initiation under inductive short days, whereas its silencing causes continuous flowering in both short days and noninductive long days, similar to mutants in the floral repressor Fv TERMINAL FLOWER1 (Fv TFL1). Molecular analysis of these transgenic lines revealed that Fv SOC1 activates Fv TFL1 in the shoot apex, leading to the repression of flowering in strawberry. In parallel, Fv SOC1 regulates the differentiation of axillary buds to runners or axillary leaf rosettes, probably through the activation of gibberellin biosynthetic genes. We also demonstrated that Fv SOC1 is regulated by photoperiod and Fv FLOWERING LOCUS T1, suggesting that it plays a central role in the photoperiodic control of both generative and vegetative growth in strawberry. In conclusion, we propose that Fv SOC1 is a signaling hub that regulates yearly cycles of vegetative and generative development through separate genetic pathways.

show abstract

“…These carpels are apocarpous, meaning they do not fuse with one another. Molecular communication from the fertilized carpels to the subtending receptacle triggers the receptacle growth into the edible flesh fruit (Nitsch, 1950;Kang et al, 2013). Therefore, flower development in strawberry is intimately tied to strawberry (Fragaria spp.)…”

mentioning

confidence: 99%

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

et al. 2014

View full text Add to dashboard Cite

ORCID IDs: 0000-0002-6902-740X (C.K.); 0000-0001-9969-9381 (Z.L.).Flowers are reproductive organs and precursors to fruits and seeds. While the basic tenets of the ABCE model of flower development are conserved in angiosperms, different flowering plants exhibit different and sometimes unique characteristics. A distinct feature of strawberry (Fragaria spp.) flowers is the development of several hundreds of individual apocarpous (unfused) carpels. These individual carpels are arranged in a spiral pattern on the subtending stem tip, the receptacle. Therefore, the receptacle is an integral part of the strawberry flower and is of significant agronomic importance, being the precursor to strawberry fruit. Taking advantage of next-generation sequencing and laser capture microdissection, we generated different tissue-and stage-transcriptomic profiling of woodland strawberry (Fragaria vesca) flower development. Using pairwise comparisons and weighted gene coexpression network analysis, we identified modules of coexpressed genes and hub genes of tissue-specific networks. Of particular importance is the discovery of a developing receptacle-specific module exhibiting similar molecular features to those of young floral meristems. The strawberry homologs of a number of meristem regulators, including LOST MERISTEM and WUSCHEL, are identified as hub genes operating in the developing receptacle network. Furthermore, almost 25% of the F-box genes in the genome are transiently induced in developing anthers at the meiosis stage, indicating active protein degradation. Together, this work provides important insights into the molecular networks underlying strawberry's unique reproductive developmental processes. This extensive floral transcriptome data set is publicly available and can be readily queried at the project Web site, serving as an important genomic resource for the plant biology research community.

show abstract

Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca

Cited by 280 publications

References 59 publications

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

TheFragaria vescaHomolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 Represses Flowering and Promotes Vegetative Growth

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

Contact Info

Product

Resources

About