Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria × ananassa).

Fengli Zhao,Gang Li,Panpan Hu,Liangjie Li,Houcheng Zhou,Xia Zhao

doi:10.7717/peerj.4976

Fengli Zhao, Gang Li + Show 4 more

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https://doi.org/10.7717/peerj.4976

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Abstract

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.

Highlights

The octoploid strawberry (Fragaria × ananassa) is the dominant cultivatedspecie of its high yield and nutritional value, including vitamin C, sugar and organic acid, and anthocyanin contents (Tanaka et al, 2008; Giampieri et al, 2012; Chen et al, 2016b)
40.53% of unigenes were aligned to the non-redundant protein sequences (Nr) protein database with an evalue threshold of e-5
When our transcriptome data were compared with the transcriptome assembly results of octoploid strawberry in a previous study (Sanchez-Sevilla et al, 2017), fewer clean reads were retained in this data set (Table 1) due to the sequencing technology at that time and the experimental design, but more genes with FPKM ≥ 0.3 were identified than in the previous study (Sanchez-Sevilla et al, 2017) (Table S3)

Summary

Introduction

The octoploid strawberry (Fragaria × ananassa) is the dominant cultivatedspecie of its high yield and nutritional value, including vitamin C, sugar and organic acid, and anthocyanin contents (Tanaka et al, 2008; Giampieri et al, 2012; Chen et al, 2016b). The strawberry fruit development and ripening process involves intricate metabolic event and is divided into four distinct phases: the green fruit, white fruit, turning fruit and red fruit stages (Fait et al, 2008). In the green fruit stage, fruits undergo cell division and cell expansion. In the white fruit stage, fruit growth is nearly complete, and fruits begin to enter the maturation process. Fruit development enters the turning fruit stage, as indicated by slight coloration. During the red fruit stage, the characteristics of ripening such as color, aroma, taste and softening, increase rapidly along with a massive accumulation of pigments, amino acids, and organic acids, among other compounds. Strawberry is an ideal model plant for studying the fruit development and ripening process in non-climacteric fruit (Giovannoni, 2004; Zhang et al, 2011)

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