Transcriptome Sequencing and Metabolism Analysis Reveals the role of Cyanidin Metabolism in Dark-red Onion (Allium cepa L.) Bulbs

Xiaojie Li,Chunsha Zhang,Aisong Zeng,Linjiao Cao,Guojun Chang,Yi Liang,Zongxiang Zhan

doi:10.1038/s41598-018-32472-5

Abstract

Onion (Allium cepa L.) is an important bulbous vegetable crop that possesses important properties related to health as well as extraordinary colors. Naturally white onion bulbs were used in this study to reveal the complex metabolic mechanisms that underlie phenotypic traits, especially bulb pigmentation. Six libraries (three dark-red and three white) were constructed and analyzed to elucidate differences in cyanidin (Cy) metabolism between dark-red and white onion bulbs. Libraries were screened using RNA-sequencing (RNA-seq) to reveal the differentially expressed genes (DEGs) involved in anthocyanin biosynthesis at the transcriptional level. Comparison with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database shows that a total of 27 unigenes participate in onion anthocyanin biosynthesis and 16 DEGs perform critical roles in flavonoid biosynthesis. Expression patterns of color-related flavonoid compounds associated with the onion anthocyanin biosynthesis pathway (ABP) show that flavonoid 3′,5′-hydroxylase (F3′5′H) and dihydroflavonol 4-reductase (DFR) genes play crucial roles in the biosynthesis of dark-red bulbs, the expression levels of flavonol synthase (FLS) and DFR genes may act to block blue pigmentation, and the loss of Cy from white onion bulbs might explain multibranching in the synthesis of this compound. Positive variation in the F3′5′H/F3′H ratio also affects onion bulb color diversity. The transcriptome presented here provides a basis for future onion molecular breeding based on variations in the diversity of ornamental plant pigmentation.

Highlights

Flavonoids are common plant secondary metabolites belonging to the class of phenylpropanoids class and occur in various modified forms
THC is isomerized to colorless naringenin by chalcone isomerase (CHI), naringenin is hydroxylated by flavanone 3-hydroxylase (F3H) to produce dihydrokaempferol, while flavonoid 3′,5′-hydroxylase (F3′5′H) and flavonoid 3′-hydroxylase (F3′H) catalyze the hydroxylation of dihydrokaempferol (DHM) to produce dihydromyricetin and dihydroquercetin, respectively
These flavonoids are essential for the production of Del and Cy, respectively; dihydroflavonols are reduced to lecoanthocyanidins via the effects of dihydroflavonol 4-reductase (DFR) and are converted to quercetin, kaempferol, and myricetin by flavonol synthase (FLS)

Summary

Introduction

Flavonoids are common plant secondary metabolites belonging to the class of phenylpropanoids class and occur in various modified forms. The second gene, C, is a basic color factor that is completely dominant over c and is required for the production of all colors This means that homozygous recessive (cc) plants will have white bulbs which are referred to as recessive white to distinguish them from their dominant white counterparts. Previous research has shown that the DFR gene transcript only accumulate in red onions while inactivation of this enzyme precludes the anthocyanin produced in the yellow onions[15] It is worth discussing which colors will be produced in onion bulbs by low level DFR expression. Previous reports on colored bulbous plants, including potato (Solanum tuberosum L.)[16], carrot (Daucus carota L.)[17], and radish (Raphanus sativus L.)[18], have emphasized anthocyanin metabolism These vacuolar pigments are Variety Dark-red onion White onion

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