Editorial

4 pages, 201 KiB

Open AccessEditorial

From Omics Analysis toward Physiological Mechanism Research in Plants

by Yan Lu, Sen Meng and Jie Luo

Life 2023, 13(12), 2275; https://doi.org/10.3390/life13122275 - 29 Nov 2023

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With the development of big data in system biology researches, the high-throughput omics analysis has become the most popular high technology in the fields of plant research [...] Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

Research

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12 pages, 2339 KiB

Open AccessArticle

ZmCOP1 Regulates Maize Mesocotyl Length and Plant Height through the Phytohormone Pathways

by Liping Chen, Qiuhua Li, Ming Wang, Feng Xiao, Kangshi Li, Ran Yang, Meng Sun, Haiyan Zhang, Jinjie Guo, Jingtang Chen and Fuchao Jiao

Life 2023, 13(7), 1522; https://doi.org/10.3390/life13071522 - 07 Jul 2023

Cited by 2 | Viewed by 926

Abstract

The morphogenesis of crops is critical to their yield performance. COP1 (constitutively photomorphogenic1) is one of the core regulators in plant morphogenesis and has been deeply studied in Arabidopsis thaliana. However, the function of COP1 in maize is still unclear. Here, we [...] Read more.

The morphogenesis of crops is critical to their yield performance. COP1 (constitutively photomorphogenic1) is one of the core regulators in plant morphogenesis and has been deeply studied in Arabidopsis thaliana. However, the function of COP1 in maize is still unclear. Here, we found that the mesocotyl lengths of zmcop1 loss-of-function mutants were shorter than those of wild-type B73 in darkness, while the mesocotyl lengths of lines with ZmCOP1 overexpression were longer than those of wild-type B104. The plant height with zmcop1 was shorter than that of B73 in both short- and long-day photoperiods. Using transcriptome RNA sequencing technology, we identified 33 DEGs (differentially expressed genes) between B73′s etiolated seedlings and those featuring zmcop1, both in darkness. The DEGs were mainly enriched in the plant phytohormone pathways. Our results provide direct evidence that ZmCOP1 functions in the elongation of etiolated seedlings in darkness and affects plant height in light. Our data can be applied in the improvement of maize plant architecture. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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18 pages, 2429 KiB

Open AccessArticle

The Effect of Hormone Types, Concentrations, and Treatment Times on the Rooting Traits of Morus ‘Yueshenda 10’ Softwood Cuttings

by Jiajia Sun, Hongyun Li, Hanlei Chen, Tiantian Wang, Jin’e Quan and Huitao Bi

Life 2023, 13(4), 1032; https://doi.org/10.3390/life13041032 - 17 Apr 2023

Cited by 2 | Viewed by 2261

Abstract

Enhancing the capacity of fruit trees to propagate via cuttings is an important endeavor for the high-quality development of the fruit industry. Optimizing the conditions for the cutting propagation of mulberry seedlings is an important factor that influences the industrial production of this [...] Read more.

Enhancing the capacity of fruit trees to propagate via cuttings is an important endeavor for the high-quality development of the fruit industry. Optimizing the conditions for the cutting propagation of mulberry seedlings is an important factor that influences the industrial production of this plant; however, the currently used mulberry breeding technology system is not mature. In this experiment, an orthogonal design was used to intercept semi-woody shoots of Yueshenda 10 as cuttings and set different hormone concentrations (200, 500, 800, and 1000 mg/L), different hormone types (NAA, IBA, IAA, and ABT-1), and different soaking times (10, 30, 60, and 120 min) for cuttings. The effects of the three factors on the rooting of mulberry cuttings were investigated by soaking the cuttings in clean water for 10 min as a control. The results showed that the primary and secondary order of the three factors affecting the rooting rate of cuttings was hormone concentration > hormone type > soaking time, and the concentration of exogenous hormones had a significant impact on all rooting indicators (p < 0.05). In addition, the rooting rate (66.24%), average number of roots (7.54 roots/plant), and rooting effect index (4.23) of Yueshenda 10 cuttings reached the optimal level when soaked with 800 mg/L ABT-1 for 30 min. The longest root length (10.20 cm) and average root length (4.44 cm) of cuttings achieved the best results when soaked with 800 mg/L NAA for 60 min and 500 mg/L NAA for 30 min, respectively. On balance, it is considered that the preferred solution is to soak the cuttings of Yueshenda 10 with 800 mg/L ABT1 solution for 0.5 h. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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15 pages, 3210 KiB

Open AccessArticle

Generation of Asynaptic Mutants in Potato by Disrupting StDMC1 Gene Using RNA Interference Approach

by Ashwani Kumar, Sundaresha Siddappa, Vinay Bhardwaj, Dalamu, Baljeet Singh, Neha Sharma, Bhawna Dipta, Vinod Kumar, Umesh Goutam and Salej Sood

Life 2023, 13(1), 174; https://doi.org/10.3390/life13010174 - 06 Jan 2023

Cited by 3 | Viewed by 1787

Abstract

Fixing the genomic composition and multiplication through true potato seed (TPS) is an important challenge in autotetraploid potato. Disrupted meiotic cDNA (DMC1) is a meiotic gene that plays a central role in DNA recombination through crossing over in meiosis. Using the Arabidopsis DMC1 [...] Read more.

Fixing the genomic composition and multiplication through true potato seed (TPS) is an important challenge in autotetraploid potato. Disrupted meiotic cDNA (DMC1) is a meiotic gene that plays a central role in DNA recombination through crossing over in meiosis. Using the Arabidopsis DMC1 (AtDMC1) gene sequence, we retrieved Solanum tuberosum DMC1(StDMC1) from the diploid potato genome, and subsequently, sense and antisense regions of the StDMC1 gene were amplified in potato cv. Kufri Jyoti. The sense and antisense fragments were confirmed by Sanger-sequencing and cloned in the pRI101 vector. Agrobacterium-mediated transformation of the RNAi construct resulted in 44% transformation efficiency, and a total of 137 mutant lines were obtained. These mutant lines were further validated through pollen viability testing, and selected lines were used for gene expression analysis. The acetocarmine-based pollen staining showed reduced pollen viability ranging from 14 to 21% in four DMC1 mutant lines (DMC4-37, DMC4-41, DMC6-20, and DMC6-21), as compared to the Kufri Jyoti control plants, which on average exhibited 78% pollen viability. The phenotypic data was supported by the reduced expression of the StDMC1 gene in these four mutant lines compared to the control Kufri Jyoti. The results confirmed the generation of StDMC1 knockdown lines. This is the first report of StDMC1 mutant line generation in tetraploid potatoes and will be a step forward in generating non-recombinant mutants through sexual reproduction in potatoes. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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15 pages, 5843 KiB

Open AccessArticle

Analysis of Rac/Rop Small GTPase Family Expression in Santalum album L. and Their Potential Roles in Drought Stress and Hormone Treatments

by Yu Chen, Shengkun Wang, Xiaojing Liu, Dongli Wang, Yunshan Liu, Lipan Hu and Sen Meng

Life 2022, 12(12), 1980; https://doi.org/10.3390/life12121980 - 26 Nov 2022

Cited by 1 | Viewed by 1490

Abstract

Plant-specific Rac/Rop small GTPases, also known as Rop, belong to the Rho subfamily. Rac proteins can be divided into two types according to their C-terminal motifs: Type I Rac proteins have a typical CaaL motif at the C-terminal, whereas type II Rac proteins [...] Read more.

Plant-specific Rac/Rop small GTPases, also known as Rop, belong to the Rho subfamily. Rac proteins can be divided into two types according to their C-terminal motifs: Type I Rac proteins have a typical CaaL motif at the C-terminal, whereas type II Rac proteins lack this motif but retain a cysteine-containing element for membrane anchoring. The Rac gene family participates in diverse signal transduction events, cytoskeleton morphogenesis, reactive oxygen species (ROS) production and hormone responses in plants as molecular switches. S. album is a popular semiparasitic plant that absorbs nutrients from the host plant through the haustoria to meet its own growth and development needs. Because the whole plant has a high use value, due to the high production value of its perfume oils, it is known as the “tree of gold”. Based on the full-length transcriptome data of S. album, nine Rac gene members were named SaRac1-9, and we analyzed their physicochemical properties. Evolutionary analysis showed that SaRac1-7, AtRac1-6, AtRac9 and AtRac11 and OsRac5, OsRacB and OsRacD belong to the typical plant type I Rac/Rop protein, while SaRac8-9, AtRac7, AtRac8, AtRac10 and OsRac1-4 belong to the type II Rac/ROP protein. Tissue-specific expression analysis showed that nine genes were expressed in roots, stems, leaves and haustoria, and SaRac7/8/9 expression in stems, haustoria and roots was significantly higher than that in leaves. The expression levels of SaRac1, SaRac4 and SaRac6 in stems were very low, and the expression levels of SaRac2 and SaRac5 in roots and SaRac2/3/7 in haustoria were very high, which indicated that these genes were closely related to the formation of S. album haustoria. To further analyze the function of SaRac, nine Rac genes in sandalwood were subjected to drought stress and hormone treatments. These results establish a preliminary foundation for the regulation of growth and development in S. album by SaRac. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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14 pages, 2522 KiB

Open AccessArticle

The Molecular Network behind Volatile Aroma Formation in Pear (Pyrus spp. Panguxiang) Revealed by Transcriptome Profiling via Fatty Acid Metabolic Pathways

by Huiyun Li, Jine Quan, Sohel Rana, Yanmei Wang, Zhi Li, Qifei Cai, Shuhong Ma, Xiaodong Geng and Zhen Liu

Life 2022, 12(10), 1494; https://doi.org/10.3390/life12101494 - 26 Sep 2022

Cited by 1 | Viewed by 1760

Abstract

Pears are popular table fruits, grown and consumed worldwide for their excellent color, aroma, and taste. Volatile aroma is an important factor affecting fruit quality, and the fatty acid metabolism pathway is important in synthesizing volatile aromas. Most of the white pear varieties [...] Read more.

Pears are popular table fruits, grown and consumed worldwide for their excellent color, aroma, and taste. Volatile aroma is an important factor affecting fruit quality, and the fatty acid metabolism pathway is important in synthesizing volatile aromas. Most of the white pear varieties cultivated in China are not strongly scented, which significantly affects their overall quality. Panguxiang is a white pear cultivar, but its aroma has unique components and is strong. The study of the mechanisms by which aroma is formed in Panguxiang is, therefore, essential to improving the quality of the fruit. The study analyzed physiological and transcriptome factors to reveal the molecular network behind volatile aroma formation in Panguxiang. The samples of Panguxiang fruit were collected in two (fruit development at 60, 90, 120, and 147 days, and fruit storage at 0, 7, 14, 21, and 28 days) periods. A total of nine sample stages were used for RNA extraction and paired-end sequencing. In addition, RNA quantification and qualification, library preparation and sequencing, data analysis and gene annotation, gene co-expression network analysis, and validation of DEGs through quantitative real-time PCR (qRT-;PCR) were performed in this study. The WGCNA identified yellow functional modules and several biological and metabolic pathways related to fatty acid formation. Finally, we identified seven and eight hub genes in the fatty acid synthesis and fatty acid metabolism pathways, respectively. Further analysis of the co-expression network allowed us to identify several key transcription factors related to the volatile aroma, including AP2/ERF-ERF, C3H, MYB, NAC, C2H2, GRAS, and Trihelix, which may also be involved in the fatty acid synthesis. This study lays a theoretical foundation for studying volatile compounds in pear fruits and provides a theoretical basis for related research in other fruits. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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14 pages, 3227 KiB

Open AccessArticle

Molecular Cloning and Functional Analysis of IrUGT86A1-like Gene in Medicinal Plant Isodon rubescens (Hemsl.) Hara

by Conglong Lian, Jinxu Lan, Bao Zhang, Hao Yang, Kaihua Guo, Jingjing Li and Suiqing Chen

Life 2022, 12(9), 1334; https://doi.org/10.3390/life12091334 - 28 Aug 2022

Viewed by 1353

Abstract

The synthesis of secondary metabolites in plants often includes glycosylation modifications. Often, the final step of constructing plant secondary metabolites is completed by glycosylation transferases, which are also involved in many cell processes. In this study, a UDP-glycosyltransferase gene (UGT) was [...] Read more.

The synthesis of secondary metabolites in plants often includes glycosylation modifications. Often, the final step of constructing plant secondary metabolites is completed by glycosylation transferases, which are also involved in many cell processes. In this study, a UDP-glycosyltransferase gene (UGT) was amplified from Isodon rubescens (Hemsl.) Hara with RT-PCR and named IrUGT86A1-like (GenBank: MZ913258). Here, we found that IrUGT86A1-like gene is 1450 bp in length and encodes for 479 amino acids. Bioinformatics analysis revealed that IrUGT86A1-like is a stable and hydrophilic protein, located in the cytoplasm with a transmembrane domain. Phylogenetic analysis showed that IrUGT86A1-like protein has the closest genetic relationship with the UDP-glycosyltransferase 86A1-like protein (XP_042054241.1) of Salvia splendens. RT-qPCR analysis demonstrated that the expression of IrUGT86A1-like gene varied in different tissues; leaves had the highest expression followed by flowers, stems, and roots had the lowest expression. This expression trend is similar to the distribution of oridonin content in different tissues of I. rubescens. Additionally, IrUGT86A1-like gene was found to be positively enhanced by NaCl and MeJA treatment, and in contrast was down-regulated by ABA treatment. Finally, the prokaryotic expression vector pEASY^®-Blunt E1-IrUGT86A1 was successfully used to express about 53 KD of IrUGT86A1-like protein. This research builds a foundation for further investigation on the function of this gene in the synthesis and modification of secondary metabolites. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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17 pages, 1905 KiB

Open AccessArticle

Effects of Different Growth Regulators on the Rooting of Catalpa bignonioides Softwood Cuttings

by Jin’e Quan, Ruoyi Ni, Yange Wang, Jiajia Sun, Mingyue Ma and Huitao Bi

Life 2022, 12(8), 1231; https://doi.org/10.3390/life12081231 - 15 Aug 2022

Cited by 9 | Viewed by 2653

Abstract

(1) Background: To further improve the rapid reproduction and large-scale application of Catalpa bignonioides. (2) Methods: With young softwood cuttings from a 3-year-old C. bignonioides mother plant used as materials, the effects of indole-3-acetic acid(IAA), indolebutyric acid(IBA) and rhizogenic powder-1(ABT-1) growth regulators [...] Read more.

(1) Background: To further improve the rapid reproduction and large-scale application of Catalpa bignonioides. (2) Methods: With young softwood cuttings from a 3-year-old C. bignonioides mother plant used as materials, the effects of indole-3-acetic acid(IAA), indolebutyric acid(IBA) and rhizogenic powder-1(ABT-1) growth regulators at different concentrations on cutting indexes and the dynamic changes in endogenous hormone contents during the rooting of the C. bignonioides cuttings were studied. (3) Results: The rooting of C. bignonioides cuttings could be divided into five stages. There were three types of rooting of adventitious roots. IBA treatment resulted in a high rooting rate and beneficial root morphology. The morphological indexes of the cutting roots after treatment with 1000 mg·L⁻¹ IBA had the best overall quality, which was significantly higher than that of the roots in the control (CK) group (p < 0.05). Although the average longest root length (20.51 cm) under ABT-1 was the longest, its overall average rooting rate was slightly lower than that under IBA. The rooting effect under IAA was generally lower than that under IBA and ABT-1. The endogenous hormone content of the cuttings was found to be closely related to rooting; the IAA and zeatin nucleoside (ZR) content was high, and the ratios of IAA/ABA and IAA/ZR were high. The contents of gibberellin₃ (GA₃) and abscisic acid (ABA) were low, which had a promoting effect on the rooting of the cuttings. (5) Conclusions: All three kinds of auxin can promote rooting and, of the three treatment groups, the rooting effect of cuttings in the IBA treatment group was the strongest, with 1000 mg·L⁻¹ being the optimum concentration. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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15 pages, 9473 KiB

Open AccessArticle

Identification and Functional Analysis of SabHLHs in Santalum album L.

by Ting Zhang, Xiaohong Chen, Yuping Xiong, Meiyun Niu, Yueya Zhang, Haifeng Yan, Yuan Li, Xinhua Zhang and Guohua Ma

Life 2022, 12(7), 1017; https://doi.org/10.3390/life12071017 - 08 Jul 2022

Cited by 2 | Viewed by 2096

Abstract

Santalum album L., a semi-parasitic evergreen tree, contains economically important essential oil, rich in sesquiterpenoids, such as (Z) α- and (Z) β-santalol. However, their transcriptional regulations are not clear. Several studies of other plants have shown that basic-helix-loop-helix (bHLH) [...] Read more.

Santalum album L., a semi-parasitic evergreen tree, contains economically important essential oil, rich in sesquiterpenoids, such as (Z) α- and (Z) β-santalol. However, their transcriptional regulations are not clear. Several studies of other plants have shown that basic-helix-loop-helix (bHLH) transcription factors (TFs) were involved in participating in the biosynthesis of sesquiterpene synthase genes. Herein, bHLH TF genes with similar expression patterns and high expression levels were screened by co-expression analysis, and their full-length ORFs were obtained. These bHLH TFs were named SaMYC1, SaMYC3, SaMYC4, SaMYC5, SabHLH1, SabHLH2, SabHLH3, and SabHLH4. All eight TFs had highly conserved bHLH domains and SaMYC1, SaMYC3, SaMYC4, and SaMYC5, also had highly conserved MYC domains. It was indicated that the eight genes belonged to six subfamilies of the bHLH TF family. Among them, SaMYC1 was found in both the nucleus and the cytoplasm, while SaMYC4 was only localized in the cytoplasm and the remaining six TFs were localized in nucleus. In a yeast one-hybrid experiment, we constructed decoy vectors pAbAi-SSy1G-box, pAbAi-CYP2G-box, pAbAi-CYP3G-box, and pAbAi-CYP4G-box, which had been transformed into yeast. We also constructed pGADT7-SaMYC1 and pGADT7-SabHLH1 capture vectors and transformed them into bait strains. Our results showed that SaMYC1 could bind to the G-box of SaSSy, and the SaCYP736A167 promoter, which SaSSy proved has acted as a key enzyme in the synthesis of santalol sesquiterpenes and SaCYP450 catalyzed the ligation of santalol sesquiterpenes into terpene. We have also constructed pGreenII 62-SK-SaMYC1, pGreenII 0800-LUC-SaSSy and pGreenII 0800-LUC-SaCYP736A167 via dual-luciferase fusion expression vectors and transformed them into Nicotiana benthamiana using an Agrobacterium-mediated method. The results showed that SaMYC1 was successfully combined with SaSSy or SaCYP736A167 promoter and the LUC/REN value was 1.85- or 1.55-fold higher, respectively, than that of the control group. Therefore, we inferred that SaMYC1 could activate both SaSSy and SaCYP736A167 promoters. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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Review

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14 pages, 1031 KiB

Open AccessReview

Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs

by Caixia Teng, Chunting Zhang, Fei Guo, Linhong Song and Yanni Fang

Life 2023, 13(9), 1917; https://doi.org/10.3390/life13091917 - 15 Sep 2023

Cited by 2 | Viewed by 1134

Abstract

MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of [...] Read more.

MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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13 pages, 2314 KiB

Open AccessReview

The Universally Conserved Unconventional G Protein YchF Is Critical for Growth and Stress Response

by Zhaoheng Lin, Rongfang Li, Zhiwei Han, Yi Liu, Liyang Gao, Suchang Huang, Ying Miao and Rui Miao

Life 2023, 13(4), 1058; https://doi.org/10.3390/life13041058 - 20 Apr 2023

Viewed by 1727

Abstract

The ancient guanine nucleotide-binding (G) proteins are a group of critical regulatory and signal transduction proteins, widely involved in diverse cellular processes of all kingdoms of life. YchF is a kind of universally conserved novel unconventional G protein that appears to be crucial [...] Read more.

The ancient guanine nucleotide-binding (G) proteins are a group of critical regulatory and signal transduction proteins, widely involved in diverse cellular processes of all kingdoms of life. YchF is a kind of universally conserved novel unconventional G protein that appears to be crucial for growth and stress response in eukaryotes and bacteria. YchF is able to bind and hydrolyze both adenine nucleoside triphosphate (ATP) and guanosine nucleoside triphosphate (GTP), unlike other members of the P-loop GTPases. Hence, it can transduce signals and mediate multiple biological functions by using either ATP or GTP. YchF is not only a nucleotide-dependent translational factor associated with the ribosomal particles and proteasomal subunits, potentially bridging protein biosynthesis and degradation, but also sensitive to reactive oxygen species (ROS), probably recruiting many partner proteins in response to environmental stress. In this review, we summarize the latest insights into how YchF is associated with protein translation and ubiquitin-dependent protein degradation to regulate growth and maintain proteostasis under stress conditions. Full article

(This article belongs to the Special Issue Plant Physiology: From Omic Analysis toward Physiological Mechanism Research)

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