International Journal of Molecular Sciences

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23 pages, 13233 KiB

Open AccessArticle

Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer

by Maria Gretsova, Svetlana Surkova, Alexander Kanapin, Anastasia Samsonova, Maria Logacheva, Andrey Shcherbakov, Anton Logachev, Mikhail Bankin, Sergey Nuzhdin and Maria Samsonova

Int. J. Mol. Sci. 2023, 24(3), 2692; https://doi.org/10.3390/ijms24032692 - 31 Jan 2023

Viewed by 2181

Abstract

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression [...] Read more.

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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29 pages, 12386 KiB

Open AccessArticle

Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions

by Dejana Milić, Bojana Živanović, Jelena Samardžić, Nenad Nikolić, Caroline Cukier, Anis M. Limami and Marija Vidović

Int. J. Mol. Sci. 2023, 24(3), 2269; https://doi.org/10.3390/ijms24032269 - 23 Jan 2023

Viewed by 1807

Abstract

Plants are inevitably exposed to extreme climatic conditions that lead to a disturbed balance between the amount of absorbed energy and their ability to process it. Variegated leaves with photosynthetically active green leaf tissue (GL) and photosynthetically inactive white leaf tissue (WL) are [...] Read more.

Plants are inevitably exposed to extreme climatic conditions that lead to a disturbed balance between the amount of absorbed energy and their ability to process it. Variegated leaves with photosynthetically active green leaf tissue (GL) and photosynthetically inactive white leaf tissue (WL) are an excellent model system to study source–sink interactions within the same leaf under the same microenvironmental conditions. We demonstrated that under excess excitation energy (EEE) conditions (high irradiance and lower temperature), regulated metabolic reprogramming in both leaf tissues allowed an increased consumption of reducing equivalents, as evidenced by preserved maximum efficiency of photosystem II (Ф_PSII) at the end of the experiment. GL of the EEE-treated plants employed two strategies: (i) the accumulation of flavonoid glycosides, especially cyanidin glycosides, as an alternative electron sink, and (ii) cell wall stiffening by cellulose, pectin, and lignin accumulation. On the other hand, WL increased the amount of free amino acids, mainly arginine, asparagine, branched-chain and aromatic amino acids, as well as kaempferol and quercetin glycosides. Thus, WL acts as an important energy escape valve that is required in order to maintain the successful performance of the GL sectors under EEE conditions. Finally, this role could be an adaptive value of variegation, as no consistent conclusions about its ecological benefits have been proposed so far. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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14 pages, 2422 KiB

Open AccessArticle

Alternative Splicing of TaHsfA2-7 Is Involved in the Improvement of Thermotolerance in Wheat

by Zhenyu Ma, Mingyue Li, Huaning Zhang, Baihui Zhao, Zihui Liu, Shuonan Duan, Xiangzhao Meng, Guoliang Li and Xiulin Guo

Int. J. Mol. Sci. 2023, 24(2), 1014; https://doi.org/10.3390/ijms24021014 - 05 Jan 2023

Cited by 7 | Viewed by 1386

Abstract

High temperature has severely affected plant growth and development, resulting in reduced production of crops worldwide, especially wheat. Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism, is involved in the growth and development of eukaryotes and the adaptation to environmental changes. Previous transcriptome [...] Read more.

High temperature has severely affected plant growth and development, resulting in reduced production of crops worldwide, especially wheat. Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism, is involved in the growth and development of eukaryotes and the adaptation to environmental changes. Previous transcriptome data suggested that heat shock transcription factor (Hsf) TaHsfA2-7 may form different transcripts by AS. However, it remains unclear whether this post-transcriptional regulatory mechanism of TaHsfA2-7 is related to thermotolerance in wheat (Triticum aestivum). Here, we identified a novel splice variant, TaHsfA2-7-AS, which was induced by high temperature and played a positive role in thermotolerance regulation in wheat. Moreover, TaHsfA2-7-AS is predicted to encode a small truncated TaHsfA2-7 isoform, retaining only part of the DNA-binding domain (DBD). TaHsfA2-7-AS is constitutively expressed in various tissues of wheat. Notably, the expression level of TaHsfA2-7-AS is significantly up-regulated by heat shock (HS) during flowering and grain-filling stages in wheat. Further studies showed that TaHsfA2-7-AS was localized in the nucleus but lacked transcriptional activation activity. Ectopic expression of TaHsfA2-7-AS in yeast exhibited improved thermotolerance. Compared to non-transgenic plants, overexpression of TaHsfA2-7-AS in Arabidopsis results in enhanced tolerance to heat stress. Simultaneously, we also found that TaHsfA1 is directly involved in the transcriptional regulation of TaHsfA2-7 and TaHsfA2-7-AS. In summary, our findings demonstrate the function of TaHsfA2-7-AS splicing variant in response to heat stress and establish a link between regulatory mechanisms of AS and the improvement of thermotolerance in wheat. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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24 pages, 8384 KiB

Open AccessArticle

Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants

by Eduardo Larriba, Míriam Nicolás-Albujer, Ana Belén Sánchez-García and José Manuel Pérez-Pérez

Int. J. Mol. Sci. 2022, 23(24), 16112; https://doi.org/10.3390/ijms232416112 - 17 Dec 2022

Cited by 1 | Viewed by 2057

Abstract

Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum “Micro-Tom” explants without the addition of exogenous hormones as a model [...] Read more.

Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum “Micro-Tom” explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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20 pages, 3719 KiB

Open AccessArticle

Comparative Ubiquitination Proteomics Revealed the Salt Tolerance Mechanism in Sugar Beet Monomeric Additional Line M14

by He Liu, Jialin Zhang, Jinna Li, Bing Yu, Sixue Chen, Chunquan Ma and Haiying Li

Int. J. Mol. Sci. 2022, 23(24), 16088; https://doi.org/10.3390/ijms232416088 - 17 Dec 2022

Viewed by 1594

Abstract

Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the [...] Read more.

Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the ubiquitination proteome changes in the salt-tolerant sugar beet monomeric additional line M14 under salt stress treatments. Based on the expression of the key genes of the ubiquitination system and the ubiquitination-modified proteins before and after salt stress, 30 min of 200 mM NaCl treatment and 6 h of 400 mM NaCl treatment were selected as time points. Through label-free proteomics, 4711 and 3607 proteins were identified in plants treated with 200 mM NaCl and 400 mM NaCl, respectively. Among them, 611 and 380 proteins were ubiquitinated, with 1085 and 625 ubiquitination sites, in the two salt stress conditions, respectively. A quantitative analysis revealed that 70 ubiquitinated proteins increased and 47 ubiquitinated proteins decreased. At the total protein level, 42 were induced and 20 were repressed with 200 mM NaCl, while 28 were induced and 27 were repressed with 400 mM NaCl. Gene ontology, KEGG pathway, protein interaction, and PTM crosstalk analyses were performed using the differentially ubiquitinated proteins. The differentially ubiquitinated proteins were mainly involved in cellular transcription and translation processes, signal transduction, metabolic pathways, and the ubiquitin/26S proteasome pathway. The uncovered ubiquitinated proteins constitute an important resource of the plant stress ubiquitinome, and they provide a theoretical basis for the marker-based molecular breeding of crops for enhanced stress tolerance. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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16 pages, 3684 KiB

Open AccessArticle

A Protective Role of Phenylalanine Ammonia-Lyase from Astragalus membranaceus against Saline-Alkali Stress

by Lijuan Fan, Gongfa Shi, Juan Yang, Guiling Liu, Zhaoqian Niu, Wangbin Ye, Songquan Wu, Ling Wang and Qingjie Guan

Int. J. Mol. Sci. 2022, 23(24), 15686; https://doi.org/10.3390/ijms232415686 - 10 Dec 2022

Cited by 4 | Viewed by 1497

Abstract

Phenylalanine ammonia-lyase (PAL, E.C.4.3.1.5) catalyzes the benzene propane metabolism and is the most extensively studied enzyme of the phenylpropanoid pathway. However, the role of PAL genes in Astragalus membranaceus, a non-model plant showing high capability toward abiotic stress, is less studied. Here, [...] Read more.

Phenylalanine ammonia-lyase (PAL, E.C.4.3.1.5) catalyzes the benzene propane metabolism and is the most extensively studied enzyme of the phenylpropanoid pathway. However, the role of PAL genes in Astragalus membranaceus, a non-model plant showing high capability toward abiotic stress, is less studied. Here, we cloned AmPAL and found that it encodes a protein that resides in the cytoplasmic membrane. The mRNA of AmPAL was strongly induced by NaCl or NaHCO₃ treatment, especially in the root. Overexpressing AmPAL in Nicotiana tabacum resulted in higher PAL enzyme activities, lower levels of malondialdehyde (MDA), and better root elongation in the seedlings under stress treatment compared to the control plants. The protective role of AmPAL under saline-alkali stress was also observed in 30-day soil-grown plants, which showed higher levels of superoxide dismutase (SOD), proline, and chlorophyll compared to wild-type N. Tabacum. Collectively, we provide evidence that AmPAL is responsive to multiple abiotic stresses and that manipulating the expression of AmPAL can be used to increase the tolerance to adverse environmental factors in plants. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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15 pages, 4992 KiB

Open AccessArticle

Genome-Wide Identification of ATG Gene Family Members in Fagopyrum tataricum and Their Expression during Stress Responses

by Yue Fang, Shuang Wang, Hula Wu, Chenglei Li, Haixia Zhao, Hui Chen, Xiaoli Wang and Qi Wu

Int. J. Mol. Sci. 2022, 23(23), 14845; https://doi.org/10.3390/ijms232314845 - 27 Nov 2022

Cited by 2 | Viewed by 2163

Abstract

Abiotic stresses such as drought and salinity are major environmental factors limiting plant productivity. Autophagy-related genes are extensively involved in plant growth, development, and adverse stress responses, which have not yet been characterized in Tartary buckwheat (Fagopyrum tataricum, TB). In this study, [...] Read more.

Abiotic stresses such as drought and salinity are major environmental factors limiting plant productivity. Autophagy-related genes are extensively involved in plant growth, development, and adverse stress responses, which have not yet been characterized in Tartary buckwheat (Fagopyrum tataricum, TB). In this study, we verified that drought stress could induce autophagy in TB roots. Next, 49 FtATGs in the whole genome of TB were identified. All FtATGs were randomly distributed in 8 known chromosomes, while 11 FtATGs were predictably segmental repeats. As the core component of autophagy, there were 8 FtATG8s with similar gene structures in TB, while FtATG8s showed high expression at the transcription level under drought and salt stresses. The cis-acting element analysis identified that all FtATG8 promoters contain light-responsive and MYB-binding elements. FtATG8s showed a cell-wide protein interaction network and strongly correlated with distinct stress-associated transcription factors. Furthermore, overexpression of FtATG8a and FtATG8f enhanced the antioxidant enzyme activities of TB under adverse stresses. Remarkably, FtATG8a and FtATG8f may be vital candidates functioning in stress resistance in TB. This study prominently aids in understanding the biological role of FtATG genes in TB. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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22 pages, 1990 KiB

Open AccessArticle

Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration

by Alexander Kanapin, Tatyana Rozhmina, Mikhail Bankin, Svetlana Surkova, Maria Duk, Ekaterina Osyagina and Maria Samsonova

Int. J. Mol. Sci. 2022, 23(23), 14536; https://doi.org/10.3390/ijms232314536 - 22 Nov 2022

Cited by 3 | Viewed by 1227

Abstract

In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in [...] Read more.

In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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20 pages, 5523 KiB

Open AccessArticle

Combined Metabolomic and Transcriptomic Analysis Reveals Allantoin Enhances Drought Tolerance in Rice

by Shuai Lu, Zichang Jia, Xiangfeng Meng, Yaoyu Chen, Surong Wang, Chaozhen Fu, Lei Yang, Rong Zhou, Baohua Wang and Yunying Cao

Int. J. Mol. Sci. 2022, 23(22), 14172; https://doi.org/10.3390/ijms232214172 - 16 Nov 2022

Cited by 4 | Viewed by 1724

Abstract

Drought is a misfortune for agriculture and human beings. The annual crop yield reduction caused by drought exceeds the sum of all pathogens. As one of the gatekeepers of China’s “granary”, rice is the most important to reveal the key drought tolerance factors [...] Read more.

Drought is a misfortune for agriculture and human beings. The annual crop yield reduction caused by drought exceeds the sum of all pathogens. As one of the gatekeepers of China’s “granary”, rice is the most important to reveal the key drought tolerance factors in rice. Rice seedlings of Nipponbare (Oryza sativa L. ssp. Japonica) were subjected to simulated drought stress, and their root systems were analyzed for the non-targeted metabolome and strand-specific transcriptome. We found that both DEGs and metabolites were enriched in purine metabolism, and allantoin accumulated significantly in roots under drought stress. However, few studies on drought tolerance of exogenous allantoin in rice have been reported. We aimed to further determine whether allantoin can improve the drought tolerance of rice. Under the treatment of exogenous allantoin at different concentrations, the drought resistant metabolites of plants accumulated significantly, including proline and soluble sugar, and reactive oxygen species (ROS) decreased and reached a significant level in 100 μmol L⁻¹. To this end, a follow-up study was identified in 100 μmol L⁻¹ exogenous allantoin and found that exogenous allantoin improved the drought resistance of rice. At the gene level, under allantoin drought treatment, we found that genes of scavenge reactive oxygen species were significantly expressed, including peroxidase (POD), catalase (CATA), ascorbate peroxidase 8 (APX8) and respiratory burst oxidase homolog protein F (RbohF). This indicates that plants treated by allantoin have better ability to scavenge reactive oxygen species to resist drought. Alternative splicing analysis revealed a total of 427 differentially expressed alternative splicing events across 320 genes. The analysis of splicing factors showed that gene alternative splicing could be divided into many different subgroups and play a regulatory role in many aspects. Through further analysis, we restated the key genes and enzymes in the allantoin synthesis and catabolism pathway, and found that the expression of synthetase and hydrolase showed a downward trend. The pathway of uric acid to allantoin is completed by uric acid oxidase (UOX). To find out the key transcription factors that regulate the expression of this gene, we identified two highly related transcription factors OsERF059 and ONAC007 through correlation analysis. They may be the key for allantoin to enhance the drought resistance of rice. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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14 pages, 3928 KiB

Open AccessArticle

Genome-Wide Association Study Reveals Novel QTLs and Candidate Genes for Grain Number in Rice

by Peiyuan Li, Qing Li, Xueli Lu, Liping Dai, Long Yang, Yifeng Hong, Tiancai Yan, Lan Shen, Qiang Zhang, Deyong Ren, Li Zhu, Jiang Hu, Guojun Dong, Guangheng Zhang, Qian Qian and Dali Zeng

Int. J. Mol. Sci. 2022, 23(21), 13617; https://doi.org/10.3390/ijms232113617 - 06 Nov 2022

Viewed by 2031

Abstract

Grain number per panicle (GNPP), determined mainly by panicle branching, is vital for rice yield. The dissection of the genetic basis underlying GNPP could help to improve rice yield. However, genetic resources, including quantitative trait loci (QTL) or genes for breeders to enhance [...] Read more.

Grain number per panicle (GNPP), determined mainly by panicle branching, is vital for rice yield. The dissection of the genetic basis underlying GNPP could help to improve rice yield. However, genetic resources, including quantitative trait loci (QTL) or genes for breeders to enhance rice GNPP, are still limited. Here, we conducted the genome-wide association study (GWAS) on the GNPP, primary branch number (PBN), and secondary branch number (SBN) of 468 rice accessions. We detected a total of 18 QTLs, including six for GNPP, six for PBN, and six for SBN, in the whole panel and the indica and japonica subpanels of 468 accessions. More importantly, qPSG1 was a common QTL for GNPP, PBN, and SBN and was demonstrated by chromosome segment substitution lines (CSSLs). Considering gene annotation, expression, and haplotype analysis, seven novel and strong GNPP-related candidate genes were mined from qPSG1. Our results provide clues to elucidate the molecular regulatory network of GNPP. The identified QTLs and candidate genes will contribute to the improvement of GNPP and rice yield via molecular marker-assisted selection (MAS) breeding and genetic engineering techniques. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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22 pages, 3820 KiB

Open AccessArticle

Identification of Key Genes during Ethylene-Induced Adventitious Root Development in Cucumber (Cucumis sativus L.)

by Yuzheng Deng, Chunlei Wang, Meiling Zhang, Lijuan Wei and Weibiao Liao

Int. J. Mol. Sci. 2022, 23(21), 12981; https://doi.org/10.3390/ijms232112981 - 26 Oct 2022

Cited by 4 | Viewed by 1619

Abstract

Ethylene (ETH), as a key plant hormone, plays critical roles in various processes of plant growth and development. ETH has been reported to induce adventitious rooting. Moreover, our previous studies have shown that exogenous ETH may induce plant adventitious root development in cucumber [...] Read more.

Ethylene (ETH), as a key plant hormone, plays critical roles in various processes of plant growth and development. ETH has been reported to induce adventitious rooting. Moreover, our previous studies have shown that exogenous ETH may induce plant adventitious root development in cucumber (Cucumis sativus L.). However, the key genes involved in this process are still unclear. To explore the key genes in ETH-induced adventitious root development, we employed a transcriptome technique and revealed 1415 differentially expressed genes (DEGs), with 687 DEGs up-regulated and 728 DEGs down-regulated. Using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we further identified critical pathways that were involved in ETH-induced adventitious root development, including carbon metabolism (starch and sucrose metabolism, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis, and fatty acid degradation), secondary metabolism (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced the content of sucrose, glucose, starch, the activity of sucrose synthase (SS), sucrose–phosphate synthase (SPS) and hexokinase (HK), and the expressions of CsHK2, pyruvate kinase2 (CsPK2), and CsCYP86A1, whereas it enhanced the expressions of β-amylase 1 (CsBAM1) and β-amylase 3 (CsBAM3). In secondary metabolism, the transcript levels of phenylalanine ammonia-lyase (CsPAL) and flavonoid 3′-monooxygenase (CsF3′M) were negatively regulated, and that of primary-amine oxidase (CsPAO) was positively regulated by ETH. Additionally, the indole-3-acetic acid (IAA) content and the expressions of auxin and ETH signaling transduction-related genes (auxin transporter-like protein 5 (CsLAX5), CsGH3.17, CsSUAR50, and CsERS) were suppressed, whereas the abscisic acid (ABA) content and the expressions of ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, BRI1-associated kinase 1 (CsBAK1), and CsXTH3) were promoted by ETH. Furthermore, the mRNA levels of these genes were confirmed by real-time PCR (RT-qPCR). These results indicate that genes related to carbon metabolism, secondary metabolite biosynthesis, and plant hormone signaling transduction are involved in ETH-induced adventitious root development. This work identified the key pathways and genes in ETH-induced adventitious rooting in cucumber, which may provide new insights into ETH-induced adventitious root development and will be useful for investigating the molecular roles of key genes in this process in further studies. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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16 pages, 9560 KiB

Open AccessArticle

Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering

by Guiling Liu, Fengyi Li, Gongfa Shi, Lei Wang, Ling Wang and Lijuan Fan

Int. J. Mol. Sci. 2022, 23(17), 9950; https://doi.org/10.3390/ijms23179950 - 01 Sep 2022

Cited by 5 | Viewed by 1535

Abstract

Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential [...] Read more.

Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential for producing I. laevigata of desirable flowering properties. A prerequisite is to identify and characterize key flowering control genes, the identity of which remains largely unknown in I. laevigata due to the lack of genome information. To fill this knowledge gap, we used sequencing data of the I. laevigata transcriptome to identify MADS-box gene-encoding transcription factors that have been shown to play key roles in developmental processes, including flowering. Our data revealed 41 putative MADS-box genes, which consisted of 8 type I (5 Mα and 3 Mβ, respectively) and 33 type II members (2 MIKC* and 31 MIKC^C, respectively). We then selected IlSEP3 and IlSVP for functional studies and found that both are localized to the nucleus and that they interact physically in vitro. Ectopic expression of IlSEP3 in Arabidopsis resulted in early flowering (32 days) compared to that of control plants (36 days), which could be mediated by modulating the expression of FT, SOC1, AP1, SVP, SPL3, VRN1, and GA20OX. By contrast, plants overexpressing IlSVP were phenotypically similar to that of wild type. Our functional validation of IlSEP3 was consistent with the notion that SEP3 promotes flowering in multiple plant species and indicated that IlSEP3 regulates flowering in I. laevigata. Taken together, this work provided a systematic identification of MADS-box genes in I. laevigata and demonstrated that the flowering time of I. laevigata can be genetically controlled by altering the expression of key MADS-box genes. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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16 pages, 7850 KiB

Open AccessArticle

Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery

by Xiaoming Song, Nan Li, Yingchao Zhang, Yi Liang, Rong Zhou, Tong Yu, Shaoqin Shen, Shuyan Feng, Yu Zhang, Xiuqing Li, Hao Lin and Xiyin Wang

Int. J. Mol. Sci. 2022, 23(16), 8986; https://doi.org/10.3390/ijms23168986 - 12 Aug 2022

Cited by 2 | Viewed by 1494

Abstract

Celery (Apium graveolens L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics [...] Read more.

Celery (Apium graveolens L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chlorophyll and carotenoid-related genes in celery and six representative species. Significantly, different contents and gene expression patterns were found among three celery varieties. In total, 237 and 290 chlorophyll and carotenoid-related genes were identified in seven species. No notable gene expansion of chlorophyll biosynthesis was detected in examined species. However, the gene encoding ζ-carotene desaturase (ZDS) enzyme in carotenoid was expanded in celery. Comparative genomics and RNA-seq analyses revealed 16 and 5 key genes, respectively, regulating chlorophyll and carotenoid. An intriguing finding is that chlorophyll and carotenoid-related genes were coordinately regulated by transcriptional factors, which could be distinctively classified into positive- and negative-regulation groups. Six CONSTANS (CO)-like transcription factors co-regulated chlorophyll and carotenoid-related genes were identified in celery. In conclusion, this study provides new insights into the regulation of chlorophyll and carotenoid by transcription factors. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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12 pages, 4081 KiB

Open AccessArticle

Transcriptome and Quasi-Targeted Metabolome Analyze Overexpression of 4-Hydroxyphenylpyruvate Dioxygenase Alleviates Fungal Toxicity of 9-Phenanthrol in Magnaporthe oryzae

by Yi Wang, Ziyi Wang, Sauban Musa Jibril, Mian Wei, Xin Pu, Chao Yang, Chan Ma, Qi Wu, Lina Liu, Yiji Quan and Chengyun Li

Int. J. Mol. Sci. 2022, 23(13), 7116; https://doi.org/10.3390/ijms23137116 - 27 Jun 2022

Cited by 3 | Viewed by 1738

Abstract

Magnaporthe oryzae, the causal agent of rice blast disease, produces devastating damage to global rice production. It is urgent to explore novel strategies to overcome the losses caused by this disease. 9-phenanthrol is often used as a transient receptor potential melastatin 4 [...] Read more.

Magnaporthe oryzae, the causal agent of rice blast disease, produces devastating damage to global rice production. It is urgent to explore novel strategies to overcome the losses caused by this disease. 9-phenanthrol is often used as a transient receptor potential melastatin 4 (TRPM4) channel inhibitor for animals, but we found its fungal toxicity to M. oryzae. Thus, we explored the antimicrobial mechanism through transcriptome and metabolome analyses. Moreover, we found that overexpression of a gene encoding 4-hydroxyphenylpyruvate dioxygenase involved in the tyrosine degradative pathway enhanced the tolerance of 9-phenanthrol in M. oryzae. Thus, our results highlight the potential fungal toxicity mechanism of 9-phenanthrol at metabolic and transcriptomic levels and identify a gene involving 9-phenanthrol alleviation. Importantly, our results demonstrate the novel mechanism of 9-phenanthrol on fungal toxicity that will provide new insights of 9-phenanthrol for application on other organisms. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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Review

Jump to: Research

11 pages, 405 KiB

Open AccessReview

Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs

by Tatiana N. Erokhina, Dmitriy Y. Ryazantsev, Sergey K. Zavriev and Sergey Y. Morozov

Int. J. Mol. Sci. 2023, 24(3), 2114; https://doi.org/10.3390/ijms24032114 - 20 Jan 2023

Cited by 2 | Viewed by 1748

Abstract

This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities [...] Read more.

This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed together with a brief description of the methods to identify pri-miRNA ORFs and the encoded protein products. Generally, miPEPs have been identified in many plant species of several families and in a few animal species. Importantly, molecular mechanisms of the miPEP action are often quite different between flowering plants and metazoan species. Requirement for the additional studies in these directions is highlighted by alternative findings concerning negative or positive regulation of pri-miRNA/miRNA expression by miPEPs in plants and animals. Additionally, the question of how miPEPs are distributed in non-flowering plant taxa is very important for understanding the evolutionary origin of such micropeptides. Evidently, further extensive studies are needed to explore the functions of miPEPs and the corresponding ORFs and to understand the full set of their roles in eukaryotic organisms. Thus, we address the most recent integrative views of different genomic, physiological, and molecular aspects concerning the expression of miPEPs and their possible fine functions. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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Multi-Omics Uncover the Mechanism of Wheat under Heavy Metal Stress

by Min Zhou and Shigang Zheng

Int. J. Mol. Sci. 2022, 23(24), 15968; https://doi.org/10.3390/ijms232415968 - 15 Dec 2022

Cited by 6 | Viewed by 3021

Abstract

Environmental pollution of heavy metals has received growing attention in recent years. Heavy metals such as cadmium, lead and mercury can cause physiological and morphological disturbances which adversely affect the growth and quality of crops. Wheat (Triticum aestivum L.) can accumulate high [...] Read more.

Environmental pollution of heavy metals has received growing attention in recent years. Heavy metals such as cadmium, lead and mercury can cause physiological and morphological disturbances which adversely affect the growth and quality of crops. Wheat (Triticum aestivum L.) can accumulate high contents of heavy metals in its edible parts. Understanding wheat response to heavy metal stress and its management in decreasing heavy metal uptake and accumulation may help to improve its growth and grain quality. Very recently, emerging advances in heavy metal toxicity and phytoremediation methods to reduce heavy metal pollution have been made in wheat. Especially, the molecular mechanisms of wheat under heavy metal stress are increasingly being recognized. In this review, we focus on the recently described epigenomics, transcriptomics, proteomics, metabolomics, ionomics and multi-omics combination, as well as functional genes uncovering heavy metal stress in wheat. The findings in this review provide some insights into challenges and future recommendations for wheat under heavy metal stress. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants)

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