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15 pages, 4270 KiB

Open AccessArticle

Locating Appropriate Reference Genes in Heteroblastic Plant Ottelia cordata for Quantitative Real-Time PCR Normalization

by Panyang Guo, Runan Li, Jiaquan Huang and Liyan Yin

Horticulturae 2025, 11(3), 313; https://doi.org/10.3390/horticulturae11030313 - 13 Mar 2025

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Abstract

Selecting the right reference genes for data normalization is the only way to ensure the precision and reproducibility of gene expression measurement using qRT-PCR. Ottelia cordata is a member of the Hydrocharitaceae family in aquatic plants that exhibits both floating and submerged leaf [...] Read more.

Selecting the right reference genes for data normalization is the only way to ensure the precision and reproducibility of gene expression measurement using qRT-PCR. Ottelia cordata is a member of the Hydrocharitaceae family in aquatic plants that exhibits both floating and submerged leaf forms. It has recently drawn interest as a possible model plant for research into non-KRANZ C₄ photosynthesis and heteroblastic leaves. Our earlier research has demonstrated bias in gene expression analysis when actin or GAPDH, two common reference genes, are used for normalization. Furthermore, there has been no study on the Hydrocharitaceae family reference gene selection published to date. To standardize qRT-PCR in O. cordata, seven genes were chosen from a transcriptome database: ACT7, EF1_α, GAPDH, BRCC36, PP2A, UBC7, and UBQ. We conducted qRT-PCR experiments in various tissues, leaves in different developmental stages, leaves in high/low carbon treatment, and leaves in high/low temperature treatment. After analyzing the stability using five statistical methods (geNorm, normFinder, comparative ΔCt, bestKeeper, and comprehensive analysis), PP2A and UBQ were identified as the most stable genes. BRCC36 was identified as a new reference gene in plants. Finally, by contrasting the expression patterns of pepc2, a crucial gene connected to C₄ photosynthesis, in floating and submerged leaves, PP2A, UBQ, and UBC7 were verified. Of these, PP2A and UBQ were shown to be the superior gene for the precise qRT-PCR data normalization. The results of this study offer the initial information concerning reference gene identification for O. cordata as well as the first data in Hydrocharitaceae plants. It will make it easier to do more gene function and molecular biology research on O. cordata and other closely related species. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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18 pages, 5177 KiB

Open AccessArticle

Identification and Expression Analysis of miR166 Gene Family in Response to Salt Stress in Chrysanthemum

by Di Wang, Shuheng Wang, Dongyang Zhang, Yuan Meng, Ying Qian, Siyu Feng, Yun Bai and Yunwei Zhou

Horticulturae 2025, 11(2), 141; https://doi.org/10.3390/horticulturae11020141 - 29 Jan 2025

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Abstract

cgr-miR166 was observed to be significantly enhanced in Chrysanthemum under 200 mM NaCl treatment. Here, ten family members were identified by aligning cgr-miR166 with scaffold sequences from the Chrysanthemum nankingense genome database, naming them from cgr-miR166a to cgr-miR166j, and their precursors could [...] Read more.

cgr-miR166 was observed to be significantly enhanced in Chrysanthemum under 200 mM NaCl treatment. Here, ten family members were identified by aligning cgr-miR166 with scaffold sequences from the Chrysanthemum nankingense genome database, naming them from cgr-miR166a to cgr-miR166j, and their precursors could form stable stem-loop structures. The mature regions were observed to be highly conserved, with the 3′ end being more conserved than the 5′ end. miR166s promoters have been found to contain cis-acting elements responsive to diverse stimuli like the phytohormones ABA and IAA. qRT-RCR results demonstrated that the transcriptome sequencing results were reliable and miR166 was present at different levels in the roots, stems, leaves and flowers of Chrysanthemum. Furthermore, the HD-ZipIII transcription factor was validated to be the target gene of Chrysanthemum miR166s by degradome sequencing. Taken together, the cgr-miR166 family exhibited both evolutionary conservation and diversification. The expression level of miR166 was upregulated in root under salt stress, while the expression level of the target gene HD-ZipIII was downregulated. These findings established the foundation for further understanding the mechanism of miR166-HD-ZipIII modules in salt response and tolerance. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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14 pages, 1859 KiB

Open AccessArticle

Genetic Diversity and Structure of a Critically Endangered Ornamental Species, Rhododendron farinosum, with Extremely Small Populations

by Fengjuan Li, Linyuan Fan, Jingli Zhang, Wen Liu, Wei Li, Yongpeng Ma and Hong Ma

Horticulturae 2025, 11(1), 51; https://doi.org/10.3390/horticulturae11010051 - 7 Jan 2025

Cited by 1 | Viewed by 694

Abstract

A comprehensive study of the genetic characteristics of endangered species is a prerequisite for their effective conservation and management. Rhododendron farinosum is an endangered ornamental species with extremely small populations located in northeastern Yunnan Province. To unravel the reasons behind the endangerment of [...] Read more.

A comprehensive study of the genetic characteristics of endangered species is a prerequisite for their effective conservation and management. Rhododendron farinosum is an endangered ornamental species with extremely small populations located in northeastern Yunnan Province. To unravel the reasons behind the endangerment of this species and provide guidance for the rational conservation of this species, this study obtained a large number of SNP loci by using double-digest restriction-site-associated DNA sequencing (ddRAD-seq) to evaluate the genetic diversity and genetic structure of R. farinosum, as well as to infer the population history of this species. Our findings reveal that, at the population level, R. farinosum exhibited a high genetic diversity (π = 0.1948 ± 0.0020, H_E = 0.1880 ± 0.0020). The F_ST values (0.1383–0.2231) indicated high genetic differentiation among the three populations. The AMOVA revealed that 62.83% of the genetic variation originated within populations and 37.17% between populations. The PCA, Structure, and UPGMA consistently depicted that the three populations of R. farinosum are clearly distinguished into three clusters. Furthermore, the effective population size of R. farinosum was inferred to date back to 95,000 years ago using the stairway plot, with a continuous decline from 3292 years. Based on these findings, we propose conservation strategies and management measures for R. farinosum. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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20 pages, 5960 KiB

Open AccessArticle

RNA-Seq Analysis Uncovered Transcriptomic Changes in Poncirus trifoliata Roots Under Long-Term Soil Drought Conditions

by Chuncao Song, Xingying Zeng, Lin Zheng, Qin Huang, Lingshan Zhong, Yong Zhou, Hengfu Yin and Yanjie Peng

Horticulturae 2024, 10(12), 1319; https://doi.org/10.3390/horticulturae10121319 - 11 Dec 2024

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Abstract

Drought is one of the most serious abiotic stresses in citrus plantations. It is thus imperative to fully understand the drought-resistant mechanisms in these plants. Here, RNA-seq was used to analyze the transcriptomic changes in the roots of Poncirus trifoliata, a widely [...] Read more.

Drought is one of the most serious abiotic stresses in citrus plantations. It is thus imperative to fully understand the drought-resistant mechanisms in these plants. Here, RNA-seq was used to analyze the transcriptomic changes in the roots of Poncirus trifoliata, a widely used rootstock in citrus plantations, under a 72-day soil drought and a 7-day recovery stage. Our results showed that the genes upregulated under drought were only enriched in the galactose metabolism and protein processing in endoplasmic reticulum pathways. In the galactose metabolism pathway, four genes related to the synthesis of raffinose family oligosaccharides, which act as osmoprotectants and ROS scavengers, were significantly upregulated under long-term drought. Several heat-shock protein (HSP) family genes were significantly upregulated under drought, leading to increased levels of HSPs to alleviate the endoplasmic reticulum-associated degradation of misfolded proteins induced by drought stress. Some other upregulated genes under drought, like late embryogenesis-abundant family genes and lipid transfer protein family genes, might also be crucial to the drought resistance of P. trifoliata roots. MSYJ196370 (heat-shock factor family gene) was the top hub gene in the protein–protein interaction analysis of upregulated genes under drought. These findings supplement the transcriptomic response of P. trifoliata root under long-term drought stress. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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12 pages, 4020 KiB

Open AccessArticle

Transcriptome and miRNA Reveal the Key Factor Regulating the Somatic Embryogenesis of Camellia oleifera

by Qinqin Xing, Kailiang Wang, Henfu Yin, Chaochen Yang and Minyan Wang

Horticulturae 2024, 10(12), 1291; https://doi.org/10.3390/horticulturae10121291 - 4 Dec 2024

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Abstract

The key genes involved in plant regeneration play a crucial role in enhancing reproductive capabilities, plant genetic transformation, and gene editing efficiency. Camellia oleifera, a vital woody oil crop, faces challenges in genetic improvement efficiency due to its slow growth and the [...] Read more.

The key genes involved in plant regeneration play a crucial role in enhancing reproductive capabilities, plant genetic transformation, and gene editing efficiency. Camellia oleifera, a vital woody oil crop, faces challenges in genetic improvement efficiency due to its slow growth and the difficulties it experiences during the regeneration process. This study focused on the expression levels of mRNA and miRNA during the somatic embryogenesis of C. oleifera, and the core genes of plant regeneration involved in the C. oleifera somatic embryogenesis process were identified, including WUSCHEL-related homeobox 4 (WOX4), WOX13, and DNA-Binding One Zinc Finger 5.6 (DOF5.6) during the somatic embryo callus induction phase; WOX11, PLETHORA2 (PLT2), and Growth-regulating factor (GRF) during the somatic embryogenesis and bud regeneration phase; and miRNAs such as miR156, miR319, and miR394. These key regulatory factors may participate in the regulation of plant auxin and cytokinin and play a core role in the regeneration process of C. oleifera. The research data elucidate the process of somatic embryogenesis in C. oleifera at the molecular level. The key regulatory genes identified provide potential targets for improving the regeneration efficiency of C. oleifera and other woody oilseed plants. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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13 pages, 3852 KiB

Open AccessArticle

Multi-Approach Unveils Potential Gene Introgression of Oil Camellias

by Menglong Fan, Zhixin Song, Ying Zhang, Xinlei Li and Zhenyuan Sun

Horticulturae 2024, 10(12), 1252; https://doi.org/10.3390/horticulturae10121252 - 26 Nov 2024

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Abstract

The complex phylogenetic relationship of polyploid species provides an opportunity for a comprehensive study of gene introgression. Oil camellias refer to a class of important woody oil plant in the camellia genus, including octoploid, hexaploid, tetraploid, and diploid plants, but the phylogeny relationship [...] Read more.

The complex phylogenetic relationship of polyploid species provides an opportunity for a comprehensive study of gene introgression. Oil camellias refer to a class of important woody oil plant in the camellia genus, including octoploid, hexaploid, tetraploid, and diploid plants, but the phylogeny relationship of these species remains poorly investigated. Here, based on multiple types of evidence, including phylogenetic conflict, gene flow analysis, and representative metabolite, we reconstructed the phylogenetic relationship of oil camellias. Camellia shensiensis and C. grijsii formed a distinct branch. Phylogenetic conflict suggested that hexaploid C. oleifera probably originated from hybridization and clustered with diploid C. kissi and tetraploid C. meiocarpa. Tetraploid C. confusa probably originated from crossing the ancestor of C. kissi and C. brevistyla, and C. brevistyla probably was the maternal progenitor of hexaploid C. sasanqua. Furthermore, the composition of anthocyanin in tender leaves showed a strong correlation with phylogenetic distinctions. This study proves the feasibility of using iconic metabolic components to solve phylogenetic relationships and lays a foundation for analyzing genetic breeding and utilizing oil camellia resources. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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20 pages, 9113 KiB

Open AccessArticle

A C2H2-Type Zinc Finger Protein from Mentha canadensis, McZFP1, Negatively Regulates Epidermal Cell Patterning and Salt Tolerance

by Xiaowei Zheng, Yichuan Xu, Li Li, Xiwu Qi, Xu Yu, Chun Qin, Dongmei Liu, Zequn Chen and Yang Bai

Horticulturae 2024, 10(11), 1139; https://doi.org/10.3390/horticulturae10111139 - 25 Oct 2024

Viewed by 1135

Abstract

C2H2-type zinc finger protein (C2H2-ZFP) transcription factors play evident roles in regulating plant growth and development and abiotic stress responses. However, the role of C2H2-ZFP from Mentha canadensis remains uncertain. We identified the multifunctional C2H2-ZFP gene McZFP1 from M. canadensis based on phylogenetic [...] Read more.

C2H2-type zinc finger protein (C2H2-ZFP) transcription factors play evident roles in regulating plant growth and development and abiotic stress responses. However, the role of C2H2-ZFP from Mentha canadensis remains uncertain. We identified the multifunctional C2H2-ZFP gene McZFP1 from M. canadensis based on phylogenetic analysis. The McZFP1 gene was highly expressed in stems, responding to abiotic stress and phytohormone treatments. McZFP1 localized in the nucleus and showed no transcriptional autoactivation activity in yeast. McZFP1 overexpression in Arabidopsis thaliana significantly reduced the number of trichomes and root hairs, root hair length, and salt stress tolerance. Further study revealed that McZFP1 overexpression increased the expression of negative regulator genes and decreased that of positive regulator genes to inhibit plant trichome and root hair development. Malondialdehyde accumulation was promoted, but the proline content and catalase, superoxide dismutase, and peroxidase activities were reduced and the expression of stress response genes was inhibited in McZFP1 overexpression lines under salt treatment, thereby compromising plant salt tolerance. Overall, these results indicate that McZFP1 is a novel C2H2-ZFP transcription factor that plays negative roles in trichome and root hair development and salt stress tolerance. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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Review

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11 pages, 632 KiB

Open AccessReview

The Sucrose Regulation of Plant Shoot Branching

by Shifa Xiong, Yangdong Wang, Yicun Chen, Xiang Shi and Liwen Wu

Horticulturae 2024, 10(12), 1348; https://doi.org/10.3390/horticulturae10121348 - 15 Dec 2024

Viewed by 1116

Abstract

The branching characteristics of plants represent crucial agronomic traits that significantly influence both yield and economic value. The formation of branches involves several stages, including the initiation of axillary meristems and the activation and continued growth of lateral buds. These processes are collaboratively [...] Read more.

The branching characteristics of plants represent crucial agronomic traits that significantly influence both yield and economic value. The formation of branches involves several stages, including the initiation of axillary meristems and the activation and continued growth of lateral buds. These processes are collaboratively regulated by genetic factors, hormones, nutritional availability, and environmental conditions. Recently, sucrose has emerged as a significant factor impacting plant branching characteristics. Sucrose not only serves as a carbon source, providing essential nutrition and energy for branching growth, but also integrates multiple regulatory factors to jointly influence branching development. This review summarizes the structural enzyme genes involved in the sucrose synthesis pathway and the key co-factors in signal transduction pathways, the interactions between sucrose and plant hormones and transcription factors, and the regulatory role of sucrose metabolites in plant branching. Furthermore, it highlights critical issues that require further investigation regarding the role of sucrose in regulating branching. Full article

(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)

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