The Asia lotus (Nelumbo nucifera Gaertn.) is an ornamental aquatic plant with high economic value. Flower colour is an important ornamental trait, with much of N. nucifera breeding focusing on its yellow flowers. To explore the yellow flower colouration mechanism in N. nucifera, we analysed its pigment constituents and content, as well as gene expression in the flavonoid pathway, in two N. nucifera cultivars. We performed metabolomic and gene expression analyses in two N. nucifera cultivars with yellow and white flowers, Molinqiuse (MLQS) and Yeguangbei (YGB), respectively, at five stages of flower colouration. Based on phenotypic observation and metabolite analyses, the later stages of flower colouration (S3–S5) were determined to be key periods for differences between MLQS and YGB, with dihydroflavonols and flavonols differing significantly between cultivars. Dihydroquercetin, dihydrokaempferol, and isorhamnetin were significantly higher in MLQS than in YGB, whereas kaempferol was significantly higher in YGB. Most of the key homologous structural genes in the flavonoid pathway were significantly more active in MLQS than in YGB at stages S1–S4. In this study, we performed the first analyses of primary and secondary N. nucifera metabolites during flower colouration, and found that isorhamnetin and kaempferol shunting resulted in petal colour differences between MLQS and YGB. Based on our data integration analyses of key enzyme expression in the putative flavonoid pathways of the two N. nucifera cultivars, NnFLS gene substrate specificity and differential expression of NnOMTs may be related to petal colour differences between MLQS and YGB. These results will contribute to determining the mechanism of yellow flower colouration in N. nucifera, and will improve yellow petal colour breeding in lotus species.

Lotus (Nelumbo nuciferaGaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115NnbHLHswere identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115NnbHLHswere further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted.NnbHLHswere predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15NnbHLHswere further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles ofNnbHLHsin four tissues indicated that manyNnbHLHsshowed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution ofNnbHLHs, and identifies candidate genes for stress resistance in lotus.

The lotus (Nelumbo nucifera Gaertn.) is one of the most economically and ornamentally important perennial aquatic plants. Plant architecture is an important trait for lotus classification, cultivation, breeding, and applications. In this study, traits representing plant architecture were measured in 390 lotus germplasms for 3 years. According to the phenotypic distribution, 21 large architecture (LA) and 22 small architecture (SA) germplasms exhibiting extreme phenotypes were selected as representatives of plant architecture. Microscopy analyses revealed that LA lotuses possessed far more vertical cells and longer cell lengths than SA lotuses, and there was a closer linear relationship between vertical cell number and plant architecture than cell length and plant architecture. Furthermore, based on whole genome re-sequencing data from 10 LA and 10 SA lotus germplasms, fixation index (F_ST) genome scan identified 11.02 Mb of genomic regions that were highly differentiated between the LA and SA lotus groups. Chi-square test revealed that 17,154 single nucleotide polymorphisms (SNPs) and 1,554 insertions and deletions (InDels) showed distinct allelic distribution between the LA and SA lotus groups within these regions. A total of 126 variants with distinct allelic distribution in the highly differentiated region were predicted to cause amino acid changes in 60 genes. Among the 41 genes with functional annotation, the expression patterns of six genes involved in cell division and cell wall construction were confirmed using quantitative reverse-transcription PCR (qRT-PCR). In addition, 34 plant architecture-associated InDel markers were developed and verified in the remaining 11 LA and 12 SA lotus plant architecture representatives. This study identified promising functional markers and candidates for molecular breeding and will facilitate further elucidation of the genetic mechanisms underlying plant architecture in the lotus.

Prunus mume is a traditional ornamental plant, which owed a unique floral scent. However, the diversity of the floral scent in P. mume cultivars with different aroma types was not identified. In this study, the floral scent of eight P. mume cultivars was studied using headspace solid-phase microextraction (HS-SPME) and organic solvent extraction (OSE), combined with gas chromatography-mass spectrometry (GC-MS). In total, 66 headspace volatiles and 74 endogenous extracts were putatively identified, of which phenylpropanoids/benzenoids were the main volatile organic compounds categories. As a result of GC-MS analysis, benzyl acetate (1.55–61.26%), eugenol (0.87–6.03%), benzaldehyde (5.34–46.46%), benzyl alcohol (5.13–57.13%), chavicol (0–5.46%), and cinnamyl alcohol (0–6.49%) were considered to be the main components in most varieties. However, the volatilization rate of these main components was different. Based on the variable importance in projection (VIP) values in the orthogonal partial least-squares discriminate analysis (OPLS-DA), differential components of four aroma types were identified as biomarkers, and 10 volatile and 12 endogenous biomarkers were screened out, respectively. The odor activity value (OAV) revealed that several biomarkers, including (Z)-2-hexen-1-ol, pentyl acetate, (E)-cinnamaldehyde, methyl salicylate, cinnamyl alcohol, and benzoyl cyanide, contributed greatly to the strong-scented, fresh-scented, sweet-scented, and light-scented types of P. mume cultivars. This study provided a theoretical basis for the floral scent evaluation and breeding of P. mume cultivars.

Prunus mume is an early spring flower of Rosaceae, which owns high application value in gardens. Being an excellent ornamental trait, the double flower trait has always been one of the important breeding goals of plant breeders. However, the key regulatory genes of double flower traits of P. mume are still unclear at present. The floral organs’ morphological differences of 20 single and 20 double flower cultivars of P. mume were compared firstly. And it was found that double flower trait of P. mume were often accompanied by petaloid stamen, multiple carpels and an increase in the total number of floral organs. Then, transcriptome sequencing of two representative cultivars P. mume ‘Danban Lve’ and P. mume ‘Xiao Lve’ were conducted at 3 Stage of flower bud development with distinct morphological differentiation. 3256 differentially expression genes (DEGs) were detected, and 20 candidate genes for double flower trait of P. mume were screened out including hub genes PmAP1–1 and PmAG-2 based on DEGs function analysis and WGCNA analysis. And it was found that epigenetic and hormone related genes may also play an important role in the process of double flower. This study suggested that the double flower trait of P.mume is more like accumulation origin based on morphological observation. 20 genes and co-expression network related to the formation of double flower P. mume were preliminarily screened through transcriptomics analysis. The results provided a reference for further understanding of the molecular mechanism of double flower trait in P. mume.