A comparative transcriptomics and eQTL approach identifiesSlWD40as a tomato fruit ripening regulator

Abstract

Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors, recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and eQTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing (VIGS) analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital transcription factors including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2 and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared to the WT, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase (PSY), pectate lyase (PL), and branched chain amino transferase 2 (BCAT2), in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.

The time is ripe for eQTLs: Transcriptomic identification of a tomato fruit ripening regulator

“…Silencing of several candidate genes, including the transcriptional regulator SlWD40 (WD-40 repeats) , prevented fruit ripening. SlWD40 was previously identified as a target of RIN ( Fujisawa et al, 2013 ), and Zhu et al (2022) found SLWD40 expression increases during fruit maturation similarly to RIN expression patterns. The authors generated SlWD40 transgenic lines, and through visual analysis and quantification of chlorophyll and carotenoid levels they found that overexpression of SlWD40 accelerated ripening while RNAi-mediated knockdown of SlWD40 delayed ripening ( Figure 1B ).…”

“…In this issue of Plant Physiology , Zhu et al (2022) compare the distinct ripening processes in tomato ( Solanum lycopersicum ) and its wild relative Solanum pennellii . Tomato characteristically has red, fleshy fruit, while S. pennellii has much smaller, hard, green fruit ( Eshed and Zamir, 1995 ).…”

“…eQTL analyses use mapping populations to determine the genetic loci of expression differences between the introgressed species ( Ranjan et al, 2016 ). Zhu et al (2022) selected differentially expressed genes whose high expression in tomato fruit decreased specifically in ILs that contained S. pennellii genome segments in the candidate gene’s genome position—i.e. these genes’ high expression depended on the cis-regulatory sequence from the tomato genome ( Figure 1A ).…”

“…B, Representative fruit of wild-type (WT), transgenic SlWD40 RNAi-knockdown and SlWD40 overexpression lines at several different days post-anthesis (DPA). Figures adapted from Zhu et al (2022) .…”

“…Through an innovative, expression-based application of a remarkable historical mapping population, Zhu et al (2022) elucidated the evolutionarily diverged ripening programs in tomato and its wild relative S. pennellii . This work provides insight into key molecular processes associated with desirable fruit crop traits, such as the modification of fruit texture through cell wall remodeling and fruit flavor through drastic global changes in the metabolome of ripening fruit.…”