Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type

Abstract

Fruit ripening is a genetically programmed process. Transcription factors (TFs) play key roles in plant development and ripening by temporarily and spatially regulating the transcription of their target genes. In this study, a total of 159 TFs were identified from a spontaneous late-ripening mutant 'Fengwan' (C. sinensis L. Osbeck) sweet orange (MT) and its wild-type counterpart ('Fengjie 72–1', WT) along the ripening period via the Transcription Factor Prediction of PlantTFDB 3.0. Fifty-two differentially expressed TFs were identified between MT and WT; 92 and 120 differentially expressed TFs were identified in WT and MT, respectively. The Venn diagram analysis showed that 16 differentially expressed TFs were identified between MT and WT and during the ripening of WT and MT. These TFs were primarily assigned to the families of C2H2, Dof, bHLH, ERF, MYB, NAC and LBD. Particularly, the number of TFs of the ERF family was the greatest between MT and WT. According to the results of the WGCNA analysis, a weighted correlation network analysis tool, several important TFs correlated to abscisic acid (ABA), citric acid, fructose, glucose and sucrose were identified, such as RD26, NTT, GATA7 and MYB21/62/77. Hierarchical cluster analysis and the expression analysis conducted at five fruit ripening stages further validated the pivotal TFs that potentially function during orange fruit development and ripening.

Research Article Comparative analysis and expression of Dof genes in Citrus sinensis during fruit development

“…Pêra during the sampling period (maximum size and weight of 43 mm diameter and 36.5 g, respectively) was similar to the data obtained by Araujo (2010) for fruits of the cultivar Valencia. As expected, based on the expression of Dof transcripts in sweet orange and other fruit species (Cai et al, 2013;Feng et al, 2016, Wu et al, 2016b, the CsDof genes analyzed showed different mRNA levels during the early stages of sweet orange fruit development analyzed here ( Figure 6). Expression of CsDof17 transcripts was the highest at all stages analyzed, indicating that this gene probably plays an important role in the development of sweet orange fruits.…”

“…In the case of CsDof9, we detected a further decrease in its mRNA expression as fruit ripening progressed. It is interesting to mention that CsDof9 (orange1.1g025998m) was found to be significantly down-regulated in a bud late-ripening mutant in comparison with its wild-type counterpart (Fengjie 72-1') during a later sampling period (150 -240 DAF) than the one used in this work (Wu et al, 2016b).…”

“…Various studies have shown their great diversity both in terms of number and functions (Lijavetzky et al, 2003;Kushwaha et al, 2011;Cai et al, 2013;Ma et al, 2015, Zhang et al, 2017Cheng et al, 2018;Garcia et al, 2018). However, there are few reports on these transcription factors in fruit trees of economic interest (Wu et al, 2016b). Thus, in this work, we performed a comprehensive study of the Dof gene family in C. sinensis, including phylogenetic, chromosomal location, gene structure and expression profiling analyses at the early stages of fruit development.…”

“…This highly complex process involves important changes in the color, flavor, aroma, texture and nutritional content of the pulp, being controlled by transcriptional regulation networks that involve several transcription factors (Gapper et al, 2013;Seymour et al, 2013;Cherian et al, 2014). Therefore, over the last few years, more and more studies have been reported on the function of transcription factors families in sweet orange and other species during fruit ripening and development (Karlova et al, 2014;Wu et al, 2016b). Since gene expression patterns can provide valuable information on their function, we analyzed the transcriptional profile of 12 CsDof genes, reported as having higher normalized RPKM values in fruits relative to other tissues in a publicly available developmental transcriptome RNA-seq normalized RPKM dataset (Jiao et al, 2013), at the early stages of fruit development.…”

“…For example, it is known that during the development and ripening processes of citrus fruits, the transcriptional patterns of a large number of genes are specifically regulated by several transcription factors (TFs) (Wu et al, 2014). As such, being a highly controlled and complex biological process, fruit development in C. sinensis involve the participation of several families of TFs, such as WRKY, MADS, MYB, MYC, bHLH, HD-Zip and Dof (Ye et al, 2010;Wu et al, 2016b).…”