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

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.

Genome‐wide analysis of PmTCP4 transcription factor binding sites by ChIP‐Seq during pistil abortion in Japanese apricot

“…et. Zucc) is an important fruit and ornamental plant with great economic importance as a preserved or value-added product (Ni et al, 2018). (Wollmann, Mica, Todesco, Long, & Weigel, 2010).…”

“…et. Zucc) is an important fruit and ornamental plant with great economic importance as a preserved or value‐added product (Ni et al., 2018). Flower development is an important stage of plant growth and development and is affected by various environmental and genetic factors.…”

“…Japanese apricot belongs to the family Rosaceae and is a prominent fruit tree of great importance as an ornamental plant due to its eye‐catching red color (Ni et al., 2018; Zhang et al., 2012). The problem of pistil abortion is very common and affects plant yield in Japanese apricot (Wang et al., 2017), however, the molecular mechanism of this phenomenon is quite unknown.…”

Comprehensive transcriptome profiling to identify genes involved in pistil abortion of Japanese apricot

“…et Zucc) is a prominent berry as well as an ornamental plant of the Rosaceae family, which originated from China about three centuries ago. Japanese apricot is regarded as famous deciduous fruit because of its economic importance, eyecatching red-skinned color, and used in value-added products (Ni et al 2018;Sun et al 2013;Wu et al 2019). Two flower categories have been described in the Japanese apricot: perfect and imperfect.…”

Transcriptomic dynamics changes related to anthocyanin accumulation in the fleshy roots of carmine radish (Raphanus sativus L.) characterized using RNA-Seq

“…In this study, UDP-glycosyltransferase 75C1-like ( RsUGT75C1 : Cluster_2736) and UDP-glycosyltransferase 78D2-like ( RsUGT78D2 : Cluster_11854) were significantly upregulated in different fleshy root types with the development of dynamic growth stages of fleshy roots from the seedling stage to the full-bloom stage but decreased in the podding stage. Further modifications involving glycosylation, acylation or methylation can be made; for example, anthocyanin is formed through a reaction catalyzed by a cyanidin 3-O-glycosyltransferase ( Ni et al, 2018 ). Here, anthocyanidin 3-O-glucoside 2′″-O-xylosyltransferase ( Rs3GGT1 : Cluster_9270), coumaroyl-CoA:anthocyanidin 3-O-glucoside-6″-O-coumaroyltransferase 1-like ( Rs3AT2 : cluster_9270) were expressed as key regulatory enzymes for the formation of anthocyanins in carmine radish.…”