Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum)

Abstract

Fruit set involves the developmental transition of an unfertilized quiescent ovary in the pistil into a fruit. While fruit set is known to involve the activation of signals (including various plant hormones) in the ovary, many biological aspects of this process remain elusive. To further expand our understanding of this process, we identified genes that are specifically expressed in tomato (Solanum lycopersicum L.) pistils during fruit set through comprehensive RNA-seq-based transcriptome analysis using 17 different tissues including pistils at six different developmental stages. First, we identified 532 candidate genes that are preferentially expressed in the pistil based on their tissue-specific expression profiles. Next, we compared our RNA-seq data with publically available transcriptome data, further refining the candidate genes that are specifically expressed within the pistil. As a result, 108 pistil-specific genes were identified, including several transcription factor genes that function in reproductive development. We also identified genes encoding hormone-like peptides with a secretion signal and cysteine-rich residues that are conserved among some Solanaceae species, suggesting that peptide hormones may function as signaling molecules during fruit set initiation. This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set.

Evaluation of internal control genes for quantitative realtime PCR analyses for studying fruit development of dwarf tomato cultivar ‘Micro-Tom’

“…In pistils, the expression level of SlYABBY2a was shown to elevate, and reached the highest at 7-day-after-flowering stage. Its expression was maintained in mature green fruit stage, and decreased in red fruit stage (Ezura et al 2017). In comparison to SlYABBY2a, SlYABBY1a is predominantly expressed in floral organs.…”

“…In comparison to SlYABBY2a, SlYABBY1a is predominantly expressed in floral organs. The expression of SlYABBY1a in pistils was kept high before flowering, and then decreased after anthesis, whereas its expression level in the stamen was elevated after anthesis (Ezura et al 2017).…”

“…SlYABBY2a and SlYABBY1a show notable expression profiles in developing pistils and stamens. The RNA-seq analysis indicated that SlYABBY2a was expressed in wide range of floral organs including pistils, stamens, petals, and sepals, and its expression was also monitored in mature green and red fruits (Ezura et al 2017). In pistils, the expression level of SlYABBY2a was shown to elevate, and reached the highest at 7-day-after-flowering stage.…”

“…In Arabidopsis thaliana, INO and CRC are reported as the reproductive YABBYs expressed specifically in pistils (Alvarez and Smyth 1999;Villanueva et al 1999). Tomato has nine YABBY genes and eight of which (SlCRCa,SlCRCb,SlINO,SlYABBY1a,SlYABBY1b,SlYABBY2a,FAS/SlYABBY2b and SlYABBY5a) are expressed in floral organs (Ezura et al 2017;Huang et al 2013). SlYABBY2a and SlYABBY1a show notable expression profiles in developing pistils and stamens.…”

“…To compare the expression profiles normalized by different internal control gene candidates, we firstly performed relative quantitation of SlYABBY2a expressions. The RNA-seq analysis indicated that there were approximately 2-folds differences in SlYABBY2a expression between young pistils in 1-2 mm bud and mature green fruit (Ezura et al 2017). When we normalized the expression level of SlYABBY2a against EXPRESSED and TIP41, the stable internal control gene candidates, the fold-changes in SlYABBY2a expression from "4.5 mm pistil" to "mature green fruit" stages were 2.8-folds for SlYABBY2a/EXPRESSED ( Figure 4A) and 1.8-folds for SlYABBY2a/TIP41 ( Figure 4B).…”