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17 pages, 3085 KiB

Open AccessArticle

Transcriptional Changes in Damask Rose Suspension Cell Culture Revealed by RNA Sequencing

by Won Kyong Cho, Hoseong Choi, Soo-Yun Kim, Euihyun Kim, Seung Hye Paek, Jiyeon Kim, Jihyeok Song, Kyoungyeon Heo, Jiae Min, Yeonhwa Jo, Jeong Hun Lee and Sang Hyun Moh

Plants 2024, 13(5), 602; https://doi.org/10.3390/plants13050602 - 22 Feb 2024

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Abstract

Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by [...] Read more.

Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by RNA sequencing to reveal transcriptional changes during rose suspension cell culture. Of the 580 coding RNAs (1.3%) highly expressed in the suspension rose cells, 68 encoded cell wall-associated proteins. However, most RNAs encoded by the chloroplasts and mitochondria are not expressed. Many highly expressed coding RNAs are involved in translation, catalyzing peptide synthesis in ribosomes. Moreover, the amide metabolic process producing naturally occurring alkaloids was the most abundant metabolic process during the propagation of rose suspension cells. During rose cell propagation, coding RNAs involved in the stress response were upregulated at an early stage, while coding RNAs associated with detoxification and transmembrane transport were upregulated at the late stage. We used transcriptome analyses to reveal important biological processes and molecular mechanisms during rose suspension cell culture. Most non-coding (nc) RNAs were not expressed in the rose suspension cells, but a few ncRNAs with unknown functions were highly expressed. The expression of ncRNAs and their target coding RNAs was highly correlated. Taken together, we revealed significant biological processes and molecular mechanisms occurring during rose suspension cell culture using transcriptome analyses. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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16 pages, 3081 KiB

Open AccessArticle

Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors

by Pavlína Pírek, Karolína Kryštofová, Ingrid Kováčová, Anna Kromerová, Dagmar Zachová, Ondřej Helia, Klára Panzarová, Jiří Fajkus, Zbyněk Zdráhal, Gabriela Lochmanová and Miloslava Fojtová

Plants 2023, 12(24), 4177; https://doi.org/10.3390/plants12244177 - 15 Dec 2023

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Abstract

The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, [...] Read more.

The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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15 pages, 3300 KiB

Open AccessArticle

Unveiling the Role of Sorghum RPAP3 in the Function of R2TP Complex: Insights into Protein Assembly in Plants

by Larissa Machado Antonio, Gustavo Henrique Martins, Annelize Zambon Barbosa Aragão, Natália Galdi Quel, Gabriel Zazeri, Walid A. Houry and Carlos Henrique Inacio Ramos

Plants 2023, 12(16), 2925; https://doi.org/10.3390/plants12162925 - 12 Aug 2023

Cited by 1 | Viewed by 1111

Abstract

The chaperone R2TP has multiple subunits that assist in the proper folding, assembly, and stabilization of various protein complexes in cells and its study can offer valuable insights into the regulation and maintenance of protein assemblies in plant systems. The ‘T’ component of [...] Read more.

The chaperone R2TP has multiple subunits that assist in the proper folding, assembly, and stabilization of various protein complexes in cells and its study can offer valuable insights into the regulation and maintenance of protein assemblies in plant systems. The ‘T’ component of R2TP is Tah1 in yeast, consisting of 111 residues, while its counterpart in humans is RPAP3, with 665 residues. RPAP3 acts as a co-chaperone of Hsp90 and facilitates interactions between RUVBL proteins and other complex components, enhancing the recruitment of client proteins by the R2TP complex. These facts further underscore the relevance of studying this complex in different organisms. The putative gene corresponding to the RPAP3 in Sorghum bicolor, a monocotyledon plant, was cloned, and the protein (396 residues) purified for biochemical characterization. SbRPAP3 exists as a folded monomer and has a RPAP3 domain, which is present in human RPAP3 but absent in yeast Tah1. SbRPAP3 retains its functional capabilities, including binding with RUVBLs, Hsp90, and Hsp70. By elucidating the role of RPAP3 in plant R2TP complex, we can further comprehend the molecular mechanisms underlying plant-specific protein assembly and contribute to advancements in plant biology and biotechnological applications. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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14 pages, 3064 KiB

Open AccessArticle

A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea

by Jeehyoung Shim, Su Young Hong, Jae-Hyuk Han, Yeisoo Yu, Eunae Yoo, Jungsook Sung, Joong Hyoun Chin and O New Lee

Plants 2023, 12(14), 2702; https://doi.org/10.3390/plants12142702 - 20 Jul 2023

Viewed by 1264

Abstract

Milk thistle (Silybum marianum) belongs to the Asteraceae family and is a medicinal plant native to the Mediterranean Basin. Silymarin in achene is a widely used herbal product for chronic liver disease. There is growing interest in natural medicine using milk [...] Read more.

Milk thistle (Silybum marianum) belongs to the Asteraceae family and is a medicinal plant native to the Mediterranean Basin. Silymarin in achene is a widely used herbal product for chronic liver disease. There is growing interest in natural medicine using milk thistle in Korea, but the raw material completely relies on imports. Despite its economic importance, phenotypic evaluations of native resources of milk thistle in Korea have not been carried out. In addition, genomic research and molecular marker development are very limited in milk thistle. In this study, we evaluated 220 milk thistle resources consisting of 172 accessions collected from the domestic market, and 48 accessions isolated from 6 accessions distributed by the National Agrobiodiversity Center in Korea. Six plant characteristics (height, seed weight, number of flowers, seed weight per flower, spine length, and color at harvest) were measured, and six samples (M01–M06) were selected to represent the genetic diversity of the population for genomic research. To develop PCR-based and co-dominant insertion/deletion (InDel) markers, we performed genome-wide InDel detection by comparing the whole-genome resequencing data of the six selected accessions with the reference genome sequence (GCA_001541825). As a result, 177 InDel markers with high distinguishability and reproducibility were selected from the 30,845 InDel variants. Unknowingly imported alien plant resources could easily be genetically mixed, and jeopardized seed purity can cause continuous difficulties in the development of high value-added agricultural platforms utilizing natural products. The selected plant materials and 177 validated InDel markers developed via whole-genome resequencing analysis could be valuable resources for breeding, conservation, and ecological studies of natives to Korea, along with acceleration of Silybum marianum industrialization. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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24 pages, 9284 KiB

Open AccessArticle

An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency

by Yin-Hua Lai, Ming-Yi Peng, Rong-Yu Rao, Wen-Shu Chen, Wei-Tao Huang, Xin Ye, Lin-Tong Yang and Li-Song Chen

Plants 2023, 12(14), 2680; https://doi.org/10.3390/plants12142680 - 18 Jul 2023

Cited by 2 | Viewed by 1113

Abstract

Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the [...] Read more.

Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the ability to keep phosphate homeostasis by elevating the abundances of metabolites containing phosphorus and the compartmentation of phosphate in plastids, and/or downregulating low-phosphate-inducible genes; (b) improving the ability to keep N homeostasis by lowering the levels of metabolites containing N but not phosphorus, upregulating N compound degradation, the root/shoot ratio, and the expression of genes involved in N uptake, and resulting in transitions from N-rich alkaloids to carbon (C)-rich phenylpropanoids and phenolic compounds (excluding indole alkaloids) and from N-rich amino acids to C-rich carbohydrates and organic acids; (c) upregulating the ability to maintain energy homeostasis by increasing energy production (tricarboxylic acid cycle, glycolysis/gluconeogenesis, oxidative phosphorylation, and ATP biosynthetic process) and decreasing energy utilization for amino acid and protein biosynthesis and new root building; (d) elevating the transmembrane transport of metabolites, thus enhancing the remobilization and recycling of useful compounds; and (e) activating protein processing in the endoplasmic reticulum. RN0 had a higher ability to detoxify reactive oxygen species and aldehydes, thus protecting RN0 against oxidative injury and delaying root senescence. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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15 pages, 1792 KiB

Open AccessArticle

Genomic Analysis Highlights Putative Defective Susceptibility Genes in Tomato Germplasm

by Ruiling Li, Alex Maioli, Sergio Lanteri, Andrea Moglia, Yuling Bai and Alberto Acquadro

Plants 2023, 12(12), 2289; https://doi.org/10.3390/plants12122289 - 12 Jun 2023

Viewed by 1182

Abstract

Tomato (Solanum lycopersicum L.) is one of the most widely grown vegetables in the world and is impacted by many diseases which cause yield reduction or even crop failure. Breeding for disease resistance is thus a key objective in tomato improvement. Since [...] Read more.

Tomato (Solanum lycopersicum L.) is one of the most widely grown vegetables in the world and is impacted by many diseases which cause yield reduction or even crop failure. Breeding for disease resistance is thus a key objective in tomato improvement. Since disease arises from a compatible interaction between a plant and a pathogen, a mutation which alters a plant susceptibility (S) gene facilitating compatibility may induce broad-spectrum and durable plant resistance. Here, we report on a genome-wide analysis of a set of 360 tomato genotypes, with the goal of identifying defective S-gene alleles as a potential source for the breeding of resistance. A set of 125 gene homologs of 10 S-genes (PMR 4, PMR5, PMR6, MLO, BIK1, DMR1, DMR6, DND1, CPR5, and SR1) were analyzed. Their genomic sequences were examined and SNPs/indels were annotated using the SNPeff pipeline. A total of 54,000 SNPs/indels were identified, among which 1300 were estimated to have a moderate impact (non-synonymous variants), while 120 were estimated to have a high impact (e.g., missense/nonsense/frameshift variants). The latter were then analyzed for their effect on gene functionality. A total of 103 genotypes showed one high-impact mutation in at least one of the scouted genes, while in 10 genotypes, more than 4 high-impact mutations in as many genes were detected. A set of 10 SNPs were validated through Sanger sequencing. Three genotypes carrying high-impact homozygous SNPs in S-genes were infected with Oidium neolycopersici, and two highlighted a significantly reduced susceptibility to the fungus. The existing mutations fall within the scope of a history of safe use and can be useful to guide risk assessment in evaluating the effect of new genomic techniques. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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15 pages, 4720 KiB

Open AccessArticle

BIC2, a Cryptochrome Function Inhibitor, Is Involved in the Regulation of ABA Responses in Arabidopsis

by Yating Wang, Wei Wang, Qiming Jia, Hainan Tian, Xutong Wang, Yingying Li, Saddam Hussain, Hadia Hussain, Tianya Wang and Shucai Wang

Plants 2023, 12(11), 2220; https://doi.org/10.3390/plants12112220 - 05 Jun 2023

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Abstract

The plant hormone ABA (abscisic acid) is able to regulate plant responses to abiotic stresses via regulating the expression of ABA response genes. BIC1 (Blue-light Inhibitor of Cryptochromes 1) and BIC2 have been identified as the inhibitors of plant cryptochrome functions, and are [...] Read more.

The plant hormone ABA (abscisic acid) is able to regulate plant responses to abiotic stresses via regulating the expression of ABA response genes. BIC1 (Blue-light Inhibitor of Cryptochromes 1) and BIC2 have been identified as the inhibitors of plant cryptochrome functions, and are involved in the regulation of plant development and metabolism in Arabidopsis . In this study, we report the identification of BIC2 as a regulator of ABA responses in Arabidopsis . RT-PCR (Reverse Transcription-Polymerase Chain Reaction) results show that the expression level of BIC1 remained largely unchanged, but that of BIC2 increased significantly in response to ABA treatment. Transfection assays in Arabidopsis protoplasts show that both BIC1 and BIC2 were mainly localized in the nucleus, and were able to activate the expression of the co-transfected reporter gene. Results in seed germination and seedling greening assays show that ABA sensitivity was increased in the transgenic plants overexpressing BIC2, but increased slightly, if any, in the transgenic plants overexpressing BIC1. ABA sensitivity was also increased in the bic2 single mutants in seedling greening assays, but no further increase was observed in the bic1 bic2 double mutants. On the other hand, in root elongation assays, ABA sensitivity was decreased in the transgenic plants overexpressing BIC2, as well as the bic2 single mutants, but no further decrease was observed in the bic1 bic2 double mutants. By using qRT-PCR (quantitative RT-PCR), we further examined how BIC2 may regulate ABA responses in Arabidopsis , and found that inhibition of ABA on the expression of the ABA receptor genes PYL4 (PYR1-Like 4) and PYL5 were decreased, but promotion of ABA on the expression of the protein kinase gene SnRK2.6 (SNF1-Related Protein Kinases 2.6) was enhanced in both the bic1 bic2 double mutants and 35S:BIC2 overexpression transgenic plants. Taken together, our results suggest that BIC2 regulates ABA responses in Arabidopsis possibly by affecting the expression of ABA signaling key regulator genes. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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21 pages, 5662 KiB

Open AccessArticle

Identification and Expression Analysis of Phosphatidylinositol Transfer Proteins Genes in Rice

by Mengtian Pei, Xuze Xie, Baoyi Peng, Xinchi Chen, Yixuan Chen, Ya Li, Zonghua Wang and Guodong Lu

Plants 2023, 12(11), 2122; https://doi.org/10.3390/plants12112122 - 26 May 2023

Cited by 1 | Viewed by 1132

Abstract

The family of phosphatidylinositol transfer proteins (PITPs) is able to bind specific lipids to carry out various biological functions throughout different stages of plant life. But the function of PITPs in rice plant is unclear. In this study, 30 PITPs were identified from [...] Read more.

The family of phosphatidylinositol transfer proteins (PITPs) is able to bind specific lipids to carry out various biological functions throughout different stages of plant life. But the function of PITPs in rice plant is unclear. In this study, 30 PITPs were identified from rice genome, which showed differences in physicochemical properties, gene structure, conservation domains, and subcellular localization. The promoter region of the OsPITPs genes included at least one type of hormone response element, such as methyl jasmonate (Me JA) and salicylic acid (SA). Furthermore, the expression level of OsML-1, OsSEC14-3, OsSEC14-4, OsSEC14-15, and OsSEC14-19 genes were significantly affected by infection of rice blast fungus Magnaporthe oryzae. Based on these findings, it is possible that OsPITPs may be involved in rice innate immunity in response to M. oryzae infection through the Me JA and SA pathway. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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17 pages, 2725 KiB

Open AccessArticle

The Carrot Phytoene Synthase 2 (DcPSY2) Promotes Salt Stress Tolerance through a Positive Regulation of Abscisic Acid and Abiotic-Related Genes in Nicotiana tabacum

by Orlando Acevedo, Rodrigo A. Contreras and Claudia Stange

Plants 2023, 12(10), 1925; https://doi.org/10.3390/plants12101925 - 09 May 2023

Cited by 1 | Viewed by 1392

Abstract

Background: Carotenoids, which are secondary metabolites derived from isoprenoids, play a crucial role in photo-protection and photosynthesis, and act as precursors for abscisic acid, a hormone that plays a significant role in plant abiotic stress responses. The biosynthesis of carotenoids in higher plants [...] Read more.

Background: Carotenoids, which are secondary metabolites derived from isoprenoids, play a crucial role in photo-protection and photosynthesis, and act as precursors for abscisic acid, a hormone that plays a significant role in plant abiotic stress responses. The biosynthesis of carotenoids in higher plants initiates with the production of phytoene from two geranylgeranyl pyrophosphate molecules. Phytoene synthase (PSY), an essential catalytic enzyme in the process, regulates this crucial step in the pathway. In Daucus carota L. (carrot), two PSY genes (DcPSY1 and DcPSY2) have been identified but only DcPSY2 expression is induced by ABA. Here we show that the ectopic expression of DcPSY2 in Nicotiana tabacum L. (tobacco) produces in L3 and L6 a significant increase in total carotenoids and chlorophyll a, and a significant increment in phytoene in the T₁L6 line. Tobacco transgenic T₁L3 and T₁L6 lines subjected to chronic NaCl stress showed an increase of between 2 and 3- and 6-fold in survival rate relative to control lines, which correlates directly with an increase in the expression of endogenous carotenogenic and abiotic-related genes, and with ABA levels. Conclusions: These results provide evidence of the functionality of DcPSY2 in conferring salt stress tolerance in transgenic tobacco T₁L3 and T₁L6 lines. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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14 pages, 3248 KiB

Open AccessArticle

Genome-Editing of FtsZ1 for Alteration of Starch Granule Size in Potato Tubers

by Alexander C. Pfotenhauer, Alessandro Occhialini, Stacee A. Harbison, Li Li, Agnieszka A. Piatek, Curtis R. Luckett, Yongil Yang, C. Neal Stewart, Jr. and Scott C. Lenaghan

Plants 2023, 12(9), 1878; https://doi.org/10.3390/plants12091878 - 04 May 2023

Viewed by 1441

Abstract

Genome-editing has enabled rapid improvement for staple food crops, such as potato, a key beneficiary of the technology. In potato, starch contained within tubers represents the primary product for use in food and non-food industries. Starch granules are produced in the plastids of [...] Read more.

Genome-editing has enabled rapid improvement for staple food crops, such as potato, a key beneficiary of the technology. In potato, starch contained within tubers represents the primary product for use in food and non-food industries. Starch granules are produced in the plastids of tubers with plastid size correlated with the size of starch grana. The division of plastids is controlled by proteins, including the tubulin-like GTPase FtsZ1. The altered expression of FtsZ1 has been shown to disrupt plastid division, leading to the production of “macro-plastid”-containing plants. These macro-chloroplast plants are characterized by cells containing fewer and enlarged plastids. In this work, we utilize CRISPR/Cas9 to generate FtsZ1 edited potato lines to demonstrate that genome-editing can be used to increase the size of starch granules in tubers. Altered plastid morphology was comparable to the overexpression of FtsZ1 in previous work in potato and other crops. Several lines were generated with up to a 1.98-fold increase in starch granule size that was otherwise phenotypically indistinguishable from wild-type plants. Further, starch paste from one of the most promising lines showed a 2.07-fold increase in final viscosity. The advantages of enlarged starch granules and the potential of CRISPR/Cas9-based technologies for food crop improvement are further discussed. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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23 pages, 4272 KiB

Open AccessArticle

Genetic Mapping of Flavonoid Grain Pigments in Durum Wheat

by Natalia Sgaramella, Domenica Nigro, Antonella Pasqualone, Massimo Antonio Signorile, Barbara Laddomada, Gabriella Sonnante, Emanuela Blanco, Rosanna Simeone and Antonio Blanco

Plants 2023, 12(8), 1674; https://doi.org/10.3390/plants12081674 - 17 Apr 2023

Cited by 3 | Viewed by 1609

Abstract

Pigmented cereal grains with high levels of flavonoid compounds have attracted the attention of nutritional science backing the development of functional foods with claimed health benefits. In this study, we report results on the genetic factors controlling grain pigmentation in durum wheat using [...] Read more.

Pigmented cereal grains with high levels of flavonoid compounds have attracted the attention of nutritional science backing the development of functional foods with claimed health benefits. In this study, we report results on the genetic factors controlling grain pigmentation in durum wheat using a segregant population of recombinant inbred lines (RILs) derived from a cross between an Ethiopian purple grain accession and an Italian amber grain cultivar. The RIL population was genotyped by the wheat 25K SNP array and phenotyped for total anthocyanin content (TAC), grain color, and the L*, a*, and b* color index of wholemeal flour, based on four field trials. The mapping population showed a wide variation for the five traits in the different environments, a significant genotype x environment interaction, and high heritability. A total of 5942 SNP markers were used for constructing the genetic linkage map, with an SNP density ranging from 1.4 to 2.9 markers/cM. Two quantitative trait loci (QTL) were identified for TAC mapping on chromosome arms 2AL and 7BS in the same genomic regions of two detected QTL for purple grain. The interaction between the two QTL was indicative of an inheritance pattern of two loci having complementary effects. Moreover, two QTL for red grain color were detected on chromosome arms 3AL and 3BL. The projection of the four QTL genomic regions on the durum wheat Svevo reference genome disclosed the occurrence of the candidate genes Pp-A3, Pp-B1, R-A1, and R-B1 involved in flavonoid biosynthetic pathways and encoding of transcription factors bHLH (Myc-1) and MYB (Mpc1, Myb10), previously reported in common wheat. The present study provides a set of molecular markers associated with grain pigments useful for the selection of essential alleles for flavonoid synthesis in durum wheat breeding programs and enhancement of the health-promoting quality of derived foods. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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16 pages, 3428 KiB

Open AccessArticle

ASR1 and ASR2, Two Closely Related ABA-Induced Serine-Rich Transcription Repressors, Function Redundantly to Regulate ABA Responses in Arabidopsis

by Hadia Hussain, Yuxin Cheng, Yating Wang, Yuan Yuan, Adnan, Yingying Li, Hainan Tian, Saddam Hussain, Siyu Chen, Rao Lin, Tianya Wang and Shucai Wang

Plants 2023, 12(4), 852; https://doi.org/10.3390/plants12040852 - 14 Feb 2023

Cited by 1 | Viewed by 1750

Abstract

The plant hormone abscisic acid (ABA) is able to regulate the expression of ABA-responsive genes via signaling transduction, and thus plays an important role in regulating plant responses to abiotic stresses. Hence, characterization of unknown ABA response genes may enable us to identify [...] Read more.

The plant hormone abscisic acid (ABA) is able to regulate the expression of ABA-responsive genes via signaling transduction, and thus plays an important role in regulating plant responses to abiotic stresses. Hence, characterization of unknown ABA response genes may enable us to identify novel regulators of ABA and abiotic stress responses. By using RT-PCR analysis, we found that the expression levels of ABA-induced Serine-rich Repressor 1 (ASR1)and ASR2, two closely related unknown function genes, were increased in response to ABA treatment. Amino acid sequence analyses show that ASR1 contains an L×L×L motif and both ASR1 and ASR2 are enriched in serine. Transfection assays in Arabidopsis leaf protoplasts show that ASR1 and ASR2 were predominantly localized in the nucleus and were able to repress the expression of the reporter gene. The roles of ASRs in regulating ABA responses were examined by generating transgenic Arabidopsis plants over-expressing ASR1 and ASR2, respectively, and CRISPR/Cas9 gene-edited single and double mutants for ASR1 and ASR2. In both the seed germination and cotyledon greening assays, ABA sensitivity remained largely unchanged in the over-expression transgenic plants and the single mutants of ASR1 and ASR2, but greatly increased ABA sensitivity was observed in the asr1 asr2 double mutants. In root elongation assays, however, decreased ABA sensitivity was observed in the 35S:ASR1 and 35S:ASR2 transgenic plants, whereas increased ABA sensitivity was observed in the asr1 and asr2 single mutants, and ABA sensitivity was further increased in the asr1 asr2 double mutants. Transcriptome analysis show that the differentially expressed genes (DEGs) down-regulated in the 35S:ASR1 transgenic plant seedlings, but up-regulated in the asr1 asr2 double mutant seedlings were highly enriched in processes including responses to plant hormones and stress stimuli. Taken together, our results show that ASR1 and ASR2 are closely related ABA response genes, ASR1 and ASR2 are serine-rich novel transcription repressors, and they negatively regulate ABA responses in Arabidopsis in a redundant manner. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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15 pages, 2865 KiB

Open AccessArticle

Small Heat Shock Protein (sHSP) Gene Family from Sweet Pepper (Capsicum annuum L.) Fruits: Involvement in Ripening and Modulation by Nitric Oxide (NO)

by Salvador González-Gordo, José M. Palma and Francisco J. Corpas

Plants 2023, 12(2), 389; https://doi.org/10.3390/plants12020389 - 13 Jan 2023

Cited by 9 | Viewed by 2251

Abstract

Small heat shock proteins (sHSPs) are usually upregulated in plants under diverse environmental stresses. These proteins have been suggested to function as molecular chaperones to safeguard other proteins from stress-induced damage. The ripening of pepper (Capsicum annuum L.) fruit involves important phenotypic, [...] Read more.

Small heat shock proteins (sHSPs) are usually upregulated in plants under diverse environmental stresses. These proteins have been suggested to function as molecular chaperones to safeguard other proteins from stress-induced damage. The ripening of pepper (Capsicum annuum L.) fruit involves important phenotypic, physiological, and biochemical changes, which have associated endogenous physiological nitro-oxidative stress, but they can also be significantly affected by environmental conditions, such as temperature. Based on the available pepper genome, a total of 41 sHSP genes were identified in this work, and their distributions in the 12 pepper chromosomes were determined. Among these genes, only 19 sHSP genes were found in the transcriptome (RNA-Seq) of sweet pepper fruits reported previously. This study aims to analyze how these 19 sHSP genes present in the transcriptome of sweet pepper fruits are modulated during ripening and after treatment of fruits with nitric oxide (NO) gas. The time-course expression analysis of these genes during fruit ripening showed that 6 genes were upregulated; another 7 genes were downregulated, whereas 6 genes were not significantly affected. Furthermore, NO treatment triggered the upregulation of 7 sHSP genes and the downregulation of 3 sHSP genes, whereas 9 genes were unchanged. These data indicate the diversification of sHSP genes in pepper plants and, considering that sHSPs are important in stress tolerance, the observed changes in sHSP expression support that pepper fruit ripening has an associated process of physiological nitro-oxidative stress, such as it was previously proposed. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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11 pages, 3289 KiB

Open AccessArticle

Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene

by Hee Kyoung Kim, Jin Young Kim, Jong Hee Kim, Ji Yun Go, Yoo-Seob Jung, Hyo Ju Lee, Mi-Jeong Ahn, Jihyeon Yu, Sangsu Bae, Ho Soo Kim, Sang-Soo Kwak, Me-Sun Kim, Yong-Gu Cho, Yu Jin Jung and Kwon Kyoo Kang

Plants 2023, 12(1), 56; https://doi.org/10.3390/plants12010056 - 22 Dec 2022

Cited by 1 | Viewed by 1791

Abstract

We generated an orange-colored (OC) rice callus line by targeted mutagenesis of the orange gene (OsOr) using the CRISPR-Cas9 system. The OC line accumulated more lutein, β-carotene, and two β-carotene isomers compared to the WT callus line. We also [...] Read more.

We generated an orange-colored (OC) rice callus line by targeted mutagenesis of the orange gene (OsOr) using the CRISPR-Cas9 system. The OC line accumulated more lutein, β-carotene, and two β-carotene isomers compared to the WT callus line. We also analyzed the expression levels of carotenoid biosynthesis genes by qRT-PCR. Among the genes encoding carotenoid metabolic pathway enzymes, the number of transcripts of the PSY2, PSY3, PDS, ZDS and β-LCY genes were higher in the OC line than in the WT line. In contrast, transcription of the ε-LCY gene was downregulated in the OC line compared to the WT line. In addition, we detected increases in the transcript levels of two genes involved in carotenoid oxidation in the OC lines. The developed OC lines also showed increased tolerance to salt stress. Collectively, these findings indicate that targeted mutagenesis of the OsOr gene via CRISPR/Cas9-mediated genome editing results in β-carotene accumulation in rice calli. Accordingly, we believe that this type of genome-editing technology could represent an effective alternative approach for enhancing the β-carotene content of plants. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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18 pages, 5119 KiB

Open AccessArticle

Phylogenetic and Phylodynamic Analyses of Soybean Mosaic Virus Using 305 Coat Protein Gene Sequences

by Hoseong Choi, Yeonhwa Jo, Hyunjung Chung, Soo Yeon Choi, Sang-Min Kim, Jin-Sung Hong, Bong Choon Lee and Won Kyong Cho

Plants 2022, 11(23), 3256; https://doi.org/10.3390/plants11233256 - 27 Nov 2022

Cited by 2 | Viewed by 1533

Abstract

Soybean mosaic virus (SMV) of the family Potyviridae is the most devastating virus that infects soybean plants. In this study, we obtained 83 SMV coat protein (CP) sequences from seven provinces in Korea using RT-PCR and Sanger sequencing. Phylogenetic and haplotype analyses revealed [...] Read more.

Soybean mosaic virus (SMV) of the family Potyviridae is the most devastating virus that infects soybean plants. In this study, we obtained 83 SMV coat protein (CP) sequences from seven provinces in Korea using RT-PCR and Sanger sequencing. Phylogenetic and haplotype analyses revealed eight groups of 83 SMV isolates and a network of 50 SMV haplotypes in Korea. The phylogenetic tree using 305 SMV CP sequences available worldwide revealed 12 clades that were further divided into two groups according to the plant hosts. Recombination rarely occurred in the CP sequences, while negative selection was dominant in the SMV CP sequences. Genetic diversity analyses revealed that plant species had a greater impact on the genetic diversity of SMV CP sequences than geographical origin or location. SMV isolates identified from Pinellia species in China showed the highest genetic diversity. Phylodynamic analysis showed that the SMV isolates between the two Pinellia species diverged in the year 1248. Since the divergence of the first SMV isolate from Glycine max in 1486, major clades for SMV isolates infecting Glycine species seem to have diverged from 1791 to 1886. Taken together, we provide a comprehensive overview of the genetic diversity and divergence of SMV CP sequences. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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Open AccessArticle

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L.

by Manica Balant, Roi Rodríguez González, Sònia Garcia, Teresa Garnatje, Jaume Pellicer, Joan Vallès, Daniel Vitales and Oriane Hidalgo

Plants 2022, 11(20), 2736; https://doi.org/10.3390/plants11202736 - 16 Oct 2022

Cited by 5 | Viewed by 2167

Abstract

Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge [...] Read more.

Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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Review

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Open AccessReview

Current Insights into m⁶A RNA Methylation and Its Emerging Role in Plant Circadian Clock

by Nguyen Nguyen Chuong, Phan Phuong Thao Doan, Lanshuo Wang, Jin Hee Kim and Jeongsik Kim

Plants 2023, 12(3), 624; https://doi.org/10.3390/plants12030624 - 31 Jan 2023

Cited by 2 | Viewed by 2419

Abstract

N6-adenosine methylation (m⁶A) is a prevalent form of RNA modification found in the expressed transcripts of many eukaryotic organisms. Moreover, m⁶A methylation is a dynamic and reversible process that requires the functioning of various proteins and their complexes [...] Read more.

N6-adenosine methylation (m⁶A) is a prevalent form of RNA modification found in the expressed transcripts of many eukaryotic organisms. Moreover, m⁶A methylation is a dynamic and reversible process that requires the functioning of various proteins and their complexes that are evolutionarily conserved between species and include methylases, demethylases, and m⁶A-binding proteins. Over the past decade, the m⁶A methylation process in plants has been extensively studied and the understanding thereof has drastically increased, although the regulatory function of some components relies on information derived from animal systems. Notably, m⁶A has been found to be involved in a variety of factors in RNA processing, such as RNA stability, alternative polyadenylation, and miRNA regulation. The circadian clock in plants is a molecular timekeeping system that regulates the daily and rhythmic activity of many cellular and physiological processes in response to environmental changes such as the day-night cycle. The circadian clock regulates the rhythmic expression of genes through post-transcriptional regulation of mRNA. Recently, m⁶A methylation has emerged as an additional layer of post-transcriptional regulation that is necessary for the proper functioning of the plant circadian clock. In this review, we have compiled and summarized recent insights into the molecular mechanisms behind m⁶A modification and its various roles in the regulation of RNA. We discuss the potential role of m⁶A modification in regulating the plant circadian clock and outline potential future directions for the study of mRNA methylation in plants. A deeper understanding of the mechanism of m⁶A RNA regulation and its role in plant circadian clocks will contribute to a greater understanding of the plant circadian clock. Full article

(This article belongs to the Special Issue Trends and Prospects of Genetic and Molecular Research in Plant)

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