scholarly journals Exploring PIF4 's contribution to early flowering in plants under daily variable temperature and its tissue‐specific flowering gene network

Plant Direct ◽  
2021 ◽  
Author(s):  
Jutapak Jenkitkonchai ◽  
Poppy Marriott ◽  
Weibing Yang ◽  
Napaporn Sriden ◽  
Jae‐Hoon Jung ◽  
...  
Keyword(s):  
Gene Network ◽  
Variable Temperature ◽  
Early Flowering ◽  
Tissue Specific

scholarly journals Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elise Bizouerne ◽  
Julia Buitink ◽  
Benoît Ly Vu ◽  
Joseph Ly Vu ◽  
Eddi Esteban ◽  
...  
Keyword(s):  
Desiccation Tolerance ◽  
Genome Stability ◽  
Gene Network ◽  
Regulatory Networks ◽  
Progressive Increase ◽  
Tissue Level ◽  
Seed Maturation ◽  
Tomato Seed ◽  
Seed Vigour ◽  
Tissue Specific

Abstract Background During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. Results During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1–2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. Conclusion The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.

scholarly journals Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

2020 ◽  
Author(s):  
Elise Bizouerne ◽  
Julia Buitink ◽  
Benoît Ly-Vu ◽  
Joseph Ly-Vu ◽  
Eddi Esteban ◽  
...  
Keyword(s):  
Desiccation Tolerance ◽  
Genome Stability ◽  
Gene Network ◽  
Regulatory Networks ◽  
Progressive Increase ◽  
Tissue Level ◽  
Seed Maturation ◽  
Tomato Seed ◽  
Seed Vigour ◽  
Tissue Specific

Abstract Background During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. Results During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. Conclusion The spatio-temporal co-expression atlas of seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.

scholarly journals Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

2021 ◽  
Author(s):  
Elise Bizouerne ◽  
Julia Buitink ◽  
Benoît Ly-Vu ◽  
Joseph Ly-Vu ◽  
Eddi Esteban ◽  
...  
Keyword(s):  
Desiccation Tolerance ◽  
Genome Stability ◽  
Gene Network ◽  
Regulatory Networks ◽  
Progressive Increase ◽  
Tissue Level ◽  
Seed Maturation ◽  
Tomato Seed ◽  
Seed Vigour ◽  
Tissue Specific

Abstract Background During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy.Results During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. Conclusion The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.

Expression of sunflower cytochrome c mRNA is tissue-specific and controlled by nitrate and light

1997 ◽  
Vol 99 (2) ◽  
pp. 342-347 ◽  
Author(s):  
Silvina A. Felitti ◽  
Raquel L. Chan ◽  
Gabriela Gago ◽  
Estela M. Valle ◽  
Daniel H. Gonzalez
Keyword(s):  
Cytochrome C ◽  
Tissue Specific

Dissecting the meiotic gene network in female embryonic germ cells

2014 ◽  
Author(s):  
Emilie Abby ◽  
Sophie Tourpin ◽  
Marie-Justine Guerquin ◽  
Bouffant Ronan Le ◽  
Rene Habert ◽  
...  
Keyword(s):  
Germ Cells ◽  
Gene Network ◽  
Embryonic Germ Cells ◽  
Meiotic Gene
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