Research

15 pages, 3763 KiB

Open AccessArticle

Unraveling the Molecular Basis of Color Variation in Dioscorea alata Tubers: Integrated Transcriptome and Metabolomics Analysis

by Yue Wang, Rui-Sen Lu, Ming-Han Li, Xin-Yu Lu, Xiao-Qin Sun and Yan-Mei Zhang

Int. J. Mol. Sci. 2024, 25(4), 2057; https://doi.org/10.3390/ijms25042057 - 08 Feb 2024

Viewed by 494

Abstract

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms [...] Read more.

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms of color variation. Flavonoids, a group of polyphenols known to influence plant color and exhibit antioxidant properties, were of particular interest. The total phenol and total flavonoid analyses revealed that purple tubers (PTs) have a significantly higher content of these metabolites than white tubers (WTs) and a higher antioxidant activity than WTs, suggesting potential health benefits of PT D. alata. The transcriptome analysis identified 108 differentially expressed genes associated with the flavonoid synthesis pathway, with 57 genes up-regulated in PTs, including CHS, CHI, DFR, FLS, F3H, F3′5′H, LAR, ANS, and ANR. The metabolomics analysis demonstrated that 424 metabolites, including 104 flavonoids and 8 tannins, accumulated differentially in PTs and WTs. Notably, five of the top ten up-regulated metabolites were flavonoids, including 6-hydroxykaempferol-7-O-glucoside, pinocembrin-7-O-(6″-O-malonyl)glucoside, 6-hydroxykaempferol-3,7,6-O-triglycoside, 6-hydroxykaempferol-7-O-triglycoside, and cyanidin-3-O-(6″-O-feruloyl)sophoroside-5-O-glucoside, with the latter being a precursor to anthocyanin synthesis. Integrating transcriptome and metabolomics data revealed that the 57 genes regulated 20 metabolites within the flavonoid synthesis pathway, potentially influencing the tubers’ color variation. The high polyphenol content and antioxidant activity of PTs indicate their suitability as nutritious and health-promoting food sources. Taken together, the findings of this study provide insights into the molecular basis of tuber color variation in D. alata and underscore the potential applications of purple tubers in the food industry and human health promotion. The findings contribute to the understanding of flavonoid biosynthesis and pigment accumulation in D. alata tubers, opening avenues for future research on enhancing the nutritional quality of D. alata cultivars. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

16 pages, 31734 KiB

Open AccessArticle

Phenotypic Variation in Flower Color and Morphology in the Gerbera (Gerbera hybrida) F₁ Hybrid Population and Their Association with EST-SSR Markers

by Yiwei Zhou, Xinru Zou, Fulong Yan, Jingjuan He, Sixian Zeng, Yunyi Yu, Xiaoshuang Tang, Xuanguo Liang, Xiuping Cai, Rangcai Yu and Yanping Fan

Int. J. Mol. Sci. 2024, 25(1), 203; https://doi.org/10.3390/ijms25010203 - 22 Dec 2023

Cited by 1 | Viewed by 635

Abstract

Gerbera (Gerbera hybrida) is a widely cultivated ornamental plant. However, its genetic improvement is limited by the lack of genetic analysis and molecular markers for traits. In this study, we analyzed the phenotypic and genotypic variation of 140 F₁ progeny [...] Read more.

Gerbera (Gerbera hybrida) is a widely cultivated ornamental plant. However, its genetic improvement is limited by the lack of genetic analysis and molecular markers for traits. In this study, we analyzed the phenotypic and genotypic variation of 140 F₁ progeny from two gerbera varieties with different flower types and colors. We evaluated the flower’s morphology, color, and pigment content of the F₁ population and performed cluster principal component analysis (PCA) and correlation analysis. The results showed that the main ornamental traits of the hybrid progeny varied greatly. The segregation ratios of single and double flowers and ligulate and split ray florets were both 1:1. The flower colors of the F₁ progeny were mainly red and purple-red, similar to the male parent’s color. Furthermore, we conducted a genetic analysis of the hybrid progeny using EST-SSR markers and performed association analysis with phenotypic traits. We identified 2, 2, 3, 1, and 2 loci to be associated with peduncle length (PL), ray floret length (RFL), and outer ray floret; the level of apex relative to the top of involucre (LAI); outer corolla lips (OCL); and the b* of ray floret color, respectively. Our results reveal the genetic patterns of important ornamental traits and provide a theoretical basis and practical tools for gerbera genetic breeding. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

17 pages, 6015 KiB

Open AccessArticle

Association Analysis of Transcriptome and Targeted Metabolites Identifies Key Genes Involved in Iris germanica Anthocyanin Biosynthesis

by Xiaojie Zhao, Yumeng Wu, Xiaoyu Zhang, Feng Tian, Fang Yu, Xue Li and Dazhuang Huang

Int. J. Mol. Sci. 2023, 24(22), 16462; https://doi.org/10.3390/ijms242216462 - 17 Nov 2023

Viewed by 817

Abstract

The anthocyanin biosynthetic pathway is the main pathway regulating floral coloration in Iris germanica, a well-known ornamental plant. We investigated the transcriptome profiles and targeted metabolites to elucidate the relationship between genes and metabolites in anthocyanin biosynthesis in the bitone flower cultivar [...] Read more.

The anthocyanin biosynthetic pathway is the main pathway regulating floral coloration in Iris germanica, a well-known ornamental plant. We investigated the transcriptome profiles and targeted metabolites to elucidate the relationship between genes and metabolites in anthocyanin biosynthesis in the bitone flower cultivar ‘Clarence’, which has a deep blue outer perianth and nearly white inner perianth. In this study, delphinidin-, pelargonidin-, and cyanidin-based anthocyanins were detected in the flowers. The content of delphinidin-based anthocyanins increased with the development of the flower. At full bloom (stage 3), delphinidin-based anthocyanins accounted for most of the total anthocyanin metabolites, whereas the content of pelargonidin- and cyanidin-based anthocyanins was relatively low. Based on functional annotations, a number of novel genes in the anthocyanin pathway were identified, which included early biosynthetic genes IgCHS, IgCHI, and IgF3H and late biosynthetic genes Ig F3′5′H, IgANS, and IgDFR. The expression of key structural genes encoding enzymes, such as IgF3H, Ig F3′5′H, IgANS, and IgDFR, was significantly upregulated in the outer perianth compared to the inner perianth. In addition, most structural genes exhibited their highest expression at the half-color stage rather than at the full-bloom stage, which indicates that these genes function ahead of anthocyanins synthesis. Moreover, transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) related to the regulation of anthocyanin biosynthesis were identified. Among 56 R2R3-MYB genes, 2 members belonged to subgroup 4, with them regulating the expression of late biosynthetic genes in the anthocyanin biosynthetic pathway, and 4 members belonged to subgroup 7, with them regulating the expression of early biosynthetic genes in the anthocyanin biosynthetic pathway. Quantitative real-time PCR (qRT-PCR) analysis was used to validate the data of RNA sequencing (RNA-Seq). The relative expression profiles of most candidate genes were consistent with the FPKM of RNA-seq. This study identified the key structural genes encoding enzymes and TFs that affect anthocyanin biosynthesis, which provides a basis and reference for the regulation of plant anthocyanin biosynthesis in I. germanica. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

21 pages, 4992 KiB

Open AccessArticle

CpCAF1 from Chimonanthus praecox Promotes Flowering and Low-Temperature Tolerance When Expressed in Arabidopsis thaliana

by Yimeng Lv, Mingfang Xie, Shiqing Zhou, Bixia Wen, Shunzhao Sui, Mingyang Li and Jing Ma

Int. J. Mol. Sci. 2023, 24(16), 12945; https://doi.org/10.3390/ijms241612945 - 18 Aug 2023

Viewed by 845

Abstract

CCR4-associated factor I (CAF1) is a deadenylase that plays a critical role in the initial step of mRNA degradation in most eukaryotic cells, and in plant growth and development. Knowledge of CAF1 proteins in woody plants remains limited. Wintersweet (Chimonanthus praecox) [...] Read more.

CCR4-associated factor I (CAF1) is a deadenylase that plays a critical role in the initial step of mRNA degradation in most eukaryotic cells, and in plant growth and development. Knowledge of CAF1 proteins in woody plants remains limited. Wintersweet (Chimonanthus praecox) is a highly ornamental woody plant. In this study, CpCAF1 was isolated from wintersweet. CpCAF1 belongs to the DEDDh (Asp-Glu-Asp-Asp-His) subfamily of the DEDD (Asp-Glu-Asp-Asp) nuclease family. The amino acid sequence showed highest similarity to the homologous gene of Arabidopsis thaliana. In transgenic Arabidopsis overexpressing CpCAF1, the timing of bolting, formation of the first rosette, and other growth stages were earlier than those of the wild-type plants. Root, lateral branch, rosette leaf, and silique growth were positively correlated with CpCAF1 expression. FLOWERING LOCUS T (FT) and SUPPRESSOROF OVEREXPRESSION OF CO 1 (SOC1) gene expression was higher while EARLY FLOWERING3 (ELF3) and FLOWERING LOCUS C (FLC) gene expression of transgenic Arabidopsis was lower than the wild type grown for 4 weeks. Plant growth and flowering occurrences were earlier in transgenic Arabidopsis overexpressing CpCAF1 than in the wild-type plants. The abundance of the CpCAF1 transcript grew steadily, and significantly exceeded the initial level under 4 °C in wintersweet after initially decreasing. After low-temperature exposure, transgenic Arabidopsis had higher proline content and stronger superoxide dismutase activity than the wild type, and the malondialdehyde level in transgenic Arabidopsis was decreased significantly by 12 h and then increased in low temperature, whereas it was directly increased in the wild type. A higher potassium ion flux in the root was detected in transgenic plants than in the wild type with potassium deficiency. The CpCAF1 promoter was a constitutive promoter that contained multiple cis-acting regulatory elements. The DRE, LTR, and MYB elements, which play important roles in response to low temperature, were identified in the CpCAF1 promoter. These findings indicate that CpCAF1 is involved in flowering and low-temperature tolerance in wintersweet, and provide a basis for future genetic and breeding research on wintersweet. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

13 pages, 3533 KiB

Open AccessArticle

Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes

by Jinliao Chen, Fei Wang, Chengyuan Zhou, Sagheer Ahmad, Yuzhen Zhou, Minghe Li, Zhongjian Liu and Donghui Peng

Int. J. Mol. Sci. 2023, 24(15), 12473; https://doi.org/10.3390/ijms241512473 - 05 Aug 2023

Cited by 2 | Viewed by 1123

Abstract

Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes [...] Read more.

Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes and colors. Although the morphological boundaries of Aerides are clearly defined, the relationship between Aerides and other closely related genera is still ambiguous in terms of phylogeny. To better understand their phylogenetic relationships, this study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of this taxonomic unit using genetic information from six Aerides plastid genomes. The quadripartite-structure plastomes ranged from 147,244 bp to 148,391 bp and included 120 genes. Among them, 74 were protein coding genes, 38 were tRNA genes and 8 were rRNA genes, while the ndh genes were pseudogenized or lost. Four non-coding mutational hotspots (rpl20–rpl33, psbM, petB, rpoB–trnC^GCA, Pi > 0.06) were identified. A total of 71–77 SSRs and 19–46 long repeats (>30 bp) were recognized in Aerides plastomes, which were mostly located in the large single-copy region. Phylogenetic analysis indicated that Aerides was monophylic and sister to Renanthera. Moreover, our results confirmed that six Aerides species can be divided into three major clades. These findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contributes to future research on the phylogenomics of Orchidaceae. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

16 pages, 6139 KiB

Open AccessArticle

IRAPs in Combination with Highly Informative ISSRs Confer Effective Potentials for Genetic Diversity and Fidelity Assessment in Rhododendron

by Sulin Wen, Hong Zhao, Manying Zhang, Guang Qiao and Xiaohui Shen

Int. J. Mol. Sci. 2023, 24(8), 6902; https://doi.org/10.3390/ijms24086902 - 07 Apr 2023

Cited by 2 | Viewed by 1160

Abstract

The species belonging to the Rhododendron genus are well-known for their colorful corolla. Molecular marker systems have the potential to elucidate genetic diversity as well as to assess genetic fidelity in rhododendrons. In the present study, the reverse transcription domains of long terminal [...] Read more.

The species belonging to the Rhododendron genus are well-known for their colorful corolla. Molecular marker systems have the potential to elucidate genetic diversity as well as to assess genetic fidelity in rhododendrons. In the present study, the reverse transcription domains of long terminal repeat retrotransposons were cloned from rhododendrons and used to develop an inter-retrotransposon amplified polymorphism (IRAP) marker system. Subsequently, 198 polymorphic loci were generated from the IRAP and inter-simple sequence repeat (ISSR) markers, of which 119 were derived from the IRAP markers. It was shown that in rhododendrons, IRAP markers were superior to the ISSRs in some polymorphic parameters, such as the average number of polymorphic loci (14.88 versus 13.17). The combination of the IRAP and ISSR systems was more discriminative for detecting 46 rhododendron accessions than each of the systems on their own. Furthermore, IRAP markers demonstrated more efficiency in genetic fidelity detection of in-vitro-grown R. bailiense Y.P.Ma, C.Q.Zhang and D.F.Chamb, an endangered species recently recorded in Guizhzhou Province, China. The available evidence revealed the distinct properties of IRAP and ISSR markers in the rhododendron-associated applications, and highlighted the availability of highly informative ISSR and IRAP markers in the evaluation of genetic diversity and genetic fidelity of rhododendrons, which may facilitate preservation and genetic breeding of rhododendron plants. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

15 pages, 4363 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

by Jie Huang, Gui-Zhen Chen, Sagheer Ahmad, Yang Hao, Jin-Liao Chen, Yu-Zhen Zhou, Si-Ren Lan, Zhong-Jian Liu and Dong-Hui Peng

Int. J. Mol. Sci. 2023, 24(2), 1261; https://doi.org/10.3390/ijms24021261 - 09 Jan 2023

Cited by 5 | Viewed by 2177

Abstract

Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the [...] Read more.

Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

16 pages, 5857 KiB

Open AccessArticle

Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans

by Yong Ye, Shanshan Cao, Lixiao Shen, Yiguang Wang, Shiwei Zhong, Liyuan Yang, Zheng Xiao, Qiu Fang, Hongbo Zhao and Bin Dong

Int. J. Mol. Sci. 2022, 23(23), 15363; https://doi.org/10.3390/ijms232315363 - 06 Dec 2022

Cited by 1 | Viewed by 1489

Abstract

CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this [...] Read more.

CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

24 pages, 10734 KiB

Open AccessArticle

Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata

by Guanghao Cheng, Fengjiao Zhang, Xiaochun Shu, Ning Wang, Tao Wang, Weibing Zhuang and Zhong Wang

Int. J. Mol. Sci. 2022, 23(22), 14036; https://doi.org/10.3390/ijms232214036 - 14 Nov 2022

Cited by 3 | Viewed by 1482

Abstract

The transition from vegetative to reproductive growth is important for controlling the flowering of Lycoris radiata. However, the genetic control of this complex developmental process remains unclear. In this study, 18 shoot apical meristem (SAM) samples were collected from early-, mid- and [...] Read more.

The transition from vegetative to reproductive growth is important for controlling the flowering of Lycoris radiata. However, the genetic control of this complex developmental process remains unclear. In this study, 18 shoot apical meristem (SAM) samples were collected from early-, mid- and late-flowering populations during floral bud differentiation. The histological analysis of paraffin sections showed that the floral bud differentiation could be divided into six stages; the differentiation time of the early group was earlier than that of the middle and late groups, and the late group was the latest. In different populations, some important differential genes affecting the flowering time were identified by transcriptome profiles of floral bud differentiation samples. Weighted gene co-expression network analysis (WGCNA) was performed to enrich the gene co-expression modules of diverse flowering time populations (FT) and floral bud differentiation stages (ST). In the MEyellow module, five core hub genes were identified, including CO14, GI, SPL8, SPL9, and SPL15. The correlation network of hub genes showed that they interact with SPLs, AP2, hormone response factors (auxin, gibberellin, ethylene, and abscisic acid), and several transcription factors (MADS-box transcription factor, bHLH, MYB, and NAC3). It suggests the important role of these genes and the complex molecular mechanism of floral bud differentiation and flowering time in L. radiata. These results can preliminarily explain the molecular mechanism of floral bud differentiation and provide new candidate genes for the flowering regulation of Lycoris. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

17 pages, 7281 KiB

Open AccessArticle

Integrated Transcriptome and Metabolome Analysis of Color Change and Low-Temperature Response during Flowering of Prunus mume

by Bin Dong, Zifei Zheng, Shiwei Zhong, Yong Ye, Yiguang Wang, Liyuan Yang, Zheng Xiao, Qiu Fang and Hongbo Zhao

Int. J. Mol. Sci. 2022, 23(21), 12831; https://doi.org/10.3390/ijms232112831 - 24 Oct 2022

Cited by 4 | Viewed by 1690

Abstract

In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume [...] Read more.

In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume to expand the scope of its cultivation. We used the integrated transcriptomic and metabolomic analysis of a cold-resistant variety of P. mume ‘Meiren’, to identify key genes and metabolites associated with low temperatures during flowering. The ‘Meiren’ cultivar responded in a timely manner to temperature by way of a low-temperature signal transduction pathway. After experiencing low temperatures, the petals fade and wilt, resulting in low ornamental value. At the same time, in the cold response pathway, the activities of related transcription factors up- or downregulate genes and metabolites related to low temperature-induced proteins, osmotic regulators, protective enzyme systems, and biosynthesis and metabolism of sugars and acids. Our findings promote research on the adaptation of P. mume to low temperatures during wintering and early flowering for domestication and breeding. Full article

(This article belongs to the Special Issue Research Advances in Ornamental Plants Breeding and Biotechnology)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Research Advances in Ornamental Plants Breeding and Biotechnology

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (10 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI