Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour

Xiang Luo,Diguang Zhao,Lina Chen,Juan Niu,Haoxian Li,Da Cao,Hui Xue,Shangyin Cao,Fuhong Zhang

doi:10.1038/s41598-018-30088-3

Xiang Luo, Diguang Zhao + Show 7 more

Open Access

https://doi.org/10.1038/s41598-018-30088-3

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Abstract

Peel colour is an important factor affecting the marketability of pomegranate fruits. Therefore, elucidating the genetic mechanism of fruit peel colour development may be useful for breeding pomegranate cultivars with enhanced fruit peel colours. In this study, we combined an iTRAQ-based proteome-level analysis with an RNA sequencing-based transcriptome-level analysis to detect the proteins and genes related to fruit peel colour development in pomegranate. We analysed the ‘Tunisia’ (red fruit) and ‘White’ (white fruit) pomegranate cultivars at two stages of fruit development. A total of 27 differentially abundant proteins (increased abundance) and 54 differentially expressed genes (16 up-regulated and 38 down-regulated) were identified from our proteomics and transcriptomics data. The identified proteins and genes contribute to pomegranate fruit peel colour by participating in the biosynthesis of anthocyanins, stilbenoids, diarylheptanoids, gingerols, flavonoids, and phenylpropanoids. Several candidate proteins and genes corresponded to enzymes related to general reactions (PAL, 4CL, DFR, LDOX/ANS, CHS, and F3′5′H) and glycosylation (GT1 and UGAT) of compounds and pigments related to the colour of pomegranate fruit peel. Complementary proteome- and transcriptome-level analyses revealed a complex molecular network controlling fruit peel colour. The candidate genes identified in this study may be useful for the marker-based breeding of new pomegranate cultivars.

Highlights

Pomegranate originated in Central Asia, including Iran, Afghanistan, and Caucasia, and is one of the oldest cultivated fruits
There were nearly twice as many differentially abundant proteins (DAPs) in SP2_TP2 than in SP1 and TP1 (SP1_TP1). These results indicated that many proteins showed differential abundance between the two fruit development stages, with more DAPs at the second analysed stage
Elucidating the genetic mechanism of the regulation of fruit peel colour may be useful for breeders interested in generating new pomegranate cultivars with enhanced fruit colours

Summary

Introduction

Pomegranate originated in Central Asia, including Iran, Afghanistan, and Caucasia, and is one of the oldest cultivated fruits. Light induces the expression of a MYB transcription factor gene associated with anthocyanin biosynthesis, and its expression level is related to the final fruit skin colour[9]. The pear MYB transcription factor gene PcMYB10 (an ortholog of MdMYBa/MdMYB10, which controls the pigmentation of apple fruit skin) is not directly responsible for mediating fruit colour[9]. The isobaric tags for relative and absolute quantitation (iTRAQ) method represents a powerful option for analysing actively produced proteins. We combined iTRAQ-based proteomics and RNA sequencing-based transcriptomics analyses to identify the proteins and genes related to fruit peel colour during two fruit development stages in two pomegranate cultivars, ‘Tunisia’ and ‘White’. We comprehensively characterised the development of pomegranate fruit peel colour at the proteome and transcriptome levels. The identified candidate genes may be useful for molecular marker-assisted pomegranate breeding

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