Recent Advances in Horticultural Plant Genomics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 September 2024 | Viewed by 18623

Special Issue Editors


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Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: horticultural crops; genomics; tissue culture;molecular biology; germplasm; somatic embryogenesis

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: genomics and biotechnology; plant tissue culture; non-coding RNA; molecular biology; somatic embryogenesis
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: tea processing; tea biotechnology; tea biochemistry; genomics; molecular biology

Special Issue Information

Dear Colleagues,

Whole-genome sequencing of plants and animals has developed rapidly over the past 20 years. With the development of sequencing technologies and the reduction of sequencing costs, more and more plant genomes have been sequenced and many results have been obtained, especially with the advent and applications of second- and third-generation sequencing technologies and Hi-C technologies, which have made sequencing  a reality in many complex plant genomes. By the end of 2022, more than 400 plant genome sequences have become available, most of them of horticultural plants. The development and applications of sequencing technologies has not only reduced the time and cost of whole-genome sequencing, but has also brought the study and understanding of plants to the whole-genome level, providing a new perspective on understanding gene structure, composition, and function, gene regulation, and species evolution at the molecular level. With advances in high-throughput sequencing technology, multiomics, such as pan-genomics,  transcriptomics and genome-wide non-coding RNAs, have been rapidly developed. Genomic research tools are widely used in horticultural plants such as fruit trees, vegetables, flowers, tea plants and Chinese herbs for molecular breeding and analysis of growth and development patterns, providing a new perspective on horticultural plant research, which would assist greater  understanding of the evolutionary histories of plant species and provide genomic resources for molecular studies on the economically important traits of horticultural plants.

Dr. Zhongxiong Lai
Prof. Dr. Yuling Lin
Dr. Yuqiong Guo
Guest Editors

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Keywords

  • genomics
  • non-coding RNA
  • transcriptomics

Published Papers (16 papers)

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16 pages, 4357 KiB  
Article
Genome-Wide Investigation of Class III Peroxidase Genes in Brassica napus Reveals Their Responsiveness to Abiotic Stresses
by Obaid Ullah Shah, Latif Ullah Khan, Sana Basharat, Lingling Zhou, Muhammad Ikram, Jiantao Peng, Wasi Ullah Khan, Pingwu Liu and Muhammad Waseem
Plants 2024, 13(7), 942; https://doi.org/10.3390/plants13070942 - 25 Mar 2024
Viewed by 834
Abstract
Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members [...] Read more.
Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members of the oxidoreductase enzyme family, play a critical role in protecting plants against abiotic stresses. This study demonstrated a comprehensive investigation of the POD gene family in B. napus. As a result, a total of 109 POD genes were identified across the 19 chromosomes and classified into five distinct subgroups. Further, 44 duplicate events were identified; of these, two gene pairs were tandem and 42 were segmental. Synteny analysis revealed that segmental duplication was more prominent than tandem duplication among POD genes. Expression pattern analysis based on the RNA-seq data of B. napus indicated that BnPOD genes were expressed differently in various tissues; most of them were expressed in roots rather than in other tissues. To validate these findings, we performed RT-qPCR analysis on ten genes; these genes showed various expression levels under abiotic stresses. Our findings not only furnish valuable insights into the evolutionary dynamics of the BnPOD gene family but also serve as a foundation for subsequent investigations into the functional roles of POD genes in B. napus. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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19 pages, 8521 KiB  
Article
Analysis of the UDP-Glucosyltransferase (UGT) Gene Family and Its Functional Involvement in Drought and Salt Stress Tolerance in Phoebe bournei
by Hengfeng Guan, Yanzi Zhang, Jingshu Li, Zhening Zhu, Jiarui Chang, Almas Bakari, Shipin Chen, Kehui Zheng and Shijiang Cao
Plants 2024, 13(5), 722; https://doi.org/10.3390/plants13050722 - 4 Mar 2024
Viewed by 846
Abstract
Uridine diphosphate glycosyltransferases (UDP-GTs, UGTs), which are regulated by UGT genes, play a crucial role in glycosylation. In vivo, the activity of UGT genes can affect the availability of metabolites and the rate at which they can be eliminated from the body. UGT [...] Read more.
Uridine diphosphate glycosyltransferases (UDP-GTs, UGTs), which are regulated by UGT genes, play a crucial role in glycosylation. In vivo, the activity of UGT genes can affect the availability of metabolites and the rate at which they can be eliminated from the body. UGT genes can exert their regulatory effects through mechanisms such as post-transcriptional modification, substrate subtype specificity, and drug interactions. Phoebe bournei is an economically significant tree species that is endemic to southern China. Despite extensive studies on the UGT gene family in various species, a comprehensive investigation of the UGT family in P. bournei has not been reported. Therefore, we conducted a systematic analysis to identify 156 UGT genes within the entire P. bournei genome, all of which contained the PSPG box. The PbUGT family consists of 14 subfamilies, consistent with Arabidopsis thaliana. We observed varying expression levels of PbUGT genes across different tissues in P. bournei, with the following average expression hierarchy: leaf > stem xylem > stem bark > root xylem > root bark. Covariance analysis revealed stronger covariance between P. bournei and closely related species. In addition, we stressed the seedlings with 10% NaCl and 10% PEG-6000. The PbUGT genes exhibited differential expression under drought and salt stresses, with specific expression patterns observed under each stress condition. Our findings shed light on the transcriptional response of PbUGT factors to drought and salt stresses, thereby establishing a foundation for future investigations into the role of PbUGT transcription factors. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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22 pages, 5894 KiB  
Article
Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones
by Conglong Lian, Jinxu Lan, Rui Ma, Jingjing Li, Fei Zhang, Bao Zhang, Xiuyu Liu and Suiqing Chen
Plants 2024, 13(5), 564; https://doi.org/10.3390/plants13050564 - 20 Feb 2024
Viewed by 845
Abstract
Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant [...] Read more.
Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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15 pages, 4137 KiB  
Article
Functional and Transcriptome Analysis Reveal Specific Roles of Dimocarpus longan DlRan3A and DlRan3B in Root Hair Development, Reproductive Growth, and Stress Tolerance
by Qilin Tian, Xiying Xie, Ruilian Lai, Chunzhen Cheng, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin and Zhongxiong Lai
Plants 2024, 13(4), 480; https://doi.org/10.3390/plants13040480 - 7 Feb 2024
Cited by 1 | Viewed by 810
Abstract
Ran GTPases play essential roles in plant growth and development. Our previous studies revealed the nuclear localization of DlRan3A and DlRan3B proteins and proposed their functional redundancy and distinction in Dimocarpus longan somatic embryogenesis, hormone, and abiotic stress responses. To further explore the [...] Read more.
Ran GTPases play essential roles in plant growth and development. Our previous studies revealed the nuclear localization of DlRan3A and DlRan3B proteins and proposed their functional redundancy and distinction in Dimocarpus longan somatic embryogenesis, hormone, and abiotic stress responses. To further explore the possible roles of DlRan3A and DlRan3B, gene expression analysis by qPCR showed that their transcripts were both more abundant in the early embryo and pulp in longan. Heterologous expression of DlRan3A driven by its own previously cloned promoter led to stunted growth, increased root hair density, abnormal fruits, bigger seeds, and enhanced abiotic stress tolerance. Conversely, constitutive promoter CaMV 35S (35S)-driven expression of DlRan3A, 35S, or DlRan3B promoter-controlled expression of DlRan3B did not induce the alterations in growth phenotype, while they rendered different hypersensitivities to abiotic stresses. Based on the transcriptome profiling of longan Ran overexpression in tobacco plants, we propose new mechanisms of the Ran-mediated regulation of genes associated with cell wall biosynthesis and expansion. Also, the transgenic plants expressing DlRan3A or DlRan3B genes controlled by 35S or by their own promoter all exhibited altered mRNA levels of stress-related and transcription factor genes. Moreover, DlRan3A overexpressors were more tolerant to salinity, osmotic, and heat stresses, accompanied by upregulation of oxidation-related genes, possibly involving the Ran-RBOH-CIPK network. Analysis of a subset of selected genes from the Ran transcriptome identified possible cold stress-related roles of brassinosteroid (BR)-responsive genes. The marked presence of genes related to cell wall biosynthesis and expansion, hormone, and defense responses highlighted their close regulatory association with Ran. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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18 pages, 9289 KiB  
Article
Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species
by Huiyue Ji, Junnan Liu, Yineng Chen, Xinyi Yu, Chenlu Luo, Luxi Sang, Jiayu Zhou and Hai Liao
Plants 2024, 13(4), 468; https://doi.org/10.3390/plants13040468 - 6 Feb 2024
Viewed by 795
Abstract
Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus [...] Read more.
Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus, Brassica rapa, and Camelina sativa, that were identified from the Ensembl plants database, and we subsequently investigated their CUB. As a result, the base composition analysis revealed that the overall GC content of HSP20 genes was below 50%. The overall GC content significantly correlated with the constituents at three codon positions, implying that both mutation pressure and natural selection might contribute to the CUB. The relatively high ENc values suggested that the CUB of the HSP20 genes in four cruciferous species was relatively weak. Subsequently, ENc exhibited a negative correlation with gene expression levels. Analyses, including ENc-plot analysis, neutral analysis, and PR2 bias, revealed that natural selection mainly shaped the CUB patterns of HSP20 genes in these species. In addition, a total of 12 optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified across the four species. A neighbor-joining phylogenetic analysis based on coding sequences (CDS) showed that the 140 HSP20 genes were strictly and distinctly clustered into 12 subfamilies. Principal component analysis and cluster analysis based on relative synonymous codon usage (RSCU) values supported the fact that the CUB pattern was consistent with the genetic relationship at the gene level and (or) species levels. These results will not only enrich the HSP20 gene resource but also advance our understanding of the CUB of HSP20 genes, which may underlie the theoretical basis for exploration of their genetic and evolutionary pattern. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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18 pages, 6427 KiB  
Article
Identification and Validation of the miR156 Family Involved in Drought Responses and Tolerance in Tea Plants (Camellia sinensis (L.) O. Kuntze)
by Shengjing Wen, Chengzhe Zhou, Caiyun Tian, Niannian Yang, Cheng Zhang, Anru Zheng, Yixing Chen, Zhongxiong Lai and Yuqiong Guo
Plants 2024, 13(2), 201; https://doi.org/10.3390/plants13020201 - 11 Jan 2024
Viewed by 1073
Abstract
The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis [...] Read more.
The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. Herein, we identify 47 mature sequences and 28 precursor sequences in tea plants. Our evolutionary analysis and multiple sequence alignment revealed that csn-miR156s were highly conserved during evolution and that the rates of the csn-miR156 members’ evolution were different. The precursor sequences formed typical and stable stem–loop structures. The prediction of cis-acting elements in the CsMIR156s promoter region showed that the CsMIR156s had diverse cis-acting elements; of these, 12 CsMIR156s were found to be drought-responsive elements. The results of reverse transcription quantitative PCR (RT-qPCR) testing showed that csn-miR156 family members respond to drought and demonstrate different expression patterns under the conditions of drought stress. This suggests that csn-miR156 family members may be significantly involved in the response of tea plants to drought stress. Csn-miR156f-2-5p knockdown significantly reduced the Fv/Fm value and chlorophyll content and led to the accumulation of more-reactive oxygen species and proline compared with the control. The results of target gene prediction showed that csn-miR156f-2-5p targeted SQUAMOSA promoter binding protein-like (SPL) genes. Further analyses showed that CsSPL14 was targeted by csn-miR156f-2-5p, as confirmed through RT-qPCR, 5′ RLM-RACE, and antisense oligonucleotide validation. Our results demonstrate that csn-miR156f-2-5p and CsSPL14 are involved in drought response and represent a new strategy for increasing drought tolerance via the breeding of tea plants. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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17 pages, 11224 KiB  
Article
Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing
by Lele Jiang, Siyi Xie, Chengzhe Zhou, Caiyun Tian, Chen Zhu, Xiaomei You, Changsong Chen, Zhongxiong Lai and Yuqiong Guo
Plants 2024, 13(1), 100; https://doi.org/10.3390/plants13010100 - 28 Dec 2023
Viewed by 922
Abstract
Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 [...] Read more.
Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography–mass spectrometry (GC–MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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20 pages, 3242 KiB  
Article
Analysis of Characteristics in the Macro-Composition and Volatile Compounds of Understory Xiaobai White Tea
by Mengcong Zhang, Chengzhe Zhou, Cheng Zhang, Kai Xu, Li Lu, Linjie Huang, Lixuan Zhang, Huang Li, Xuefang Zhu, Zhongxiong Lai and Yuqiong Guo
Plants 2023, 12(24), 4102; https://doi.org/10.3390/plants12244102 - 7 Dec 2023
Cited by 1 | Viewed by 1088
Abstract
Understory planting affects the growth environment of tea plants, regulating the tea plant growth and the formation of secondary metabolites, which in turn affects the flavor of Xiaobai white tea. The present research adopted biochemical composition determination, widely targeted volatilities (WTV) analysis, multivariate [...] Read more.
Understory planting affects the growth environment of tea plants, regulating the tea plant growth and the formation of secondary metabolites, which in turn affects the flavor of Xiaobai white tea. The present research adopted biochemical composition determination, widely targeted volatilities (WTV) analysis, multivariate statistical analysis, and odor activity value (OAV) analysis to analyze the characteristics in the macro-composition and volatile compounds of understory white tea. The sensory evaluation results indicated that understory Xiaobai white tea (LWTs) was stronger than ordinary Xiaobai white tea (PWTs) in terms of the taste of smoothness, sweetness, and thickness as well as the aromas of the flower and sweet. Understory planting reduced light intensity and air temperature, increased air humidity, organic matter, total nitrogen, and available nitrogen contents, which improved the growth environment of tea plants. The phytochemical analysis showed that the water-extractable substances, caffeine, flavonoids, and soluble sugar contents of understory tea fresh-leaf (LF) were higher than those of ordinary fresh-leaf (PF). The phytochemical analysis showed that the free amino acids, theaflavins, thearubigins, water-extractable substances, and tea polyphenols contents of LWTs were significantly higher than those of PWTs, which may explain the higher smoothness, sweetness, and thickness scores of LWTs than those of PWTs. The 2-heptanol, 2-decane, damasone, and cedar alcohol contents were significantly higher in LWTs than in PWTs, which may result in stronger flowery and sweet aromas in LWTs than in PWTs. These results provide a firm experimental basis for the observed differences in the flavor of LWTs and PWTs. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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16 pages, 6741 KiB  
Article
Transcriptome Analysis Reveals Fruit Quality Formation in Actinidia eriantha Benth
by Peiyu Wang, Xin Feng, Jinlan Jiang, Peipei Yan, Zunwen Li, Weihong Luo, Yiting Chen and Wei Ye
Plants 2023, 12(24), 4079; https://doi.org/10.3390/plants12244079 - 6 Dec 2023
Viewed by 820
Abstract
Actinidia chinensis Planch. is a fruit tree originating from China that is abundant in the wild. Actinidia eriantha Benth. is a type of A. chinensis that has emerged in recent years. The shape of A. eriantha is an elongated oval, and the skin [...] Read more.
Actinidia chinensis Planch. is a fruit tree originating from China that is abundant in the wild. Actinidia eriantha Benth. is a type of A. chinensis that has emerged in recent years. The shape of A. eriantha is an elongated oval, and the skin is covered with dense, non-shedding milk-white hairs. The mature fruit has flesh that is bright green in colour, and the fruit has a strong flavour and a grass-like smell. It is appreciated for its rich nutrient content and unique flavour. Vitamin C, sugar, and organic acids are key factors in the quality and flavour composition of A. eriantha but have not yet been systematically analysed. Therefore, we sequenced the transcriptome of A. eriantha at three developmental stages and labelled them S1, S2, and S3, and comparisons of S1 vs. S2, S1 vs. S3, and S2 vs. S3 revealed 1218, 4019, and 3759 upregulated differentially expressed genes and 1823, 3415, and 2226 downregulated differentially expressed genes, respectively. Furthermore, the upregulated differentially expressed genes included 213 core genes, and Gene Ontology enrichment analysis showed that they were enriched in hormones, sugars, organic acids, and many organic metabolic pathways. The downregulated differentially expressed genes included 207 core genes, which were enriched in the light signalling pathway. We further constructed the metabolic pathways of sugars, organic acids, and vitamin C in A. eriantha and identified the genes involved in vitamin C, sugar, and organic acid synthesis in A. eriantha fruits at different stages. During fruit development, the vitamin C content decreased, the carbohydrate compound content increased, and the organic acid content decreased. The gene expression patterns were closely related to the accumulation patterns of vitamin C, sugars, and organic acids in A. eriantha. The above results lay the foundation for the accumulation of vitamin C, sugars, and organic acids in A. eriantha and for understanding flavour formation in A. eriantha. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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14 pages, 5180 KiB  
Article
Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Development in Rosa roxburghii
by Xiaolong Huang, Xiaoai Wu, Guilian Sun, Yu Jiang and Huiqing Yan
Plants 2023, 12(19), 3425; https://doi.org/10.3390/plants12193425 - 28 Sep 2023
Cited by 3 | Viewed by 1009
Abstract
Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii ‘Guinong 5’ at full-bloom promoted fruit size and weight, prickle [...] Read more.
Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii ‘Guinong 5’ at full-bloom promoted fruit size and weight, prickle development, seed abortion, ascorbic acid accumulation, and reduction in total soluble sugar. RNA-Seq analysis was conducted to generate 45.75 Gb clean reads from GA3- and non-treated fruits at 120 days after pollination. We obtained 4275 unigenes belonging to differently expressed genes (DEGs). Gene ontology and the Kyoto Encyclopedia of Genes and Genomes displayed that carbon metabolism and oxidative phosphorylation were highly enriched. The increased critical genes of DEGs related to pentose phosphate, glycolysis/gluconeogenesis, and citrate cycle pathways might be essential for soluble sugar degradation. Analysis of DEGs implicated in ascorbate revealed the myoinositol pathway required to accumulate ascorbic acid. Finally, DEGs involved in endogenous phytohormones and transcription factors, including R2R3 MYB, bHLH, and WRKY, were determined. These findings indicated that GA3-trigged morphological alterations might be related to the primary metabolites, hormone signaling, and transcription factors, providing potential candidate genes that could be guided to enhance the fruit development of R. roxburghii in practical approaches. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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13 pages, 6500 KiB  
Article
Transcriptome and Metabolome Reveal Sugar and Organic Acid Accumulation in Rosa roxburghii Fruit
by Liyao Su, Tian Zhang, Min Wu, Yan Zhong and Zongming (Max) Cheng
Plants 2023, 12(17), 3036; https://doi.org/10.3390/plants12173036 - 24 Aug 2023
Cited by 3 | Viewed by 1116
Abstract
Sugars and organic acids significantly impact fruit sensory quality, but their accumulation patterns and regulatory mechanisms during the development of Rosa roxburghii fruit are still unclear. We utilized transcriptomics and metabolomics to investigate genes related to sugar and organic acid metabolism in Rosa [...] Read more.
Sugars and organic acids significantly impact fruit sensory quality, but their accumulation patterns and regulatory mechanisms during the development of Rosa roxburghii fruit are still unclear. We utilized transcriptomics and metabolomics to investigate genes related to sugar and organic acid metabolism in Rosa roxburghii. Metabolomics data revealed that sucrose, glucose and fructose were the primary sugars, whereas citric acid and malic acid were the primary organic acids in Rosa roxburghii fruit. We constructed the metabolic pathways of major sugars and organic acids in Rosa roxburghii and identified five key genes involved in sugar and organic acid synthesis. In addition, we identified a module containing 132 transcription factors that was significantly associated with sucrose, citric acid and malic acid. Based on quantitative polymerase chain reaction (qPCR), we identified 13 transcription factors involved in sugar and organic acid metabolism, including the transcription factor RrANL2 and the sucrose synthase gene RrSUS3. Further yeast one-hybrid and dual luciferase assays showed that RrANL2 could bind to the promoter of RrSUS3 to increase its expression. These results provide new insights into the metabolism of sugars and organic acids in Rosa roxburghii fruit. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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21 pages, 3351 KiB  
Article
Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant (Camellia sinensis)
by Juan Hu, Qianqian Chen, Atif Idrees, Wanjun Bi, Zhongxiong Lai and Yun Sun
Plants 2023, 12(16), 2929; https://doi.org/10.3390/plants12162929 - 13 Aug 2023
Cited by 3 | Viewed by 1637
Abstract
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such [...] Read more.
MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral ‘ABCE’ model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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17 pages, 9709 KiB  
Article
Genome-Wide Identification of the MPK Gene Family and Expression Analysis under Low-Temperature Stress in the Banana
by Zhengyang Fan, Bianbian Zhao, Ruilian Lai, Huan Wu, Liang Jia, Xiaobing Zhao, Jie Luo, Yuji Huang, Yukun Chen, Yuling Lin and Zhongxiong Lai
Plants 2023, 12(16), 2926; https://doi.org/10.3390/plants12162926 - 12 Aug 2023
Viewed by 1348
Abstract
Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis [...] Read more.
Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis, respectively. These MPKs were divided into Group A, B, C, and D. Phylogenetic analysis revealed that this difference in number was due to the gene shrinkage of the Group B subfamily of Musa balbisiana and Musa textilis. KEGG annotations revealed that K14512, which is involved in plant hormone signal transduction and the plant–pathogen interaction, was the most conserved pathway of the MPKs. The results of promoter cis-acting element prediction and focTR4 (Fusarium oxysporum f. sp. cubense tropical race 4) transcriptome expression analysis preliminarily confirmed that MPKs were relevant to plant hormone and biotic stress, respectively. The expression of MPKs in Group A was significantly upregulated at 4 °C, and dramatically, the MPKs in the root were affected by low temperature. miR172, miR319, miR395, miR398, and miR399 may be the miRNAs that regulate MPKs during low-temperature stress, with miR172 being the most critical. miRNA prediction and qRT-PCR results indicated that miR172 may negatively regulate MPKs. Therefore, we deduced that MPKs might coordinate with miR172 to participate in the process of the resistance to low-temperature stress in the roots of the banana. This study will provide a theoretical basis for further analysis of the mechanism of MPKs under low-temperature stress of bananas, and this study could be applied to molecular breeding of bananas in the future. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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15 pages, 2866 KiB  
Article
Characterization of Carotenoid Cleavage Oxygenase Genes in Cerasus humilis and Functional Analysis of ChCCD1
by Chunzhen Cheng, Rui Yang, Lu Yin, Jianying Zhang, Limin Gao, Rong Lu, Yan Yang, Pengfei Wang, Xiaopeng Mu, Shuai Zhang, Bin Zhang and Jiancheng Zhang
Plants 2023, 12(11), 2114; https://doi.org/10.3390/plants12112114 - 26 May 2023
Cited by 4 | Viewed by 1385
Abstract
Carotenoid cleavage oxygenases (CCOs) are key enzymes that function in degrading carotenoids into a variety of apocarotenoids and some other compounds. In this study, we performed genome-wide identification and characterization analysis of CCO genes in Cerasus humilis. Totally, nine CCO genes could [...] Read more.
Carotenoid cleavage oxygenases (CCOs) are key enzymes that function in degrading carotenoids into a variety of apocarotenoids and some other compounds. In this study, we performed genome-wide identification and characterization analysis of CCO genes in Cerasus humilis. Totally, nine CCO genes could be classified into six subfamilies, including carotenoid cleavage dioxygenase 1 (CCD1), CCD4, CCD7, CCD8, CCD-like and nine-cis-epoxycarotenoid dioxygenase (NCED), were identified. Results of gene expression analysis showed that ChCCOs exhibited diverse expression patterns in different organs and in fruits at different ripening stages. To investigate the roles of ChCCOs in carotenoids degradation, enzyme assays of the ChCCD1 and ChCCD4 were performed in Escerichia coli BL21(DE3) that can accumulate lycopene, β-carotene and zeaxanthin. The prokaryotic expressed ChCCD1 resulted in obvious degradation of lycopene, β-carotene and zeaxanthin, but ChCCD4 did not show similar functions. To further determine the cleaved volatile apocarotenoids of these two proteins, headspace gas chromatography/mass spectrometer analysis was performed. Results showed that ChCCD1 could cleave lycopene at 5, 6 and 5′, 6′ positions to produce 6-methy-5-hepten-2-one and could catalyze β-carotene at 9, 10 and 9′, 10′ positions to generate β-ionone. Our study will be helpful for clarifying the roles of CCO genes especially ChCCD1 in regulating carotenoid degradation and apocarotenoid production in C. humilis. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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21 pages, 4940 KiB  
Article
Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei
by Jiarui Chang, Dunjin Fan, Shuoxian Lan, Shengze Cheng, Shipin Chen, Yuling Lin and Shijiang Cao
Plants 2023, 12(10), 2048; https://doi.org/10.3390/plants12102048 - 21 May 2023
Cited by 2 | Viewed by 1475
Abstract
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source [...] Read more.
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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Review

Jump to: Research

27 pages, 2972 KiB  
Review
Multi-Omics Research Accelerates the Clarification of the Formation Mechanism and the Influence of Leaf Color Variation in Tea (Camellia sinensis) Plants
by Yan-Gen Fan, Ting-Ting Zhao, Qin-Zeng Xiang, Xiao-Yang Han, Shu-Sen Yang, Li-Xia Zhang and Li-Jun Ren
Plants 2024, 13(3), 426; https://doi.org/10.3390/plants13030426 - 31 Jan 2024
Viewed by 1095
Abstract
Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential [...] Read more.
Tea is a popular beverage with characteristic functional and flavor qualities, known to be rich in bioactive metabolites such as tea polyphenols and theanine. Recently, tea varieties with variations in leaf color have been widely used in agriculture production due to their potential advantages in terms of tea quality. Numerous studies have used genome, transcriptome, metabolome, proteome, and lipidome methods to uncover the causes of leaf color variations and investigate their impacts on the accumulation of crucial bioactive metabolites in tea plants. Through a comprehensive review of various omics investigations, we note that decreased expression levels of critical genes in the biosynthesis of chlorophyll and carotenoids, activated chlorophyll degradation, and an impaired photosynthetic chain function are related to the chlorina phenotype in tea plants. For purple-leaf tea, increased expression levels of late biosynthetic genes in the flavonoid synthesis pathway and anthocyanin transport genes are the major and common causes of purple coloration. We have also summarized the influence of leaf color variation on amino acid, polyphenol, and lipid contents and put forward possible causes of these metabolic changes. Finally, this review further proposes the research demands in this field in the future. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)
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