Differentially expressed genes identified by RNA-Seq during fruit set.

<p>The number of up- and down-regulated DEGs in ovaries at 4DPAP, 4DPAT and 4DPGT with respect to (A) 2DAA and (B) 6DPE, respectively during fruit set.</p

DEGs associated with parthenocarpy induced by auxin and GA.

<p>DEGs associated with parthenocarpy induced by auxin and GA.</p

Ovaries collection for analyzing transcriptomic changes underlying fruit set in tomato.

<p>Flowers were emasculated at 2 days before anthesis (2DAA), followed by different treatments on the day just equivalent to anthesis. Then, the uniform ovaries were collected 4 days after pollination (4DPAP), 2,4-dichlorophenoxyaceticacid (2,4-D) (4DPAT) and gibberellin application (4DPGT), while the untreated ovaries were considered as control (6DPE).</p

Model for regulatory events underlying fruit set mainly mediated by auxin and gibberellin.

<p>(A) After pollination, the increase of auxin and GA biosynthesis and response will trigger fruit initiation. And the elevated auxin and GA would inhibit ethylene biosynthesis and response which negatively regulate fruit set. Auxin stimulates GA biosynthesis gene <i>GA20ox1</i> via down-regulating <i>KNOX</i> (<i>LeT6</i>, <i>LeT12</i>) in partially, subsequently influences GA response by regulating <i>GID1</i> and <i>GRAS</i>. Some Aux/IAAs may be degraded by the 26S proteasome and in turn, the transcripts are increased via feedback regulation to fine-tune auxin response. Some ARFs (<i>ARF4</i>, <i>ARF9</i>) are up-regulated which could promote auxin signaling cascades. In addition, auxin response may be mediated by GA via down-regulation of <i>IAA9</i> and <i>ARF2</i> during fruit set. Accordingly, events that the activation of carbohydrate metabolism, cell division and expansion as well as the down-regulation of <i>MADS-box</i> occur to promote fruit set process. (B) After 2, 4-D application, <i>KNAT3</i> displayed down-regulation, which would interact with BLH1, thus negatively regulating parthenocarpy. In the present of GA, the transcripts of <i>DELLA</i> and <i>GID2</i> are regulated via feedback to fine-tune GA response. GA application decreased the transcripts of <i>IAA9</i> and <i>ARF8B</i>, and then led to parthenocarpy. Moreover, other factors such as <i>GRAS</i>, <i>AGL66</i> and <i>AGO10</i>, which are down-regulated after hormone application, also seem to have a regulatory role in parthenocarpy. The red and green frame shows up- and down-regulation, respectively. The red line arrow and the green line behind represent positive and negative regulation, respectively. The regular arc line represents feedback regulation. Dashed line shows suggested interactions.</p

Venn diagram of DEGs associated with fruit set.

<p>The common and distinct DEGs during the three types of fruit set with respect to two controls, 2DAA (A) and 6DPE (B), respectively. (C) The DEGs common to all the three types of fruit set with respect to both controls. C-2DAA and C-6DPE represent common DEGs with respect to 2DAA and 6DPE, respectively.</p

DEGs associated with transcription factors.

<p>(A) Cluster analysis of DEGs associated with transcription factors. (B) Pie charts show the up- and down-regulated TFs during fruit set.</p

Expression of genes associated with auxin and GA signaling in ovaries after pollination and 2,4-D/GA₃ treatments.

<p>Expression of genes associated with auxin and GA signaling in ovaries after pollination and 2,4-D/GA₃ treatments.</p

DEGs involved in MADS-box and homeobox family during fruit set.

<p>The fold-change value is represented by the Log2 Ratio.</p><p>DEGs involved in MADS-box and homeobox family during fruit set.</p

DEGs associated with hormone biosynthesis and signaling.

<p>(A) Cluster analysis of DEGs associated with hormone biosynthesis and signaling. (B) Pie charts show the percentages of up- and down-regulated DEGs involved in hormone biosynthesis and signaling during fruit set.</p

Summary of the RNA-Seq data in ovaries during fruit set.

<p>Summary of the RNA-Seq data in ovaries during fruit set.</p