Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume).

Xiaopeng Ni,Zhihong Gao,Song Xue,Muhammad Khalil-Ur-Rehman,Wanxu Wang,Zhaojun Ni,Shahid Iqbal

doi:10.7717/peerj.4625

Abstract

The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.

Highlights

Japanese apricot (Prunus mume Sieb. et Zucc), an attractive fruit tree, originated from Southwest China and has been extensively cultivated in all of East Asia and Japan
We found some structural genes in the flavonoid pathway which named chalcone isomerase (CHI), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), flavanone 3-hydroxylase (F3H), flavonol 3′-hydroxylase (F3′ H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX) and UDP-glucose flavonoid3-O-glycosyltransferase (UFGT)
The vertical diameter of all red-skinned were more than all green-skinned cultivars, for ‘width and flank diameter,’ ‘QJM’ and all red-skinned cultivars were close in value and had no significant difference except two green-skinned cultivars, ‘Shinano koume’ (SKM)’ and ‘YLM.’ The weights of red-skinned cultivars ‘Ruantiao hongmei’ (RHM),’ ‘XZM’ and ‘zhugan’ (XZM) and ‘Zhonghong’ (ZHM)’ were recorded as 26.68, 24.22 and 30.17 g, respectively (Table 2)

Summary

Introduction

Japanese apricot (Prunus mume Sieb. et Zucc), an attractive fruit tree, originated from Southwest China and has been extensively cultivated in all of East Asia and Japan. Et Zucc), an attractive fruit tree, originated from Southwest China and has been extensively cultivated in all of East Asia and Japan. China, being the origin of Japanese apricot, is rich in good quality germplasm with an approximately 190 fruiting cultivars (Chu, 1999). How to cite this article Ni et al (2018), Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume). Fruit colour is an significant factor for determining fruit quality, which increases its value and attracts consumer’s attention (Gao, Han & Zhang, 2003). The whole genome of Japanese apricot was sequenced in 2012 (Zhang et al, 2012), laying the foundation for detailed study of important traits related to pigmentation, flowering time, dormancy and other commercially relevant aspects. Genome-based tools can be advanced to develop breeding efficiency and carry out other functional genomic research

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