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18 pages, 7498 KiB

Open AccessArticle

Comprehensive Genome-Wide Analysis of the Receptor-like Protein Gene Family and Functional Analysis of PeRLP8 Associated with Crown Rot Resistance in Passiflora edulis

by Weijun Yu, Fan Liang, Yue Li, Wenjie Jiang, Yongkang Li, Zitao Shen, Ting Fang and Lihui Zeng

Plants 2024, 13(23), 3264; https://doi.org/10.3390/plants13233264 - 21 Nov 2024

Viewed by 289

Abstract

Passion fruit (Passiflora edulis Sims) is a Passifloraceae plant with high economic value. Crown rot caused by Rhizoctonia solani is a major fungal disease, which can seriously reduce the yield and quality of passion fruit. Receptor-like proteins (RLPs), which act as pathogen [...] Read more.

Passion fruit (Passiflora edulis Sims) is a Passifloraceae plant with high economic value. Crown rot caused by Rhizoctonia solani is a major fungal disease, which can seriously reduce the yield and quality of passion fruit. Receptor-like proteins (RLPs), which act as pathogen recognition receptors, are widely involved in plant immune responses and developmental processes. However, the role of RLP family members of passion fruit in resistance to crown rot remains unclear. In this study, evolutionary dynamics analysis and comprehensive genomic characterization of the RLP genes family were performed on passion fruit. A total of 141 PeRLPs in the genome of the ‘Zixiang’ cultivar and 79 PesRLPs in the genome of the ‘Tainong’ cultivar were identified, respectively. Evolutionary analysis showed that proximal and dispersed duplication events were the primary drivers of RLP family expansion. RNA-seq data and RT-qPCR analysis showed that PeRLPs were constitutively expressed in different tissues and induced by low temperature, JA, MeJA, and SA treatments. The PeRLP8 gene was identified as the hub gene by RNA-seq analysis of passion fruit seedlings infected by Rhizoctonia solani. The expression levels of PeRLP8 of the resistant variety Passiflora maliformis (LG) were significantly higher than those of the sensitive variety Passiflora edulis f. flavicarpa (HG). Transient overexpression of PeRLP8 tobacco and passion fruit leaves enhanced the resistance to Rhizoctonia solani, resulting in reduced lesion areas by 52.06% and 54.17%, respectively. In addition, it can increase reactive oxygen species levels and upregulated expression of genes related to active oxygen biosynthesis and JA metabolism in passion fruit leaves. Our research provides new insights into the molecular mechanism and breeding strategy of passion fruit resistance to crown rot. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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21 pages, 3964 KiB

Open AccessArticle

Emission and Transcriptional Regulation of Aroma Variation in Oncidium Twinkle ‘Red Fantasy’ Under Diel Rhythm

by Yan Chen, Shengyuan Zhong, Lan Kong, Ronghui Fan, Yan Xu, Yiquan Chen and Huaiqin Zhong

Plants 2024, 13(22), 3232; https://doi.org/10.3390/plants13223232 - 17 Nov 2024

Viewed by 339

Abstract

Oncidium hybridum is one of the important cut-flowers in the world. However, the lack of aroma in its cut-flower varieties greatly limits the sustainable development of the Oncidium hybridum cut-flowers industry. This paper is an integral investigation of the diel pattern and influencing [...] Read more.

Oncidium hybridum is one of the important cut-flowers in the world. However, the lack of aroma in its cut-flower varieties greatly limits the sustainable development of the Oncidium hybridum cut-flowers industry. This paper is an integral investigation of the diel pattern and influencing factors of the aroma release of Oncidium Twinkle ‘Red Fantasy’. GC-MS analysis revealed that the release of 3-Carene peaked at 10:00, while Butyl tiglate and Prenyl senecioate did so at 14:00, with a diel rhythm. By analyzing the correlation network between aroma component synthesis and differentially expressed genes, 15 key structural genes were detected and regulated by multiple circadian rhythm-related transcription factors. Cluster-17371.18_TPS, Cluster-65495.1_TPS, Cluster-46699.0_TPS, Cluster-60935.10_DXS, Cluster-47205.4_IDI, and Cluster-65313.7_LOX were key genes in the terpenoid and fatty acid derivative biosynthetic pathway, which were co-expressed with aroma release. Constant light/dark treatments revealed that the diurnal release of 3-Carene may be influenced by light and the circadian clock, and Butyl tiglate and Prenyl senecioate may be mainly determined by endogenous circadian clock. Under constant light treatment, the TPS, DXS, IDI, and LOX genes seem to lose their regulatory role in the release of aroma compounds from Oncidium Twinkle ‘Red Fantasy’. Under constant dark treatment, the TPS genes were consistent with the release pattern of 3-Carene, which may be a key factor in regulating the diel rhythm of 3-Carene biosynthesis. These results laid a theoretical foundation for the study of floral transcriptional regulation and genetic engineering technology breeding of Oncidium hybridum. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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19 pages, 15466 KiB

Open AccessArticle

Transcriptomic Analysis Reveals the Mechanism of Color Formation in the Peel of an Evergreen Pomegranate Cultivar ‘Danruo No.1’ During Fruit Development

by Xiaowen Wang, Chengkun Yang, Wencan Zhu, Zhongrui Weng, Feili Li, Yuanwen Teng, Kaibing Zhou, Minjie Qian and Qin Deng

Plants 2024, 13(20), 2903; https://doi.org/10.3390/plants13202903 - 17 Oct 2024

Viewed by 595

Abstract

Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of [...] Read more.

Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of ‘Danruo No. 1’ pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease–increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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17 pages, 2929 KiB

Open AccessArticle

Transcriptomic and Metabolomic Analysis Reveals the Potential Roles of Polyphenols and Flavonoids in Response to Sunburn Stress in Chinese Olive (Canarium album)

by Yu Long, Chaogui Shen, Ruilian Lai, Meihua Zhang, Qilin Tian, Xiaoxia Wei and Rujian Wu

Plants 2024, 13(17), 2369; https://doi.org/10.3390/plants13172369 - 25 Aug 2024

Viewed by 792

Abstract

Sunburn stress is one of the main environmental stress factors that seriously affects the fruit development and quality of Chinese olive, a tropical and subtropical fruit in south China. Therefore, the understanding of the changes in physiological, biochemical, metabolic, and gene expression in [...] Read more.

Sunburn stress is one of the main environmental stress factors that seriously affects the fruit development and quality of Chinese olive, a tropical and subtropical fruit in south China. Therefore, the understanding of the changes in physiological, biochemical, metabolic, and gene expression in response to sunburn stress is of great significance for the industry and breeding of Chinese olive. In this study, the different stress degrees of Chinese olive fruits, including serious sunburn injury (SSI), mild sunburn injury (MSI), and ordinary (control check, CK) samples, were used to identify the physiological and biochemical changes and explore the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) by using transcriptomics and metabolomics. Compared with CK, the phenotypes, antioxidant capacity, and antioxidant-related enzyme activities of sunburn stress samples changed significantly. Based on DEG-based KEGG metabolic pathway analysis of transcriptomics, the polyphenol and flavonoid-related pathways, including phenylpropanoid biosynthesis, sesquiterpenoid, and triterpenoid biosynthesis, monoterpene biosynthesis, carotenoid biosynthesis, isoflavonoid biosynthesis, flavonoid biosynthesis, were enriched under sunburn stress of Chinese olive. Meanwhile, 33 differentially accumulated polyphenols and 99 differentially accumulated flavonoids were identified using metabolomics. According to the integration of transcriptome and metabolome, 15 and 8 DEGs were predicted to regulate polyphenol and flavonoid biosynthesis in Chinese olive, including 4-coumarate-CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), cinnamoyl-alcohol dehydrogenase (CAD), chalcone synthase (CHS), flavanone-3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS). Additionally, the content of total polyphenols and flavonoids was found to be significantly increased in MSI and SSI samples compared with CK. Our research suggested that the sunburn stress probably activates the transcription of the structural genes involved in polyphenol and flavonoid biosynthesis in Chinese olive fruits to affect the antioxidant capacity and increase the accumulation of polyphenols and flavonoids, thereby responding to this abiotic stress. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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13 pages, 3373 KiB

Open AccessArticle

Characterization of bZIP Transcription Factors in Transcriptome of Chrysanthemum mongolicum and Roles of CmbZIP9 in Drought Stress Resistance

by Xuan Wang, Yuan Meng, Shaowei Zhang, Zihan Wang, Kaimei Zhang, Tingting Gao and Yueping Ma

Plants 2024, 13(15), 2064; https://doi.org/10.3390/plants13152064 - 26 Jul 2024

Viewed by 665

Abstract

bZIP transcription factors play important roles in regulating plant development and stress responses. Although bZIPs have been identified in many plant species, there is little information on the bZIPs in Chrysanthemum. In this study, bZIP TFs were identified from the leaf transcriptome [...] Read more.

bZIP transcription factors play important roles in regulating plant development and stress responses. Although bZIPs have been identified in many plant species, there is little information on the bZIPs in Chrysanthemum. In this study, bZIP TFs were identified from the leaf transcriptome of C. mongolicum, a plant naturally tolerant to drought. A total of 28 full-length bZIP family members were identified from the leaf transcriptome of C. mongolicum and were divided into five subfamilies based on their phylogenetic relationships with the bZIPs from Arabidopsis. Ten conserved motifs were detected among the bZIP proteins of C. mongolicum. Subcellular localization assays revealed that most of the CmbZIPs were predicted to be localized in the nucleus. A novel bZIP gene, designated as CmbZIP9, was cloned based on a sequence of the data of the C. mongolicum transcriptome and was overexpressed in tobacco. The results indicated that the overexpression of CmbZIP9 reduced the malondialdehyde (MDA) content and increased the peroxidase (POD) and superoxide dismutase (SOD) activities as well as the expression levels of stress-related genes under drought stress, thus enhancing the drought tolerance of transgenic tobacco lines. These results provide a theoretical basis for further exploring the functions of the bZIP family genes and lay a foundation for stress resistance improvement in chrysanthemums in the future. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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18 pages, 16224 KiB

Open AccessArticle

Genome-Wide Identification of the CYP716 Gene Family in Platycodon grandiflorus (Jacq.) A. DC. and Its Role in the Regulation of Triterpenoid Saponin Biosynthesis

by Wuhua Zhang, Javed Iqbal, Zhihui Hou, Yingdong Fan, Jie Dong, Chengzhi Liu, Tao Yang, Daidi Che, Jinzhu Zhang and Dawei Xin

Plants 2024, 13(14), 1946; https://doi.org/10.3390/plants13141946 - 16 Jul 2024

Viewed by 973

Abstract

The main type of saponins occurring in the root of Platycodon grandiflorus (Jacq.) A. DC. are oleanolic acid glycosides. The CYP716 gene family plays a major role in catalyzing the conversion of β-amyrin into oleanolic acid. However, studies on the CYP716 genes in [...] Read more.

The main type of saponins occurring in the root of Platycodon grandiflorus (Jacq.) A. DC. are oleanolic acid glycosides. The CYP716 gene family plays a major role in catalyzing the conversion of β-amyrin into oleanolic acid. However, studies on the CYP716 genes in P. grandiflorus are limited, and its evolutionary history remains poorly understood. In this study, 22 PgCYP716 genes were identified, distributed among seven subfamilies. Cis-acting elements of the PgCYP716 promoters were mainly involved in plant hormone regulation and responses to abiotic stresses. PgCYP716A264, PgCYP716A391, PgCYP716A291, and PgCYP716BWv3 genes were upregulated in the root and during saponin accumulation, as shown by RNA-seq analysis, suggesting that these four genes play an important role in saponin synthesis. The results of subcellular localization indicated that these four genes encoded membrane proteins. Furthermore, the catalytic activity of these four genes was proved in the yeast, which catalyzed the conversion of β-amyrin into oleanolic acid. We found that the content of β-amyrin, platycodin D, platycoside E, platycodin D3, and total saponins increased significantly when either of the four genes was over expressed in the transgenic hair root. In addition, the expression of PgSS, PgGPPS2, PgHMGS, and PgSE was also upregulated while these four genes were overexpressed. These data support that these four PgCYP716 enzymes oxidize β-amyrin to produce oleanolic acid, ultimately promoting saponin accumulation by activating the expression of upstream pathway genes. Our results enhanced the understanding of the functional variation among the PgCYP716 gene family involved in triterpenoid biosynthesis and provided a theoretical foundation for improving saponin content and enriching the saponin biosynthetic pathway in P. grandiflorus. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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19 pages, 12237 KiB

Open AccessArticle

Selection of Stable Reference Genes for QRT-PCR in Tree Peony ‘Doulv’ and Functional Analysis of PsCUC3

by Shuang Zhou, Chao Ma, Wenbin Zhou, Shuangcheng Gao, Dianyun Hou, Lili Guo and Guoan Shi

Plants 2024, 13(13), 1741; https://doi.org/10.3390/plants13131741 - 24 Jun 2024

Cited by 1 | Viewed by 931

Abstract

(1) Background: Tree peonies display extensive cultivar diversity due to widespread hybridization, resulting in a complex genetic architecture. This complexity complicates the selection of universal reference genes across different cultivars for qRT-PCR analyses. Paeonia suffruticosa ‘Doulv’, notable for its unique green blooms in [...] Read more.

(1) Background: Tree peonies display extensive cultivar diversity due to widespread hybridization, resulting in a complex genetic architecture. This complexity complicates the selection of universal reference genes across different cultivars for qRT-PCR analyses. Paeonia suffruticosa ‘Doulv’, notable for its unique green blooms in China, exhibits chlorosis post-flowering and features petaloid stamens and pistils. (2) Methods: Based on published literature and RNA-seq data from ‘Doulv’, nine candidate reference genes—ACT (Actin), TUB (β-Tubulin), UBC (Ubiquitin Conjugating Enzyme), UBQ (Ubiquitin), UPL (Ubiquitin Protein Ligase), PP2A (Protein Phosphatase 2A), PP2C (Protein Phosphatase 2C), MBF1A (Multiprotein Bridging Factor 1A), and GAPDH (Glyceraldehyde-3-Phosphate Dehydrogenase)—were selected. Their expression stability was assessed across various tissues and developmental stages of ‘Doulv’ flowers using qRT-PCR, with evaluations conducted via GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0. Gene cloning and expression analyses of PsCUC3, including its subcellular localization, were performed. (3) Results: GAPDH and ACT were identified as the most stable reference genes in petaloid stamens across various developmental stages of ‘Doulv’, whereas UBC and MBF1A were optimal across different tissues. Notably, specific conserved amino acids in PsCUC3 from ‘Doulv’ diverged from those in NAM/CUC3 proteins of other species, impacting its protein structure. PsCUC3 expression analysis revealed no correlation with chlorophyll content in petaloid stamens but an association with petaloid organ development. Furthermore, PsCUC3 was predominantly localized in the nucleus. (4) Conclusions: This study comprehensively evaluated suitable reference genes using GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0 software, establishing a robust qRT-PCR detection system for ‘Doulv’ peony. These results provide a solid experimental foundation for further research on ‘Doulv’ peony. Building on this experimental foundation, the functional analysis of the PsCUC3 gene was conducted. The findings suggest a potential association between the PsCUC3 gene and floral morphology alterations in ‘Doulv’, identifying PsCUC3 as crucial for understanding the molecular mechanisms influencing floral structure in tree peonies. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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18 pages, 2900 KiB

Open AccessArticle

Regulatory Mechanism of Proanthocyanidins in Grape Peels Using vvi-miR828a and Its Target Gene VvMYBPA1

by Lingqi Yue, Jingjing He, Tian Gan, Songtao Jiu, Muhammad Khalil-Ur-Rehman, Kunyu Liu, Miao Bai, Guoshun Yang and Yanshuai Xu

Plants 2024, 13(12), 1688; https://doi.org/10.3390/plants13121688 - 18 Jun 2024

Viewed by 836

Abstract

Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate [...] Read more.

Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars ‘Italia’ and ‘Benitaka’. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in ‘Italia’ at 10 and 11 wpf was significantly higher than that in ‘Benitaka’. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in ‘Benitaka’ was significantly higher than that in ‘Italia’; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in ‘Italia’ and ‘Benitaka’ peels at 11 wpf demonstrated that the PA content of ‘Benitaka’ was significantly higher than that of ‘Italia’. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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16 pages, 4357 KiB

Open AccessArticle

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

Cited by 2 | Viewed by 1517

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

Open AccessArticle

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

Cited by 3 | Viewed by 1867

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

Open AccessArticle

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

Cited by 4 | Viewed by 1497

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

Open AccessArticle

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 1351

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

Open AccessArticle

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

Cited by 2 | Viewed by 1373

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

Open AccessArticle

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

Cited by 1 | Viewed by 1804

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

Open AccessArticle

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

Cited by 3 | Viewed by 1608

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

Open AccessArticle

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 2 | Viewed by 1834

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

Open AccessArticle

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 1338

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

Open AccessArticle

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 5 | Viewed by 1462

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

Open AccessArticle

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 6 | Viewed by 1642

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

Open AccessEditor’s ChoiceArticle

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 4 | Viewed by 2248

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

Open AccessArticle

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

Cited by 1 | Viewed by 1828

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

Open AccessArticle

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 7 | Viewed by 1856

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

Open AccessArticle

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 3 | Viewed by 1945

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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24 pages, 1433 KiB

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Exploiting Brassica rapa L. subsp. pekinensis Genome Research

by Faujiah Nurhasanah Ritonga, Zeyu Gong, Yihui Zhang, Fengde Wang, Jianwei Gao, Cheng Li and Jingjuan Li

Plants 2024, 13(19), 2823; https://doi.org/10.3390/plants13192823 - 9 Oct 2024

Viewed by 905

Abstract

Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the [...] Read more.

Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species. Full article

(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics)

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27 pages, 2972 KiB

Open AccessReview

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

Cited by 3 | Viewed by 1881

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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