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16 pages, 4554 KiB

Open AccessArticle

Transcriptomic Analysis of Hormone Signal Transduction, Carbohydrate Metabolism, Heat Shock Proteins, and SCF Complexes before and after Fertilization of Korean Pine Ovules

by Xiaoqian Yu, Xueqing Liu, Yuanxing Wang, Yue Zhang, Hailong Shen and Ling Yang

Int. J. Mol. Sci. 2023, 24(7), 6570; https://doi.org/10.3390/ijms24076570 - 31 Mar 2023

Cited by 1 | Viewed by 1035

Abstract

The fertilization process is a critical step in plant reproduction. However, the mechanism of action and mode of regulation of the fertilization process in gymnosperms remain unclear. In this study, we investigated the molecular regulatory networks involved in the fertilization process in Korean [...] Read more.

The fertilization process is a critical step in plant reproduction. However, the mechanism of action and mode of regulation of the fertilization process in gymnosperms remain unclear. In this study, we investigated the molecular regulatory networks involved in the fertilization process in Korean pine ovules through anatomical observation, physiological and biochemical assays, and transcriptome sequencing technology. The morphological and physiological results indicated that fertilization proceeds through the demise of the proteinaceous vacuole, egg cell division, and pollen tube elongation. Auxin, cytokinin, soluble sugar, and soluble starch contents begin to decline upon fertilization. Transcriptomic data analysis revealed a large number of differentially expressed genes at different times before and after fertilization. These genes were primarily involved in pathways associated with plant hormone signal transduction, protein processing in the endoplasmic reticulum, fructose metabolism, and mannose metabolism. The expression levels of several key genes were further confirmed by qRT-PCR. These findings represent an important step towards understanding the mechanisms underlying morphological changes in the Korean pine ovule during fertilization, and the physiological and transcriptional analyses lay a foundation for in-depth studies of the molecular regulatory network of the Korean pine fertilization process. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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20 pages, 11670 KiB

Open AccessArticle

Construction of ceRNA Networks at Different Stages of Somatic Embryogenesis in Garlic

by Yunhe Bai, Min Liu, Rong Zhou, Fangling Jiang, Ping Li, Mengqian Li, Meng Zhang, Hanyu Wei and Zhen Wu

Int. J. Mol. Sci. 2023, 24(6), 5311; https://doi.org/10.3390/ijms24065311 - 10 Mar 2023

Cited by 3 | Viewed by 1502

Abstract

LncRNA (long non-coding RNA) and mRNA form a competitive endogenous RNA (ceRNA) network by competitively binding to common miRNAs. This network regulates various processes of plant growth and development at the post-transcriptional level. Somatic embryogenesis is an effective means of plant virus-free rapid [...] Read more.

LncRNA (long non-coding RNA) and mRNA form a competitive endogenous RNA (ceRNA) network by competitively binding to common miRNAs. This network regulates various processes of plant growth and development at the post-transcriptional level. Somatic embryogenesis is an effective means of plant virus-free rapid propagation, germplasm conservation, and genetic improvement, which is also a typical process to study the ceRNA regulatory network during cell development. Garlic is a typical asexual reproductive vegetable. Somatic cell culture is an effective means of virus-free rapid propagation in garlic. However, the ceRNA regulatory network of somatic embryogenesis remains unclear in garlic. In order to clarify the regulatory role of the ceRNA network in garlic somatic embryogenesis, we constructed lncRNA and miRNA libraries of four important stages (explant stage: EX; callus stage: AC; embryogenic callus stage: EC; globular embryo stage: GE) in the somatic embryogenesis of garlic. It was found that 44 lncRNAs could be used as precursors of 34 miRNAs, 1511 lncRNAs were predicted to be potential targets of 144 miRNAs, and 45 lncRNAs could be used as eTMs of 29 miRNAs. By constructing a ceRNA network with miRNA as the core, 144 miRNAs may bind to 1511 lncRNAs and 12,208 mRNAs. In the DE lncRNA-DE miRNA-DE mRNA network of adjacent stages of somatic embryo development (EX-VS-CA, CA-VS-EC, EC-VS-GE), by KEGG enrichment of adjacent stage DE mRNA, plant hormone signal transduction, butyric acid metabolism, and C5-branched dibasic acid metabolism were significantly enriched during somatic embryogenesis. Since plant hormones play an important role in somatic embryogenesis, further analysis of plant hormone signal transduction pathways revealed that the auxin pathway-related ceRNA network (lncRNAs-miR393s-TIR) may play a role in the whole stage of somatic embryogenesis. Further verification by RT-qPCR revealed that the lncRNA125175-miR393h-TIR2 network plays a major role in the network and may affect the occurrence of somatic embryos by regulating the auxin signaling pathway and changing the sensitivity of cells to auxin. Our results lay the foundation for studying the role of the ceRNA network in the somatic embryogenesis of garlic. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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19 pages, 8510 KiB

Open AccessArticle

Genome-Wide Analysis of the FBA Subfamily of the Poplar F-Box Gene Family and Its Role under Drought Stress

by Cong-Hua Feng, Meng-Xue Niu, Xiao Liu, Yu Bao, Shujing Liu, Meiying Liu, Fang He, Shuo Han, Chao Liu, Hou-Ling Wang, Weilun Yin, Yanyan Su and Xinli Xia

Int. J. Mol. Sci. 2023, 24(5), 4823; https://doi.org/10.3390/ijms24054823 - 02 Mar 2023

Cited by 3 | Viewed by 1928

Abstract

F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is [...] Read more.

F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is one of the largest subgroups of the widely prevalent F-box family and plays significant roles in plant development and stress response. However, the FBA gene family in poplar has not been systematically studied to date. In this study, a total of 337 F-box candidate genes were discovered based on the fourth-generation genome resequencing of P. trichocarpa. The domain analysis and classification of candidate genes revealed that 74 of these candidate genes belong to the FBA protein family. The poplar F-box genes have undergone multiple gene replication events, particularly in the FBA subfamily, and their evolution can be attributed to genome-wide duplication (WGD) and tandem duplication (TD). In addition, we investigated the P. trichocarpa FBA subfamily using the PlantGenIE database and quantitative real-time PCR (qRT-PCR); the results showed that they are expressed in the cambium, phloem and mature tissues, but rarely expressed in young leaves and flowers. Moreover, they are also widely involved in the drought stress response. At last, we selected and cloned PtrFBA60 for physiological function analysis and found that it played an important role in coping with drought stress. Taken together, the family analysis of FBA genes in P. trichocarpa provides a new opportunity for the identification of P. trichocarpa candidate FBA genes and elucidation of their functions in growth, development and stress response, thus demonstrating their utility in the improvement of P. trichocarpa. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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13 pages, 5575 KiB

Open AccessArticle

Application of Nicotinamide to Culture Medium Improves the Efficiency of Genome Editing in Hexaploid Wheat

by Wanxin Wang, Peipei Huang, Wenshuang Dai, Huali Tang, Yuliang Qiu, Yanan Chang, Zhiyang Han, Xi Li, Lipu Du, Xingguo Ye, Cheng Zou and Ke Wang

Int. J. Mol. Sci. 2023, 24(5), 4416; https://doi.org/10.3390/ijms24054416 - 23 Feb 2023

Cited by 3 | Viewed by 1486

Abstract

Histone acetylation is the earliest and most well-characterized of post-translation modifications. It is mediated by histone acetyltransferases (HAT) and histone deacetylases (HDAC). Histone acetylation could change the chromatin structure and status and further regulate gene transcription. In this study, nicotinamide, a histone deacetylase [...] Read more.

Histone acetylation is the earliest and most well-characterized of post-translation modifications. It is mediated by histone acetyltransferases (HAT) and histone deacetylases (HDAC). Histone acetylation could change the chromatin structure and status and further regulate gene transcription. In this study, nicotinamide, a histone deacetylase inhibitor (HDACi), was used to enhance the efficiency of gene editing in wheat. Transgenic immature and mature wheat embryos harboring a non-mutated GUS gene, the Cas9 and a GUS-targeting sgRNA were treated with nicotinamide in two concentrations (2.5 and 5 mM) for 2, 7, and 14 days in comparison with a no-treatment control. The nicotinamide treatment resulted in GUS mutations in up to 36% of regenerated plants, whereas no mutants were obtained from the non-treated embryos. The highest efficiency was achieved when treated with 2.5 mM nicotinamide for 14 days. To further validate the impact of nicotinamide treatment on the effectiveness of genome editing, the endogenous TaWaxy gene, which is responsible for amylose synthesis, was tested. Utilizing the aforementioned nicotinamide concentration to treat embryos containing the molecular components for editing the TaWaxy gene, the editing efficiency could be increased to 30.3% and 13.3%, respectively, for immature and mature embryos in comparison to the 0% efficiency observed in the control group. In addition, nicotinamide treatment during transformation progress could also improve the efficiency of genome editing approximately threefold in a base editing experiment. Nicotinamide, as a novel approach, may be employed to improve the editing efficacy of low-efficiency genome editing tools such as base editing and prime editing (PE) systems in wheat. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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24 pages, 8252 KiB

Open AccessArticle

Genome-Wide Characterization and Gene Expression Analyses of Malate Dehydrogenase (MDH) Genes in Low-Phosphorus Stress Tolerance of Chinese Fir (Cunninghamia lanceolata)

by Yawen Lin, Wanting Chen, Qiang Yang, Yajing Zhang, Xiangqing Ma and Ming Li

Int. J. Mol. Sci. 2023, 24(5), 4414; https://doi.org/10.3390/ijms24054414 - 23 Feb 2023

Cited by 5 | Viewed by 1869

Abstract

Malate dehydrogenase (MDH) genes play vital roles in developmental control and environmental stress tolerance in sessile plants by modulating the organic acid–malic acid level. However, MDH genes have not yet been characterized in gymnosperm, and their roles in nutrient deficiency are largely unexplored. [...] Read more.

Malate dehydrogenase (MDH) genes play vital roles in developmental control and environmental stress tolerance in sessile plants by modulating the organic acid–malic acid level. However, MDH genes have not yet been characterized in gymnosperm, and their roles in nutrient deficiency are largely unexplored. In this study, 12 MDH genes were identified in Chinese fir (Cunninghamia lanceolata), namely, ClMDH-1, -2, -3, …, and -12. Chinese fir is one of the most abundant commercial timber trees in China, and low phosphorus has limited its growth and production due to the acidic soil of southern China. According to the phylogenetic analysis, MDH genes were classified into five groups, and Group 2 genes (ClMDH-7, -8, -9, and 10) were only found to be present in Chinese fir but not in Arabidopsis thaliana and Populus trichocarpa. In particular, the Group 2 MDHs also had specific functional domains—Ldh_1_N (malidase NAD-binding functional domain) and Ldh_1_C (malate enzyme C-terminal functional domain)—indicating a specific function of ClMDHs in the accumulation of malate. All ClMDH genes contained the conserved MDH gene characteristic functional domains Ldh_1_N and Ldh_1_C, and all ClMDH proteins exhibited similar structures. Twelve ClMDH genes were identified from eight chromosomes, involving fifteen ClMDH homologous gene pairs, each with a Ka/Ks ratio of <1. The analysis of cis-elements, protein interactions, and transcription factor interactions of MDHs showed that the ClMDH gene might play a role in plant growth and development, and in response to stress mechanisms. The results of transcriptome data and qRT-PCR validation based on low-phosphorus stress showed that ClMDH1, ClMDH6, ClMDH7, ClMDH2, ClMDH4, ClMDH5, ClMDH10 and ClMDH11 were upregulated under low-phosphorus stress and played a role in the response of fir to low-phosphorus stress. In conclusion, these findings lay a foundation for further improving the genetic mechanism of the ClMDH gene family in response to low-phosphorus stress, exploring the potential function of this gene, promoting the improvement of fir genetics and breeding, and improving production efficiency. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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18 pages, 3679 KiB

Open AccessArticle

Transcriptomic and Proteomic Analyses of Celery Cytoplasmic Male Sterile Line and Its Maintainer Line

by Haoran Wang, Qing Cheng, Ziqi Zhai, Xiangyun Cui, Mingxuan Li, Ruiquan Ye, Liang Sun and Huolin Shen

Int. J. Mol. Sci. 2023, 24(4), 4194; https://doi.org/10.3390/ijms24044194 - 20 Feb 2023

Viewed by 1416

Abstract

Male sterility is a common phenomenon in the plant kingdom and based on the organelles harboring the male-sterility genes, it can be classified into the genic male sterility (GMS) and the cytoplasmic male sterility (CMS). In every generation, CMS can generate 100% male-sterile [...] Read more.

Male sterility is a common phenomenon in the plant kingdom and based on the organelles harboring the male-sterility genes, it can be classified into the genic male sterility (GMS) and the cytoplasmic male sterility (CMS). In every generation, CMS can generate 100% male-sterile population, which is very important for the breeders to take advantage of the heterosis and for the seed producers to guarantee the seed purity. Celery is a cross-pollinated plant with the compound umbel type of inflorescence which carries hundreds of small flowers. These characteristics make CMS the only option to produce the commercial hybrid celery seeds. In this study, transcriptomic and proteomic analyses were performed to identify genes and proteins that are associated with celery CMS. A total of 1255 differentially expressed genes (DEGs) and 89 differentially expressed proteins (DEPs) were identified between the CMS and its maintainer line, then 25 genes were found to differentially expressed at both the transcript and protein levels. Ten DEGs involved in the fleece layer and outer pollen wall development were identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, most of which were down-regulated in the sterile line W99A. These DEGs and DEPs were mainly enriched in the pathways of “phenylpropanoid/sporopollenin synthesis/metabolism”, “energy metabolism”, “redox enzyme activity” and “redox processes”. Results obtained in this study laid a foundation for the future investigation of mechanisms of pollen development as well as the reasons for the CMS in celery. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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19 pages, 15456 KiB

Open AccessArticle

Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries

by Lili Guo, Shixiong Lu, Tao Liu, Guojie Nai, Jiaxuan Ren, Huimin Gou, Baihong Chen and Juan Mao

Int. J. Mol. Sci. 2023, 24(4), 4049; https://doi.org/10.3390/ijms24044049 - 17 Feb 2023

Cited by 9 | Viewed by 1760

Abstract

Protein phosphatase 2C (PP2C) is a negative regulator of serine/threonine residue protein phosphatase and plays an important role in abscisic acid (ABA) and abiotic-stress-mediated signaling pathways in plants. The genome complexity of woodland strawberry and pineapple strawberry is different due to the difference [...] Read more.

Protein phosphatase 2C (PP2C) is a negative regulator of serine/threonine residue protein phosphatase and plays an important role in abscisic acid (ABA) and abiotic-stress-mediated signaling pathways in plants. The genome complexity of woodland strawberry and pineapple strawberry is different due to the difference in chromosome ploidy. This study conducted a genome-wide investigation of the FvPP2C (Fragaria vesca) and FaPP2C (Fragaria ananassa) gene family. Fifty-six FvPP2C genes and 228 FaPP2C genes were identified from the woodland strawberry and pineapple strawberry genomes, respectively. FvPP2Cs were distributed on seven chromosomes, and FaPP2Cs were distributed on 28 chromosomes. The size of the FaPP2C gene family was significantly different from that of the FvPP2C gene family, but both FaPP2Cs and FvPP2Cs were localized in the nucleus, cytoplasm, and chloroplast. Phylogenetic analysis revealed that 56 FvPP2Cs and 228 FaPP2Cs could be divided into 11 subfamilies. Collinearity analysis showed that both FvPP2Cs and FaPP2Cs had fragment duplication, and the whole genome duplication was the main cause of PP2C gene abundance in pineapple strawberry. FvPP2Cs mainly underwent purification selection, and there were both purification selection and positive selection effects in the evolution of FaPP2Cs. Cis-acting element analysis found that the PP2C family genes of woodland and pineapple strawberries mainly contained light responsive elements, hormone responsive elements, defense and stress responsive elements, and growth and development-related elements. The results of quantitative real-time PCR (qRT-PCR) showed that the FvPP2C genes showed different expression patterns under ABA, salt, and drought treatment. The expression level of FvPP2C18 was upregulated after stress treatment, which may play a positive regulatory role in ABA signaling and abiotic stress response mechanisms. This study lays a foundation for further investigation on the function of the PP2C gene family. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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15 pages, 4645 KiB

Open AccessArticle

A Small Subunit of Geranylgeranyl Diphosphate Synthase Functions as an Active Regulator of Carotenoid Synthesis in Nicotiana tabacum

by Chen Dong, Mei Zhang, Shanshan Song, Fang Wei, Lili Qin, Puqing Fan, Yongchun Shi, Xiaoran Wang and Ran Wang

Int. J. Mol. Sci. 2023, 24(2), 992; https://doi.org/10.3390/ijms24020992 - 04 Jan 2023

Cited by 1 | Viewed by 1534

Abstract

As one of the most imperative antioxidants in higher plants, carotenoids serve as accessory pigments to harvest light for photosynthesis and photoprotectors for plants to adapt to high light stress. Here, we report a small subunit (SSU) of geranylgeranyl diphosphate synthase (GGPPS) in [...] Read more.

As one of the most imperative antioxidants in higher plants, carotenoids serve as accessory pigments to harvest light for photosynthesis and photoprotectors for plants to adapt to high light stress. Here, we report a small subunit (SSU) of geranylgeranyl diphosphate synthase (GGPPS) in Nicotiana tabacum, NtSSU II, which takes part in the regulation carotenoid biosynthesis by forming multiple enzymatic components with NtGGPPS1 and downstream phytoene synthase (NtPSY1). NtSSU II transcript is widely distributed in various tissues and stimulated by low light and high light treatments. The confocal image revealed that NtSSU II was localized in the chloroplast. Bimolecular fluorescence complementation (BiFC) indicated that NtSSU II and NtGGPPS1 formed heterodimers, which were able to interact with phytoene synthase (NtPSY1) to channel GGPP into the carotenoid production. CRISPR/Cas9-induced ntssu II mutant exhibited decreased leaf area and biomass, along with a decline in carotenoid and chlorophyll accumulation. Moreover, the genes involved in carotenoid biosynthesis were also downregulated in transgenic plants of ntssu II mutant. Taken together, the newly identified NtSSU II could form multiple enzymatic components with NtGGPPS1 and NtPSY1 to regulate carotenoid biosynthesis in N. tabacum, in addition to the co-expression of genes in carotenoids biosynthetic pathways. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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19 pages, 7425 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Mechanisms of Tolerance to High Concentrations of Calcium Chloride Stress in Parachlorella kessleri

by Xudong Liu, Jinli Zhao, Fangru Nan, Qi Liu, Junping Lv, Jia Feng and Shulian Xie

Int. J. Mol. Sci. 2023, 24(1), 651; https://doi.org/10.3390/ijms24010651 - 30 Dec 2022

Cited by 2 | Viewed by 1499

Abstract

Salt stress is one of the abiotic stress factors that affect the normal growth and development of higher plants and algae. However, few research studies have focused on calcium stress, especially in algae. In this study, the mechanism of tolerance to high calcium [...] Read more.

Salt stress is one of the abiotic stress factors that affect the normal growth and development of higher plants and algae. However, few research studies have focused on calcium stress, especially in algae. In this study, the mechanism of tolerance to high calcium stress of a Parachlorella kessleri strain was explored by the method of transcriptomics combined with physiological and morphological analysis. Concentrations of CaCl₂ 100 times (3.6 g/L) and 1000 times (36 g/L) greater than the standard culture were set up as stresses. The results revealed the algae could cope with high calcium stress mainly by strengthening photosynthesis, regulating osmotic pressure, and inducing antioxidant defense. Under the stress of 3.6 g/L CaCl₂, the algae grew well with normal cell morphology. Although the chlorophyll content was significantly reduced, the photosynthetic efficiency was well maintained by up-regulating the expression of some photosynthesis-related genes. The cells reduced oxidative damage by inducing superoxide dismutase (SOD) activities and selenoprotein synthesis. A large number of free amino acids were produced to regulate the osmotic potential. When in higher CaCl₂ stress of 36 g/L, the growth and chlorophyll content of algae were significantly inhibited. However, the algae still slowly grew and maintained the same photosynthetic efficiency, which resulted from significant up-regulation of massive photosynthesis genes. Antioxidant enzymes and glycerol were found to resist oxidative damage and osmotic stress, respectively. This study supplied algal research on CaCl₂ stress and provided supporting data for further explaining the mechanism of plant salt tolerance. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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10 pages, 2117 KiB

Open AccessArticle

Fine Mapping and Identification of a Candidate Gene of Downy Mildew Resistance, RPF2, in Spinach (Spinacia oleracea L.)

by Shuo Gao, Tiantian Lu, Hongbing She, Zhaosheng Xu, Helong Zhang, Zhiyuan Liu and Wei Qian

Int. J. Mol. Sci. 2022, 23(23), 14872; https://doi.org/10.3390/ijms232314872 - 28 Nov 2022

Cited by 1 | Viewed by 1367

Abstract

Downy mildew is a major threat to the economic value of spinach. The most effective approach to managing spinach downy mildew is breeding cultivars with resistance genes. The resistance allele RPF2 is effective against races 1–10 and 15 of Peronospora farinosa f. sp. [...] Read more.

Downy mildew is a major threat to the economic value of spinach. The most effective approach to managing spinach downy mildew is breeding cultivars with resistance genes. The resistance allele RPF2 is effective against races 1–10 and 15 of Peronospora farinosa f. sp. Spinaciae (P. effusa) and is widely used as a resistance gene. However, the gene and the linked marker of RPF2 remain unclear, which limit its utilization. Herein, we located the RPF2 gene in a 0.61 Mb region using a BC₁ population derived from Sp39 (rr) and Sp62 (RR) cultivars via kompetitive allele specific PCR (KASP) markers. Within this region, only one R gene, Spo12821, was identified based on annotation information. The amino acid sequence analysis showed that there were large differences in the length of the LRR domain between the parents. Additionally, a molecular marker, RPF2-IN12821, was developed based on the sequence variation in the Spo12821, and the evaluation in the BC₁ population produced a 100% match with resistance/susceptibility. The finding of the study could be valuable for improving our understanding of the genetic basis of resistance against the downy mildew pathogen and breeding resistance lines in the future. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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16 pages, 3868 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit (Passiflora edulis Sims)

by Yanhui Liu, Jieyu Yuan, Dan Zhang, Kao Deng, Gaifeng Chai, Youmei Huang, Suzhuo Ma, Yuan Qin and Lulu Wang

Int. J. Mol. Sci. 2022, 23(22), 14153; https://doi.org/10.3390/ijms232214153 - 16 Nov 2022

Cited by 2 | Viewed by 2014

Abstract

The SQUAMOSA promoter binding proteins (SBPs) gene family plays important roles in plant growth and development. The SBP gene family has been identified and reported in many species, but it has not been well studied in passion fruit. In this study, a total [...] Read more.

The SQUAMOSA promoter binding proteins (SBPs) gene family plays important roles in plant growth and development. The SBP gene family has been identified and reported in many species, but it has not been well studied in passion fruit. In this study, a total of 14 SBP genes were identified in passion fruit and named from PeSBP1 to PeSBP14 based on their chromosomal distribution. The phylogenetic tree, gene structure, conserved motifs, collinearity analysis, and expression patterns of the identified SBP members were analyzed. We classified the PeSBP genes into eight groups (I to VIII) according to the phylogenetic tree, gene structure, and conserved motifs. Synteny analysis found that 5 homologous gene pairs existed in PeSBP genes and 11 orthologous gene pairs existed between passion fruit and Arabidopsis. Synonymous nucleotide substitution analysis showed that the PeSBP genes were under strong negative selection. The expression pattern of PeSBP genes in seed, root, leaf, and flower showed that nine of the PeSBP genes displayed high expression in the leaf and the flower. The expression patterns of PeSBP3/6/8/9/10 were further detected by qRT-PCR. In addition, differences in the expression levels occurred for each gene in the different flower organs and at the different developmental stages. There were large differences among SBPs based on transcriptional levels under cold, heat, salt, and osmotic stress conditions. Altogether, this study provides an overview of SBP genes in passion fruit and lays the foundation for further functional analysis. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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19 pages, 3582 KiB

Open AccessArticle

Genome-Wide Prediction and Analysis of Oryza Species NRP Genes in Rice Blast Resistance

by Dong Liang, Junjie Yu, Tianqiao Song, Rongsheng Zhang, Yan Du, Mina Yu, Huijuan Cao, Xiayan Pan, Junqing Qiao, Youzhou Liu, Zhongqiang Qi and Yongfeng Liu

Int. J. Mol. Sci. 2022, 23(19), 11967; https://doi.org/10.3390/ijms231911967 - 08 Oct 2022

Viewed by 1980

Abstract

Members of the N-rich proteins (NRPs) gene family play important roles in the plant endoplasmic reticulum stress in response, which can be triggered by plant pathogens’ infection. Previous studies of the NRP gene family have been limited to only a few plants, such [...] Read more.

Members of the N-rich proteins (NRPs) gene family play important roles in the plant endoplasmic reticulum stress in response, which can be triggered by plant pathogens’ infection. Previous studies of the NRP gene family have been limited to only a few plants, such as soybean and Arabidopsis thaliana. Thus, their evolutionary characteristics in the Oryza species and biological functions in rice defense against the pathogenic fungus Magnaporthe oryzae have remained unexplored. In the present study, we demonstrated that the NRP genes family may have originated in the early stages of plant evolution, and that they have been strongly conserved during the evolution of the Oryza species. Domain organization of NRPs was found to be highly conserved within but not between subgroups. OsNRP1, an NRP gene in the Oryza sativa japonica group, was specifically up-regulated during the early stages of rice-M. oryzae interactions-inhibited M. oryzae infection. Predicted protein-protein interaction networks and transcription-factor binding sites revealed a candidate interactor, bZIP50, which may be involved in OsNRP1-mediated rice resistance against M. oryzae infection. Taken together, our results established a basis for future studies of the NRP gene family and provided molecular insights into rice immune responses to M. oryzae. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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14 pages, 3939 KiB

Open AccessArticle

Two Conserved Amino Acids Characterized in the Island Domain Are Essential for the Biological Functions of Brassinolide Receptors

by Wenjuan Li, Jiaojiao Zhang, Xiaoyi Tian, Hui Liu, Khawar Ali, Qunwei Bai, Bowen Zheng, Guang Wu and Hongyan Ren

Int. J. Mol. Sci. 2022, 23(19), 11454; https://doi.org/10.3390/ijms231911454 - 28 Sep 2022

Cited by 1 | Viewed by 1237

Abstract

Brassinosteroids (BRs) play important roles in plant growth and development, and BR perception is the pivotal process required to trigger BR signaling. In angiosperms, BR insensitive 1 (BRI1) is the essential BR receptor, because its mutants exhibit an extremely dwarf phenotype in Arabidopsis. [...] Read more.

Brassinosteroids (BRs) play important roles in plant growth and development, and BR perception is the pivotal process required to trigger BR signaling. In angiosperms, BR insensitive 1 (BRI1) is the essential BR receptor, because its mutants exhibit an extremely dwarf phenotype in Arabidopsis. Two other BR receptors, BRI1-like 1 (BRL1) and BRI1-like 3 (BRL3), are shown to be not indispensable. All BR receptors require an island domain (ID) responsible for BR perception. However, the biological functional significance of residues in the ID remains unknown. Based on the crystal structure and sequence alignments analysis of BR receptors, we identified two residues 597 and 599 of AtBRI1 that were highly conserved within a BR receptor but diversified among different BR receptors. Both of these residues are tyrosine in BRI1, while BRL1/BRL3 fixes two phenylalanines. The experimental findings revealed that, except BRI1Y597F and BRI1Y599F, substitutions of residues 597 and 599 with the remaining 18 amino acids differently impaired BR signaling and, surprisingly, BRI1Y599F showed a weaker phenotype than BRI1Y599 did, implying that these residues were the key sites to differentiate BR receptors from a non-BR receptor, and the essential BR receptor BRI1 from BRL1/3, which possibly results from positive selection via gain of function during evolution. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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17 pages, 5714 KiB

Open AccessArticle

Brassinosteroid Signaling Downstream Suppressor BIN2 Interacts with SLFRIGIDA-LIKE to Induce Early Flowering in Tomato

by Maqsood Khan, Bote Luo, Miaomiao Hu, Shangtan Fu, Jianwei Liu, Meng Jiang, Yan Zhao, Shuhua Huang, Shufen Wang and Xiaofeng Wang

Int. J. Mol. Sci. 2022, 23(19), 11264; https://doi.org/10.3390/ijms231911264 - 24 Sep 2022

Cited by 8 | Viewed by 1495

Abstract

Brassinosteroid (BR) signaling is very important in plant developmental processes. Its various components interact to form a signaling cascade. These components are widely studied in Arabidopsis; however, very little information is available on tomatoes. Brassinosteroid Insensitive 2 (BIN2), the downstream suppressor of BR [...] Read more.

Brassinosteroid (BR) signaling is very important in plant developmental processes. Its various components interact to form a signaling cascade. These components are widely studied in Arabidopsis; however, very little information is available on tomatoes. Brassinosteroid Insensitive 2 (BIN2), the downstream suppressor of BR signaling, plays a critical role in BR signal pathway, while FRIGIDA as a key suppressor of Flowering Locus C with overexpression could cause early flowering; however, how the BR signaling regulates FRIGIDA homologous protein to adjust flowering time is still unknown. This study identified 12 FRIGIDA-LIKE proteins with a conserved FRIGIDA domain in tomatoes. Yeast two-hybrid and BiFC confirmed that SlBIN2 interacts with 4 SlFRLs, which are sub-cellularly localized in the nucleus. Tissue-specific expression of SlFRLs was observed highly in young roots and flowers. Biological results revealed that SlFRLs interact with SlBIN2 to regulate early flowering. Further, the mRNA level of SlBIN2 also increased in SlFRL-overexpressed lines. The relative expression of SlCPD increased upon SlFRL silencing, while SlDWF and SlBIN2 were decreased, both of which are important for BR signaling. Our research firstly provides molecular evidence that BRs regulate tomato flowering through the interaction between SlFRLs and SlBIN2. This study will promote the understanding of the specific pathway essential for floral regulation. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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28 pages, 6885 KiB

Open AccessArticle

A Comparative Transcriptome Analysis Reveals the Molecular Mechanisms That Underlie Somatic Embryogenesis in Peaonia ostii ‘Fengdan’

by Huiting Ci, Changyue Li, Theint Thinzar Aung, Shunli Wang, Chen Yun, Fang Wang, Xiuxia Ren and Xiuxin Zhang

Int. J. Mol. Sci. 2022, 23(18), 10595; https://doi.org/10.3390/ijms231810595 - 13 Sep 2022

Cited by 6 | Viewed by 1844

Abstract

Low propagation rate is the primary problem that limits industry development of tree peony. In this study, a highly efficient regeneration system for tree peony using somatic embryogenesis (SE) was established. The transcriptomes of zygotic embryo explants (S0), non-embryonic callus (S1), embryonic callus [...] Read more.

Low propagation rate is the primary problem that limits industry development of tree peony. In this study, a highly efficient regeneration system for tree peony using somatic embryogenesis (SE) was established. The transcriptomes of zygotic embryo explants (S0), non-embryonic callus (S1), embryonic callus (S2), somatic embryos (S3), and regenerated shoots (S4) were analyzed to determine the regulatory mechanisms that underlie SE in tree peony. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of S1-vs-S2 and S1-vs-S3, respectively. The enriched DEGs were primarily involved in hormone signal transduction, stress response and the nucleus (epigenetic modifications). The results indicated that cell division, particularly asymmetric cell division, was enhanced in S3. Moreover, the genes implicated in cell fate determination played central roles in S3. Hormone signal pathways work in concert with epigenetic modifications and stress responses to regulate SE. SERK, WOX9, BBM, FUS3, CUC, and WUS were characterized as the molecular markers for tree peony SE. To our knowledge, this is the first study of the SE of tree peony using transcriptome sequencing. These results will improve our understanding of the molecular mechanisms that underly SE in tree peony and will benefit the propagation and genetic engineering of this plant. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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15 pages, 3139 KiB

Open AccessArticle

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

by Shu-Fen Li, Hong-Bing She, Long-Long Yang, Li-Na Lan, Xin-Yu Zhang, Li-Ying Wang, Yu-Lan Zhang, Ning Li, Chuan-Liang Deng, Wei Qian and Wu-Jun Gao

Int. J. Mol. Sci. 2022, 23(17), 10158; https://doi.org/10.3390/ijms231710158 - 05 Sep 2022

Cited by 10 | Viewed by 2019

Abstract

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level [...] Read more.

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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20 pages, 4551 KiB

Open AccessArticle

A TCP Transcription Factor in Malus halliana, MhTCP4, Positively Regulates Anthocyanins Biosynthesis

by Jiaxin Meng, Jiao Yin, Han Wang and Houhua Li

Int. J. Mol. Sci. 2022, 23(16), 9051; https://doi.org/10.3390/ijms23169051 - 12 Aug 2022

Cited by 5 | Viewed by 1670

Abstract

Anthocyanins belong to a group of flavonoids, which are the most important flower pigments. Clarifying the potential anthocyanins biosynthesis molecular mechanisms could facilitate artificial manipulation of flower pigmentation in plants. In this paper, we screened a differentially expressed gene, MhTCP4, from the [...] Read more.

Anthocyanins belong to a group of flavonoids, which are the most important flower pigments. Clarifying the potential anthocyanins biosynthesis molecular mechanisms could facilitate artificial manipulation of flower pigmentation in plants. In this paper, we screened a differentially expressed gene, MhTCP4, from the transcriptome data of Malus halliana petals at different development stages and explored its role in anthocyanins biosynthesis. The transcriptome data and qRT-PCR analysis showed that the expression level of MhTCP4 gradually decreased from the flower color fades. Tissue specific expression analysis showed MhTCP4 was expressed in the petal, leaf, and fruit of M. halliana, and was highly expressed in the scarlet petal. Overexpression of MhTCP4 promoted anthocyanins accumulation and increased pigments in infected parts of M. ‘Snowdrift’ and M. ‘Fuji’ fruit peels. In contrast, when endogenous MhTCP4 was silenced, the anthocyanins accumulation was inhibited and pigments decreased in the infected peels. The qRT-PCR analysis revealed that overexpression or silence of MhTCP4 caused expression changes of a series of structural genes included in anthocyanins biosynthesis pathway. The yeast two-hybrid assays indicated that MhTCP4 did not interact with MhMYB10. Furthermore, the yeast one-hybrid assays indicated that MhTCP4 did not directly bind to the promoter of MhMYB10, but that of the anthocyanins biosynthesis genes, MhCHI and MhF3′H. Dual luciferase assays further confirmed that MhTCP4 can strongly activate the promoters of MhCHI and MhF3′H in tobacco. Overall, the results suggest that MhTCP4 positively regulates anthocyanins biosynthesis by directly activated MhCHI and MhF3′H in M. halliana flowers. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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16 pages, 1916 KiB

Open AccessArticle

Mitogen-Activated Protein Kinases Associated Sites of Tobacco Repression of Shoot Growth Regulates Its Localization in Plant Cells

by Luyao Wang, Ying Gui, Bingye Yang, Wenpan Dong, Peiling Xu, Fangjie Si, Wei Yang, Yuming Luo, Jianhua Guo, Dongdong Niu and Chunhao Jiang

Int. J. Mol. Sci. 2022, 23(16), 8941; https://doi.org/10.3390/ijms23168941 - 11 Aug 2022

Cited by 1 | Viewed by 1315

Abstract

Plant defense and growth rely on multiple transcriptional factors (TFs). Repression of shoot growth (RSG) is a TF belonging to a bZIP family in tobacco, known to be involved in plant gibberellin feedback regulation by inducing the expression of key genes. The tobacco [...] Read more.

Plant defense and growth rely on multiple transcriptional factors (TFs). Repression of shoot growth (RSG) is a TF belonging to a bZIP family in tobacco, known to be involved in plant gibberellin feedback regulation by inducing the expression of key genes. The tobacco calcium-dependent protein kinase CDPK1 was reported to interact with RSG and manipulate its intracellular localization by phosphorylating Ser-114 of RSG previously. Here, we identified tobacco mitogen-activated protein kinase 3 (NtMPK3) as an RSG-interacting protein kinase. Moreover, the mutation of the predicted MAPK-associated phosphorylation site of RSG (Thr-30, Ser-74, and Thr-135) significantly altered the intracellular localization of the NtMPK3-RSG interaction complex. Nuclear transport of RSG and its amino acid mutants (T30A and S74A) were observed after being treated with plant defense elicitor peptide flg22 within 5 min, and the two mutated RSG swiftly re-localized in tobacco cytoplasm within 30 min. In addition, triple-point mutation of RSG (T30A/S74A/T135A) mimics constant unphosphorylated status, and is predominantly localized in tobacco cytoplasm. RSG (T30A/S74A/T135A) showed no re-localization effect under the treatments of flg22, B. cereus AR156, or GA₃, and over-expression of this mutant in tobacco resulted in lower expression levels of downstream gene GA20ox1. Our results suggest that MAPK-associated phosphorylation sites of RSG regulate its localization in tobacco, and that constant unphosphorylation of RSG in Thr-30, Ser-74, and Thr-135 keeps RSG predominantly localized in cytoplasm. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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20 pages, 5808 KiB

Open AccessArticle

Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L.

by Yihan Li, Yongjun Wang, Xiaoxi Feng, Xiuting Hua, Meijie Dou, Wei Yao, Muqing Zhang and Jisen Zhang

Int. J. Mol. Sci. 2022, 23(15), 8724; https://doi.org/10.3390/ijms23158724 - 05 Aug 2022

Cited by 4 | Viewed by 1728

Abstract

Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due [...] Read more.

Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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17 pages, 4031 KiB

Open AccessArticle

Functional Characterization of Tomato ShROP7 in Regulating Resistance against Oidium neolycopersici

by Yanan Meng, Ancheng Zhang, Qing Ma and Lianxi Xing

Int. J. Mol. Sci. 2022, 23(15), 8557; https://doi.org/10.3390/ijms23158557 - 02 Aug 2022

Cited by 3 | Viewed by 1554

Abstract

ROPs (Rho-like GTPases from plants) are a unique family of small GTP-binding proteins in plants and play vital roles in numerous cellular processes, including growth and development, abiotic stress signaling, and plant defense. In the case of the latter, the role of ROPs [...] Read more.

ROPs (Rho-like GTPases from plants) are a unique family of small GTP-binding proteins in plants and play vital roles in numerous cellular processes, including growth and development, abiotic stress signaling, and plant defense. In the case of the latter, the role of ROPs as response regulators to obligate parasitism remains largely enigmatic. Herein, we isolated and identified ShROP7 and show that it plays a critical role in plant immune response to pathogen infection. Real-time quantitative PCR analysis revealed that the expression of ShROP7 was significantly increased during incompatible interactions. To establish its requirement for resistance, we demonstrate that virus-induced gene silencing (VIGS) of ShROP7 resulted in increased susceptibility of tomato to Oidium neolycopersici (On) Lanzhou strain (On-Lz). Downstream resistance signaling through H₂O₂ and the induction of the hypersensitive response (HR) in ShROP7-silenced plants were significantly reduced after inoculating with On-Lz. Taken together, with the identification of ShROP7-interacting candidates, including ShSOBIR1, we demonstrate that ShROP7 plays a positive regulatory role in tomato powdery mildew resistance. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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14 pages, 2534 KiB

Open AccessArticle

The L-Type Lectin-like Receptor Kinase Gene TaLecRK-IV.1 Regulates the Plant Height in Wheat

by Mamoudou Saidou and Zengyan Zhang

Int. J. Mol. Sci. 2022, 23(15), 8208; https://doi.org/10.3390/ijms23158208 - 26 Jul 2022

Cited by 5 | Viewed by 1428

Abstract

Dwarfing is important for the production of wheat (Triticumaestivum L.). In model plants, receptor-like kinases have been implicated in signal transduction, immunity, and development. However, functional roles of lectin receptor-like kinases in wheat are poorly understood. In this study, we identified an [...] Read more.

Dwarfing is important for the production of wheat (Triticumaestivum L.). In model plants, receptor-like kinases have been implicated in signal transduction, immunity, and development. However, functional roles of lectin receptor-like kinases in wheat are poorly understood. In this study, we identified an L-type lectin receptor-like kinase gene in wheat, designated as TaLecRK-IV.1, and revealed its role in plant height. Real time quantitative PCR analyses indicated that TaLecRK-IV.1 transcript level was lower in a dwarf wheat line harboring the Rht-D1b gene compared to its transcript level detected in a taller wheat line CI12633. Importantly, the virus-induced gene silencing results showed that silencing of TaLecRK-IV.1 in the wheat line CI12633 led to dwarf plants. The results of the disease resistance test performed after the gene silencing experiment suggest no significant role of TaLecRK-IV.1 in the resistance reaction of wheat line CI12633 to sharp eyespot. Gene expression analysis revealed that the transcript abundance of TaLecRK-IV.1 was more up-regulated after the exogenous application of gibberellic acid and auxin, two development-related phytohormones, compared to the gene transcript levels detected in the control plants (mock treatment). These findings support the potential implication of TaLecRK-IV.1 in the pathway controlling plant height rather than the disease resistance role, and suggest that TaLecRK-IV.1 may be a positive regulator of plant height through the gibberellic acid and auxin-signaling pathways. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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18 pages, 7026 KiB

Open AccessArticle

Characterization, Expression Profiling, and Biochemical Analyses of the Cinnamoyl-CoA Reductase Gene Family for Lignin Synthesis in Alfalfa Plants

by Weiti Cui, Zihan Zhuang, Peihao Jiang, Jincheng Pan, Gan Zhao, Sheng Xu and Wenbiao Shen

Int. J. Mol. Sci. 2022, 23(14), 7762; https://doi.org/10.3390/ijms23147762 - 14 Jul 2022

Cited by 3 | Viewed by 1753

Abstract

Cinnamoyl-CoA reductase (CCR) is a pivotal enzyme in plant lignin synthesis, which has a role in plant secondary cell wall development and environmental stress defense. Alfalfa is a predominant legume forage with excellent quality, but the lignin content negatively affects fodder [...] Read more.

Cinnamoyl-CoA reductase (CCR) is a pivotal enzyme in plant lignin synthesis, which has a role in plant secondary cell wall development and environmental stress defense. Alfalfa is a predominant legume forage with excellent quality, but the lignin content negatively affects fodder digestibility. Currently, there is limited information on CCR characteristics, gene expression, and its role in lignin metabolism in alfalfa. In this study, we identified 30 members in the CCR gene family of Medicago sativa. In addition, gene structure, conserved motif, and evolution analysis suggested MsCCR1–7 presumably functioned as CCR, while the 23 MsCCR-likes fell into three categories. The expression patterns of MsCCRs/MsCCR-likes suggested their role in plant development, response to environmental stresses, and phytohormone treatment. These results were consistent with the cis-elements in their promoters. Histochemical staining showed that lignin accumulation gradually deepened with the development, which was consistent with gene expression results. Furthermore, recombinant MsCCR1 and MsCCR-like1 were purified and the kinetic parameters were tested under four substrates. In addition, three-dimensional structure models of MsCCR1 and MsCCR-like1 proteins showed the difference in the substrate-binding motif H212(X)2K215R263. These results will be useful for further application for legume forage quality modification and biofuels industry engineering in the future. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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16 pages, 3985 KiB

Open AccessArticle

Nutrient Supply Is Essential for Shifting Tree Peony Reflowering Ahead in Autumn and Sugar Signaling Is Involved

by Yuqian Xue, Jingqi Xue, Xiuxia Ren, Changyue Li, Kairong Sun, Litao Cui, Yingmin Lyu and Xiuxin Zhang

Int. J. Mol. Sci. 2022, 23(14), 7703; https://doi.org/10.3390/ijms23147703 - 12 Jul 2022

Cited by 2 | Viewed by 1425

Abstract

The flowering time of tree peony is short and concentrated in spring, which limits the development of its industry. We previously achieved tree peony reflowering in autumn. Here, we further shifted its reflowering time ahead through proper gibberellin (GA) treatment plus nutrient supply. [...] Read more.

The flowering time of tree peony is short and concentrated in spring, which limits the development of its industry. We previously achieved tree peony reflowering in autumn. Here, we further shifted its reflowering time ahead through proper gibberellin (GA) treatment plus nutrient supply. GA treatment alone initiated bud differentiation, but it aborted later, whereas GA plus nutrient (G + N) treatment completed the opening process 38 days before the control group. Through microstructural observation of bud differentiation and starch grains, we concluded that GA plays a triggering role in flowering induction, whereas the nutriment supply ensured the continuous developing for final opening, and both are necessary. We further determined the expression of five floral induction pathway genes and found that PsSOC1 and PsLFY probably played key integral roles in flowering induction and nutrient supply, respectively. Considering the GA signaling, PsGA2ox may be mainly involved in GA regulation, whereas PsGAI may regulate further flower formation after nutrient application. Furthermore, G + N treatment, but not GA alone, inhibited the expression of PsTPS1, a key restricting enzyme in sugar signaling, at the early stage, indicating that sugar signaling is also involved in this process; in addition, GA treatment induced high expression of PsSnRK1, a major nutrient insufficiency indicator, and the induction of PsHXK1, a rate-limiting enzyme for synthesis of sugar signaling substances, further confirmed the nutrient shortage. In short, besides GA application, exogenous nutrient supply is essential to shift tree peony reflowering ahead in autumn under current forcing culture technologies. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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17 pages, 3800 KiB

Open AccessArticle

Molecular Evolution and Functional Divergence of Stress-Responsive Cu/Zn Superoxide Dismutases in Plants

by Guozhi Zhou, Chaochao Liu, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao and Hongjian Wan

Int. J. Mol. Sci. 2022, 23(13), 7082; https://doi.org/10.3390/ijms23137082 - 25 Jun 2022

Cited by 10 | Viewed by 1580

Abstract

Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved in [...] Read more.

Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved in many of the biological functions of plants in response to abiotic and biotic stresses. Here, we carried out a comprehensive analysis of the Cu/Zn SOD gene family in different plant species, ranging from lower plants to higher plants, and further investigated their organization, sequence features, and expression patterns in response to biotic and abiotic stresses. Our results show that plant Cu/Zn SODs can be divided into two subfamilies (group I and group II). Group II appeared to be conserved only as single- or low-copy genes in all lineages, whereas group I genes underwent at least two duplication events, resulting in multiple gene copies and forming three different subgroups (group Ia, group Ib, and group Ic). We also found that, among these genes, two important events—the loss of introns and the loss of and variation in signal peptides—occurred over the long course of their evolution, indicating that they were involved in shifts in subcellular localization from the chloroplast to cytosol or peroxisome and underwent functional divergence. In addition, expression patterns of Cu/Zn SOD genes from Arabidopsis thaliana and Solanum lycopersicum were tested in different tissues/organs and developmental stages and under different abiotic stresses. The results indicate that the Cu/Zn SOD gene family possesses potential functional divergence and may play vital roles in ROS scavenging in response to various stresses in plants. This study will help establish a foundation for further understanding these genes’ function during stress responses. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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15 pages, 4120 KiB

Open AccessArticle

Development and Molecular Cytogenetic Identification of Two Wheat-Aegilops geniculata Roth 7M^g Chromosome Substitution Lines with Resistance to Fusarium Head Blight, Powdery Mildew and Stripe Rust

by Xiaoying Yang, Maoru Xu, Yongfu Wang, Xiaofang Cheng, Chenxi Huang, Hong Zhang, Tingdong Li, Changyou Wang, Chunhuan Chen, Yajuan Wang and Wanquan Ji

Int. J. Mol. Sci. 2022, 23(13), 7056; https://doi.org/10.3390/ijms23137056 - 24 Jun 2022

Cited by 3 | Viewed by 1666

Abstract

Fusarium head blight (Fhb), powdery mildew, and stripe rust are major wheat diseases globally. Aegilops geniculata Roth (U^gU^gM^gM^g, 2n = 4x = 28), a wild relative of common wheat, is valuable germplasm [...] Read more.

Fusarium head blight (Fhb), powdery mildew, and stripe rust are major wheat diseases globally. Aegilops geniculata Roth (U^gU^gM^gM^g, 2n = 4x = 28), a wild relative of common wheat, is valuable germplasm of disease resistance for wheat improvement and breeding. Here, we report the development and characterization of two substitution accessions with high resistance to powdery mildew, stripe rust and Fhb (W623 and W637) derived from hybrid progenies between Ae. geniculata and hexaploid wheat Chinese Spring (CS). Fluorescence in situ hybridization (FISH), Genomic in situ hybridizations (GISH), and sequential FISH-GISH studies indicated that the two substitution lines possess 40 wheat chromosomes and 2 Ae. geniculata chromosomes. Furthermore, compared that the wheat addition line parent W166, the 2 alien chromosomes from W623 and W637 belong to the 7M^g chromosomes of Ae. geniculata via sequential FISH-GISH and molecular marker analysis. Nullisomic-tetrasomic analysis for homoeologous group-7 of wheat and FISH revealed that the common wheat chromosomes 7A and 7B were replaced in W623 and W637, respectively. Consequently, lines W623, in which wheat chromosomes 7A were replaced by a pair of Ae. geniculata 7M^g chromosomes, and W637, which chromosomes 7B were substituted by chromosomes 7M^g, with resistance to Fhb, powdery mildew, and stripe rust. This study has determined that the chromosome 7M^g from Ae. geniculata exists genes resistant to Fhb and powdery mildew. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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16 pages, 4942 KiB

Open AccessArticle

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

by Wei Lan, Shuai Zheng, Ping Yang, Yuhao Qiu, Yun Xu and Ying Miao

Int. J. Mol. Sci. 2022, 23(10), 5754; https://doi.org/10.3390/ijms23105754 - 20 May 2022

Cited by 3 | Viewed by 1899

Abstract

Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. [...] Read more.

Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. In this study, multi-omics proteomic analyses of ubiquitinated proteins enriched by using antibody against “di-Gly-Lys” via a free labeling were used to investigate the global changes of protein levels and ubiquitination modification levels of upl5 mutant relative to wild-type plant; subcellular localization analysis of UPL5 was found to be located in the nucleus, cytoplasm, and plastid within the cell; and the direct lysine site patterns of UPL5 were screened by the H89R substitution in the tagged ubiquitinated assay. It suggests that UPL5 acting as a candidate of organelle E3 ligase either in the nucleus or cytoplasm or plastid modifies numerous targets related to nuclear transcription and plastid photosynthesis involving in Ca²⁺ and hormone signaling pathway in plant senescence and in response to (a)biotic stress protection. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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16 pages, 2634 KiB

Open AccessArticle

InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection

by Zhenyu Wang, Zhongyin Deng, Xingchen Kong, Fang Wang, Jiantao Guan, Dada Cui, Guoliang Sun, Ruyi Liao, Mingxue Fu, Yuqing Che, Chenyang Hao, Shuaifeng Geng, Xueyong Zhang, Peng Zhou, Long Mao, Shaoshuai Liu and Aili Li

Int. J. Mol. Sci. 2022, 23(10), 5587; https://doi.org/10.3390/ijms23105587 - 17 May 2022

Cited by 3 | Viewed by 2030

Abstract

Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese [...] Read more.

Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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24 pages, 5126 KiB

Open AccessArticle

RNA-Seq Analysis Identifies Transcription Factors Involved in Anthocyanin Biosynthesis of ‘Red Zaosu’ Pear Peel and Functional Study of PpPIF8

by Zhenyu Ma, Chuangqi Wei, Yudou Cheng, Zhonglin Shang, Xiulin Guo and Junfeng Guan

Int. J. Mol. Sci. 2022, 23(9), 4798; https://doi.org/10.3390/ijms23094798 - 27 Apr 2022

Cited by 5 | Viewed by 2218

Abstract

Red-skinned pears are favored by people for their attractive appearance and abundance of anthocyanins. However, the molecular basis of anthocyanin biosynthesis in red pears remains elusive. Here, a comprehensive transcriptome analysis was conducted to explore the potential regulatory mechanism of anthocyanin biosynthesis in [...] Read more.

Red-skinned pears are favored by people for their attractive appearance and abundance of anthocyanins. However, the molecular basis of anthocyanin biosynthesis in red pears remains elusive. Here, a comprehensive transcriptome analysis was conducted to explore the potential regulatory mechanism of anthocyanin biosynthesis in ‘Red Zaosu’ pear (Pyrus pyrifolia × Pyrus communis). Gene co-expression analysis and transcription factor mining identified 263 transcription factors, which accounted for 6.59% of the total number of transcription factors in the pear genome in two gene modules that are highly correlated with anthocyanin biosynthesis. Clustering, gene network modeling with STRING-DB, and local motif enrichment analysis (CentriMo) analysis suggested that PpPIF8 may play a role in anthocyanin biosynthesis. Furthermore, eight PIFs were identified in the pear genome, of which only PpPIF8 was rapidly induced by light. Functional studies showed that PpPIF8 localizes in the nucleus and is preferentially expressed in the tissue of higher levels of anthocyanin. The overexpression of PpPIF8 in pear peel and pear calli promotes anthocyanin biosynthesis and upregulates the expression of anthocyanin biosynthesis genes. Yeast-one hybrid and transgenic analyses indicated that PpPIF8 binds to the PpCHS promoter to induce PpCHS expression. The positive effect of PpPIF8 on anthocyanin biosynthesis is different from previously identified negative regulators of PyPIF5 and MdPIF7 in pear and apple. Taken together, our data not only provide a comprehensive view of transcription events during the coloration of pear peel, but also resolved the regulatory role of PpPIF8 in the anthocyanin biosynthesis pathway. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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Review

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15 pages, 1245 KiB

Open AccessReview

Role of bZIP Transcription Factors in Plant Salt Stress

by Haotian Liu, Xun Tang, Ning Zhang, Shigui Li and Huaijun Si

Int. J. Mol. Sci. 2023, 24(9), 7893; https://doi.org/10.3390/ijms24097893 - 26 Apr 2023

Cited by 18 | Viewed by 2908

Abstract

Soil salinity has become an increasingly serious problem worldwide, greatly limiting crop development and yield, and posing a major challenge to plant breeding. Basic leucine zipper (bZIP) transcription factors are the most widely distributed and conserved transcription factors and are the main regulators [...] Read more.

Soil salinity has become an increasingly serious problem worldwide, greatly limiting crop development and yield, and posing a major challenge to plant breeding. Basic leucine zipper (bZIP) transcription factors are the most widely distributed and conserved transcription factors and are the main regulators controlling various plant response processes against external stimuli. The bZIP protein contains two domains: a highly conserved, DNA-binding alkaline region, and a diverse leucine zipper, which is one of the largest transcription factor families in plants. Plant bZIP is involved in many biological processes, such as flower development, seed maturation, dormancy, and senescence, and plays an important role in abiotic stresses such as salt damage, drought, cold damage, osmotic stress, mechanical damage, and ABA signal response. In addition, bZIP is involved in the regulation of plant response to biological stresses such as insect pests and pathogen infection through salicylic acid, jasmonic acid, and ABA signal transduction pathways. This review summarizes and discusses the structural characteristics and functional characterization of the bZIP transcription factor group, the bZIP transcription factor complex and its molecular regulation mechanisms related to salt stress resistance, and the regulation of transcription factors in plant salt stress resistance. This review provides a theoretical basis and research ideas for further exploration of the salt stress-related functions of bZIP transcription factors. It also provides a theoretical basis for crop genetic improvement and green production in agriculture. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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14 pages, 539 KiB

Open AccessReview

Alternative Splicing in the Regulatory Circuit of Plant Temperature Response

by Rong Xue, Ruirui Mo, Dongkai Cui, Wencong Cheng, Haoyu Wang, Jinxia Qin and Zhenshan Liu

Int. J. Mol. Sci. 2023, 24(4), 3878; https://doi.org/10.3390/ijms24043878 - 15 Feb 2023

Cited by 1 | Viewed by 1980

Abstract

As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have [...] Read more.

As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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17 pages, 1500 KiB

Open AccessReview

The Ubiquitin–26S Proteasome Pathway and Its Role in the Ripening of Fleshy Fruits

by Wen Jia, Gangshuai Liu, Peiyu Zhang, Hongli Li, Zhenzhen Peng, Yunxiang Wang, Tomislav Jemrić and Daqi Fu

Int. J. Mol. Sci. 2023, 24(3), 2750; https://doi.org/10.3390/ijms24032750 - 01 Feb 2023

Cited by 2 | Viewed by 3119

Abstract

The 26S proteasome is an ATP-dependent proteolytic complex in eukaryotes, which is mainly responsible for the degradation of damaged and misfolded proteins and some regulatory proteins in cells, and it is essential to maintain the balance of protein levels in the cell. The [...] Read more.

The 26S proteasome is an ATP-dependent proteolytic complex in eukaryotes, which is mainly responsible for the degradation of damaged and misfolded proteins and some regulatory proteins in cells, and it is essential to maintain the balance of protein levels in the cell. The ubiquitin–26S proteasome pathway, which targets a wide range of protein substrates in plants, is an important post-translational regulatory mechanism involved in various stages of plant growth and development and in the maturation process of fleshy fruits. Fleshy fruit ripening is a complex biological process, which is the sum of a series of physiological and biochemical reactions, including the biosynthesis and signal transduction of ripening related hormones, pigment metabolism, fruit texture changes and the formation of nutritional quality. This paper reviews the structure of the 26S proteasome and the mechanism of the ubiquitin–26S proteasome pathway, and it summarizes the function of this pathway in the ripening process of fleshy fruits. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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19 pages, 2640 KiB

Open AccessReview

Molecular and Genetic Events Determining the Softening of Fleshy Fruits: A Comprehensive Review

by Zhenzhen Peng, Gangshuai Liu, Hongli Li, Yunxiang Wang, Haiyan Gao, Tomislav Jemrić and Daqi Fu

Int. J. Mol. Sci. 2022, 23(20), 12482; https://doi.org/10.3390/ijms232012482 - 18 Oct 2022

Cited by 19 | Viewed by 2809

Abstract

Fruit softening that occurs during fruit ripening and postharvest storage determines the fruit quality, shelf life and commercial value and makes fruits more attractive for seed dispersal. In addition, over-softening results in fruit eventual decay, render fruit susceptible to invasion by opportunistic pathogens. [...] Read more.

Fruit softening that occurs during fruit ripening and postharvest storage determines the fruit quality, shelf life and commercial value and makes fruits more attractive for seed dispersal. In addition, over-softening results in fruit eventual decay, render fruit susceptible to invasion by opportunistic pathogens. Many studies have been conducted to reveal how fruit softens and how to control softening. However, softening is a complex and delicate life process, including physiological, biochemical and metabolic changes, which are closely related to each other and are affected by environmental conditions such as temperature, humidity and light. In this review, the current knowledge regarding fruit softening mechanisms is summarized from cell wall metabolism (cell wall structure changes and cell-wall-degrading enzymes), plant hormones (ETH, ABA, IAA and BR et al.), transcription factors (MADS-Box, AP2/ERF, NAC, MYB and BZR) and epigenetics (DNA methylation, histone demethylation and histone acetylation) and a diagram of the regulatory relationship between these factors is provided. It will provide reference for the cultivation of anti-softening fruits. Full article

(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2022)

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