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Plant Genomics and Genome Editing 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 44474

Special Issue Editor

Prof. Dr. Hikmet Budak

E-Mail Website
Guest Editor
Montana BioAgriculture, Inc., Missoula, MT 59802, USA
Interests: plant genomics; next generation sequencing; small RNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Scientists are able to precisely edit genomes efficiently and cost-effectively thanks to the many high-quality reference genome sequences that are currently available. Zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system have been successfully employed to edit numerous individual genes in many organisms, and CRISPR-edited plants are now on the market. The CRISPR-Cas system has been widely used to edit genetic elements in genomes for various applications—not only crop improvement, but also many gene therapy studies. In this Special Issue, we cordially invite scientists from across the world to contribute their cutting-edge research on plant genomics and genome editing. We welcome the submission of original research articles and short communications contributing to the advancement of genomics and genome editing, including techniques, applications, trait development, and enabling database and computational software. We are also inviting scientists to write reviews for this Special Issue. 

Prof. Dr. Hikmet Budak
Guest Editor

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Keywords

  • next-generation sequencing
  • structural and functional genomics
  • SNPs
  • miRNA
  • LncRNA
  • CRISPR/Cas9
  • TALEN
  • genome editing

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Published Papers (24 papers)

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16 pages, 5575 KiB  
Article
Pan-Genome Analysis of TIFY Gene Family and Functional Analysis of CsTIFY Genes in Cucumber
by Kun Liu, Haiyu Xu, Xinbin Gao, Yinghao Lu, Lina Wang, Zhonghai Ren and Chunhua Chen
Int. J. Mol. Sci. 2024, 25(1), 185; https://doi.org/10.3390/ijms25010185 - 22 Dec 2023
Viewed by 730
Abstract
Cucumbers are frequently affected by gray mold pathogen Botrytis cinerea, a pathogen that causes inhibited growth and reduced yield. Jasmonic acid (JA) plays a primary role in plant responses to biotic stresses, and the jasmonate-ZIM-Domain (JAZ) proteins are key regulators of the [...] Read more.
Cucumbers are frequently affected by gray mold pathogen Botrytis cinerea, a pathogen that causes inhibited growth and reduced yield. Jasmonic acid (JA) plays a primary role in plant responses to biotic stresses, and the jasmonate-ZIM-Domain (JAZ) proteins are key regulators of the JA signaling pathway. In this study, we used the pan-genome of twelve cucumber varieties to identify cucumber TIFY genes. Our findings revealed that two CsTIFY genes were present in all twelve cucumber varieties and showed no differences in protein sequence, gene structure, and motif composition. This suggests their evolutionary conservation across different cucumber varieties and implies that they may play a crucial role in cucumber growth. On the other hand, the other fourteen CsTIFY genes exhibited variations in protein sequence and gene structure or conserved motifs, which could be the result of divergent evolution, as these genes adapt to different cultivation and environmental conditions. Analysis of the expression profiles of the CsTIFY genes showed differential regulation by B. cinerea. Transient transfection plants overexpressing CsJAZ2, CsJAZ6, or CsZML2 were found to be more susceptible to B. cinerea infection compared to control plants. Furthermore, these plants infected by the pathogen showed lower levels of the enzymatic activities of POD, SOD and CAT. Importantly, after B. cinerea infection, the content of JA was upregulated in the plants, and cucumber cotyledons pretreated with exogenous MeJA displayed increased resistance to B. cinerea infection compared to those pretreated with water. Therefore, this study explored key TIFY genes in the regulation of cucumber growth and adaptability to different cultivation environments based on bioinformatics analysis and demonstrated that CsJAZs negatively regulate cucumber disease resistance to gray mold via multiple signaling pathways. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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12 pages, 1846 KiB  
Article
QTL Mapping of Soybean (Glycine max) Vine Growth Habit Trait
by Jian Song, Kanglin Liu, Xuezhen Yang, Yijie Chen, Yajun Xiong, Qichao Yang, Jing Wang, Zhihao Zhang, Caiyu Wu, Jun Wang and Lijuan Qiu
Int. J. Mol. Sci. 2023, 24(19), 14770; https://doi.org/10.3390/ijms241914770 - 30 Sep 2023
Viewed by 776
Abstract
The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) [...] Read more.
The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) approach was employed to study the genetic etiology of the VGH in soybean plants by integrating linkage mapping and population sequencing approaches. To develop a recombinant inbred line (RIL) population, the cultivated Zhongdou41 (ZD41) soybean cultivar was bred with ZYD02787, a wild soybean accession. The VGH status of each line in the resultant population was assessed, ultimately leading to the identification of six and nine QTLs from the BSA sequencing of the F4 population and F6-F8 population sequence mapping, respectively. One QTL shared across these analyzed generations was detected on chromosome 19. Three other QTLs detected by BSA-seq were validated and localized to the 90.93 kb, 2.9 Mb, and 602.08 kb regions of chromosomes 6 and 13, harboring 14, 53, and 4 genes, respectively. Three consistent VGH-related QTLs located on chromosomes 2 and 19 were detected in a minimum of three environments, while an additional six loci on chromosomes 2, 10, 13, and 18 were detected in at least two environments via ICIM mapping. Of all the detected loci, five had been reported previously whereas seven represent novel QTLs. Together, these data offer new insights into the genetic basis of the VGH in soybean plants, providing a rational basis to inform the use of wild accessions in future breeding efforts. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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20 pages, 3584 KiB  
Article
Combined Transcriptomic and Metabolomic Approach Revealed a Relationship between Light Control, Photoprotective Pigments, and Lipid Biosynthesis in Olives
by Tiziana Maria Sirangelo, Ivano Forgione, Samanta Zelasco, Cinzia Benincasa, Enzo Perri, Elisa Vendramin, Federica Angilè, Francesco Paolo Fanizzi, Francesco Sunseri, Amelia Salimonti and Fabrizio Carbone
Int. J. Mol. Sci. 2023, 24(19), 14448; https://doi.org/10.3390/ijms241914448 - 22 Sep 2023
Cited by 1 | Viewed by 868
Abstract
Olive possesses excellent nutritional and economic values for its main healthy products. Among them, a high content of antioxidant compounds, balanced during the ripening process, are produced under genetic and environmental control, resulting in high variability among cultivars. The genes involved in these [...] Read more.
Olive possesses excellent nutritional and economic values for its main healthy products. Among them, a high content of antioxidant compounds, balanced during the ripening process, are produced under genetic and environmental control, resulting in high variability among cultivars. The genes involved in these complex pathways are mainly known, but despite many studies which indicated the key role of light quality and quantity for the synthesis of many metabolites in plants, limited information on these topics is available in olive. We carried out a targeted gene expression profiling in three olive cultivars, Cellina di Nardò, Ruveia, and Salella, which were selected for their contrasting oleic acid and phenolic content. The –omics combined approach revealed a direct correlation between a higher expression of the main flavonoid genes and the high content of these metabolites in ‘Cellina di Nardò’. Furthermore, it confirmed the key role of FAD2-2 in the linoleic acid biosynthesis. More interestingly, in all the comparisons, a co-regulation of genes involved in photoperception and circadian clock machinery suggests a key role of light in orchestrating the regulation of these pathways in olive. Therefore, the identified genes in our analyses might represent a useful tool to support olive breeding, although further investigations are needed. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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11 pages, 2017 KiB  
Article
Characterization and Gene Mapping of an Open-Glume Oryza sativa L. Mutant
by Xingxue Mao, Xiaoyu Zheng, Wenfeng Chen and Chen Li
Int. J. Mol. Sci. 2023, 24(16), 12702; https://doi.org/10.3390/ijms241612702 - 11 Aug 2023
Viewed by 681
Abstract
Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, [...] Read more.
Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, decreased seed setting rate, and smaller rice grains. Genetic analysis showed that the open-glume phenotype might be controlled by a recessive qualitative trait locus. Employing bulked segregant analysis (BSA), one candidate region was identified on rice chromosome 1. The glume opening phenotype cosegregated with SNP (Chr1:1522703), which was located at the start codon of one transcript of OsJAG, resulting in partial loss of OsJAG function. cDNA analysis revealed that OsJAG encodes two transcript variants. Compared to normal plants, the expression of OsJAG.1 was upregulated in open-glume plants. When investigating the glume phenotype, we found that the expression of genes related to floral development changed greatly in open-glume plants. Taken together, this work increases our understanding of the developmental role of OsJAG in rice floral development. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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15 pages, 3338 KiB  
Article
ARF3-Mediated Regulation of SPL in Early Anther Morphogenesis: Maintaining Precise Spatial Distribution and Expression Level
by Qi Yang, Jianzheng Wang, Shiting Zhang, Yuyuan Zhan, Jingting Shen and Fang Chang
Int. J. Mol. Sci. 2023, 24(14), 11740; https://doi.org/10.3390/ijms241411740 - 21 Jul 2023
Viewed by 963
Abstract
Early anther morphogenesis is a crucial process for male fertility in plants, governed by the transcription factor SPL. While the involvement of AGAMOUS (AG) in SPL activation and microsporogenesis initiation is well established, our understanding of the mechanisms governing the spatial distribution and [...] Read more.
Early anther morphogenesis is a crucial process for male fertility in plants, governed by the transcription factor SPL. While the involvement of AGAMOUS (AG) in SPL activation and microsporogenesis initiation is well established, our understanding of the mechanisms governing the spatial distribution and precise expression of SPL during anther cell fate determination remains limited. Here, we present novel findings on the abnormal phenotypes of two previously unreported SPL mutants, spl-4 and spl-5, during anther morphogenesis. Through comprehensive analysis, we identified ARF3 as a key upstream regulator of SPL. Our cytological experiments demonstrated that ARF3 plays a critical role in restricting SPL expression specifically in microsporocytes. Moreover, we revealed that ARF3 directly binds to two specific auxin response elements on the SPL promoter, effectively suppressing AG-mediated activation of SPL. Notably, the arf3 loss-of-function mutant exhibits phenotypic similarities to the SPL overexpression mutant (spl-5), characterized by defective adaxial anther lobes. Transcriptomic analysis revealed differential expression of the genes involved in the morphogenesis pathway in both arf3 and spl mutants, with ARF3 and SPL exhibited opposing regulatory effects on this pathway. Taken together, our study unveils the precise role of ARF3 in restricting the spatial expression and preventing aberrant SPL levels during early anther morphogenesis, thereby ensuring the fidelity of the critical developmental process in plants. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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15 pages, 3206 KiB  
Article
Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm
by Zhipeng Li, Yiqiong Chen, Yangyan Li, Ying Zeng, Wanying Li, Xiaona Ma, Lili Huang and Yanting Shen
Int. J. Mol. Sci. 2023, 24(13), 10970; https://doi.org/10.3390/ijms241310970 - 30 Jun 2023
Viewed by 1079
Abstract
As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli’s genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on [...] Read more.
As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli’s genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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19 pages, 7269 KiB  
Article
Combined Metabolome and Transcriptome Analysis Highlights the Host’s Influence on Cistanche deserticola Metabolite Accumulation
by Ru Feng, Hongshuang Wei, Rong Xu, Sai Liu, Jianhe Wei, Kun Guo, Haili Qiao and Changqing Xu
Int. J. Mol. Sci. 2023, 24(9), 7968; https://doi.org/10.3390/ijms24097968 - 27 Apr 2023
Cited by 1 | Viewed by 1642
Abstract
The medicinal plant Cistanche deserticola Ma (Orobanchaceae) is a holoparasitic angiosperm that takes life-essential materials from Haloxylon ammodendron (C. A. Mey.) Bunge (Amaranthaceae) roots. Although many experiments have been conducted to improve the quality of C. deserticola, little attention has been paid [...] Read more.
The medicinal plant Cistanche deserticola Ma (Orobanchaceae) is a holoparasitic angiosperm that takes life-essential materials from Haloxylon ammodendron (C. A. Mey.) Bunge (Amaranthaceae) roots. Although many experiments have been conducted to improve the quality of C. deserticola, little attention has been paid to the host’s influence on metabolite accumulation. In this study, transcriptomic and metabolomic analyses were performed to unveil the host’s role in C. deserticola’s metabolite accumulation, especially of phenylethanoid glycosides (PhGs). The results indicate that parasitism by C. deserticola causes significant changes in H. ammodendron roots in relation to metabolites and genes linked to phenylalanine metabolism, tryptophan metabolism and phenylpropanoid biosynthesis pathways, which provide precursors for PhGs. Correlation analysis of genes and metabolites further confirms that C. deserticola’s parasitism affects PhG biosynthesis in H. ammodendron roots. Then we found specific upregulation of glycosyltransferases in haustoria which connect the parasites and hosts. It was shown that C. deserticola absorbs PhG precursors from the host and that glycosylation takes place in the haustorium. We mainly discuss how the host resists C. deserticola parasitism and how this medicinal parasite exploits its unfavorable position and takes advantage of host-derived metabolites. Our study highlights that the status of the host plant affects not only the production but also the quality of Cistanches Herba, which provides a practical direction for medicinal plant cultivation. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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17 pages, 5532 KiB  
Article
Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms)
by Rongming Tian, Xueyimu Aou, Boni Song, Zixuan Li, Xingjin He and Songdong Zhou
Int. J. Mol. Sci. 2023, 24(8), 7419; https://doi.org/10.3390/ijms24087419 - 18 Apr 2023
Cited by 1 | Viewed by 1454
Abstract
Ligusticopsis litangensis is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of Ligusticopsis capillacea and Ligusticopsis dielsiana, the morphological boundaries between them are explicit and have obviously distinguishable characters. [...] Read more.
Ligusticopsis litangensis is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of Ligusticopsis capillacea and Ligusticopsis dielsiana, the morphological boundaries between them are explicit and have obviously distinguishable characters. The main distinguishing features of the cryptic species are as follows: long conical multi-branched roots, very short pedicels in compound umbels, unequal rays, oblong-globose fruits, 1–2 vittae per furrow and 3–4 vittae on the commissure. The above-mentioned features differ somewhat from other species within the genus Ligusticopsis, but generally coincide with the morphological boundaries defined for the genus Ligusticopsis. To determine the taxonomic position of L. litangensis, we sequenced and assembled the plastomes of L. litangensis and compared them with the plastomes of 11 other species of the genus Ligusticopsis. Notably, both phylogenetic analyses based on ITS sequences and the complete chloroplast genome robustly supported that three accessions of L. litangensis are monophyletic clade and then nested in Ligusticopsis genus. Moreover, the plastid genomes of 12 Ligusticopsis species, including the new species, were highly conserved in terms of gene order, gene content, codon bias, IR boundaries and SSR content. Overall, the integration of morphological, comparative genomic and phylogenetic evidence indicates that Ligusticopsis litangensis actually represents a new species. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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18 pages, 16516 KiB  
Article
Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed
by Liyuan Zhang, Bo Yang, Chao Zhang, Huan Chen, Jinxiong Xu, Cunmin Qu, Kun Lu and Jiana Li
Int. J. Mol. Sci. 2023, 24(3), 2543; https://doi.org/10.3390/ijms24032543 - 28 Jan 2023
Cited by 3 | Viewed by 1757
Abstract
Argonautes (AGOs) interact with microRNAs (miRNAs) to form the RNA-induced silencing complex (RISC), which can posttranscriptionally regulate the expression of targeted genes. To date, however, the AGOs and their miRNA triggers remain elusive in rapeseed (Brassica napus). Here, we systematically performed [...] Read more.
Argonautes (AGOs) interact with microRNAs (miRNAs) to form the RNA-induced silencing complex (RISC), which can posttranscriptionally regulate the expression of targeted genes. To date, however, the AGOs and their miRNA triggers remain elusive in rapeseed (Brassica napus). Here, we systematically performed a phylogenetic analysis and examined the collinear relationships of the AGOs among four Brassicaceae species. Their physicochemical properties, gene structures, and expression patterns among 81 tissues from multiple materials and developmental stages were further analyzed. Additionally, their posttranscriptional regulation was analyzed using psRNATarget prediction, miRNA-/mRNA-Seq analyses, and a qRT-PCR verification. We finally identified 10 AtAGOs, 13 BolAGOs, 11 BraAGOs, and 24 BnaAGOs. An expression analysis of the BnaAGOs in the B. napus cultivar ZS11, as well as genotypes with extreme phenotypes in various yield-related traits, revealed the conservation and diversity of these genes. Furthermore, we speculated the posttranscriptional regulation of the B. napus miR168a–AGO1s and miR403–AGO2s modules. Combining miRNA-Seq and mRNA-Seq analyses, we found that the B. napus miR168a–AGO1s module may play an essential role in negatively regulating yield traits, whereas the miR403–AGO2s module positively impacts yield. This is the first attempt to comprehensively analyze the AGOs and their miRNA triggers in B. napus and provides a theoretical basis for breeding high-yielding varieties through the manipulation of the miRNA–AGOs modules. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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16 pages, 3773 KiB  
Article
Mutation of OsLPR3 Enhances Tolerance to Phosphate Starvation in Rice
by Hao Ai, Xiuli Liu, Zhi Hu, Yue Cao, Nannan Kong, Feiyan Gao, Siwen Hu, Xing Shen, Xianzhong Huang, Guohua Xu and Shubin Sun
Int. J. Mol. Sci. 2023, 24(3), 2437; https://doi.org/10.3390/ijms24032437 - 26 Jan 2023
Viewed by 1775
Abstract
Low Phosphate Root (LPR) encodes a protein localized to the endoplasmic reticulum (ER) and cell wall. This gene plays a key role in responding to phosphate (Pi) deprivation, especially in remodeling the root system architecture (RSA). An identification and expression analysis [...] Read more.
Low Phosphate Root (LPR) encodes a protein localized to the endoplasmic reticulum (ER) and cell wall. This gene plays a key role in responding to phosphate (Pi) deprivation, especially in remodeling the root system architecture (RSA). An identification and expression analysis of the OsLPR family in rice (Oryza sativa) has been previously reported, and OsLPR5, functioning in Pi uptake and translocation, is required for the normal growth and development of rice. However, the role of OsLPR3, one of the five members of this family in rice, in response to Pi deficiency and/or in the regulation of plant growth and development is unknown. Therefore, in this study, the roles of OsLPR3 in these processes were investigated, and some functions were found to differ between OsLPR3 and OsLPR5. OsLPR3 was found to be induced in the leaf blades, leaf sheaths, and roots under Pi deprivation. OsLPR3 overexpression strongly inhibited the growth and development of the rice but did not affect the Pi homeostasis of the plant. However, oslpr3 mutants improved RSA and Pi utilization, and they exhibited a higher tolerance to low Pi stress in rice. The agronomic traits of the oslpr3 mutants, such as 1000-grain weight and seed length, were stimulated under Pi-sufficient conditions, indicating that OsLPR3 plays roles different from those of OsLPR5 during plant growth and development, as well as in the maintenance of the Pi status of rice. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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8 pages, 1122 KiB  
Communication
Evaluation of CRISPR/Cas9 Constructs in Wheat Cell Suspension Cultures
by Krzysztof Michalski, Paulina Ziąbska, Sławomir Sowa, Janusz Zimny and Anna M. Linkiewicz
Int. J. Mol. Sci. 2023, 24(3), 2162; https://doi.org/10.3390/ijms24032162 - 21 Jan 2023
Cited by 3 | Viewed by 1941
Abstract
Despite intensive optimization efforts, developing an efficient sequence-specific CRISPR/Cas-mediated genome editing method remains a challenge, especially in polyploid cereal species such as wheat. Validating the efficacy of nuclease constructs prior to using them in planta is, thus, a major step of every editing [...] Read more.
Despite intensive optimization efforts, developing an efficient sequence-specific CRISPR/Cas-mediated genome editing method remains a challenge, especially in polyploid cereal species such as wheat. Validating the efficacy of nuclease constructs prior to using them in planta is, thus, a major step of every editing experiment. Several construct evaluation strategies were proposed, with PEG-mediated plasmid transfection of seedling-derived protoplasts becoming the most popular. However, the usefulness of this approach is affected by associated construct copy number bias and chromatin relaxation, both influencing the outcome. Therefore, to achieve a reliable evaluation of CRISPR/Cas9 constructs, we proposed a system based on an Agrobacterium-mediated transformation of established wheat cell suspension cultures. This system was used for the evaluation of a CRISPR/Cas9 construct designed to target the ABA 8′-hydroxylase 1 gene. The efficiency of editing was verified by cost-effective means of Sanger sequencing and bioinformatic analysis. We discuss advantages and potential future developments of this method in contrast to other in vitro approaches. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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15 pages, 3751 KiB  
Article
Transcriptome Analysis and Screening of Genes Associated with Flower Size in Tomato (Solanum lycopersicum)
by Yiyao Zhang, Aining Zhang, Wenhui Yang, Xinyi Jia, Qingjun Fu, Tingting Zhao, Jingbin Jiang, Jingfu Li, Huanhuan Yang and Xiangyang Xu
Int. J. Mol. Sci. 2022, 23(24), 15624; https://doi.org/10.3390/ijms232415624 - 09 Dec 2022
Cited by 1 | Viewed by 1696
Abstract
Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and [...] Read more.
Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development. In this study, RNA-seq analysis was performed on two stages of tomato flower development using the Illumina sequencing platform. A total of 8536 DEGs were obtained by sequencing, including 3873 upregulated DEGs and 4663 down-regulated DEGs. These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism. The pathways such as pentose, glucuronate interconversion, and Phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes. According to the enrichment analysis results of DEGs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply. In addition, some plant hormones, such as GA, may also have effects on flower development. Combined with previous studies, the expression levels of Solyc02g087860 and three of bZIPs were significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development. These genes were previously reported in Arabidopsis but not in tomatoes. Our next work will conduct a detailed functional analysis of the identified bZIP family genes to characterize their association with tomato flower size. This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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18 pages, 3049 KiB  
Article
Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
by Yuan Gao, Guohui Shen, Guohui Yuan and Zhihui Tian
Int. J. Mol. Sci. 2022, 23(22), 13864; https://doi.org/10.3390/ijms232213864 - 10 Nov 2022
Cited by 2 | Viewed by 1437
Abstract
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, [...] Read more.
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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17 pages, 4685 KiB  
Article
Optimization and Application of CRISPR/Cas9 Genome Editing in a Cosmopolitan Pest, Diamondback Moth
by Zhen Zhang, Lei Xiong, Chao Xie, Lingling Shen, Xuanhao Chen, Min Ye, Linyang Sun, Xiaozhen Yang, Shuyuan Yao, Zhen Yue, Zhengjiao Liang, Minsheng You and Shijun You
Int. J. Mol. Sci. 2022, 23(21), 13042; https://doi.org/10.3390/ijms232113042 - 27 Oct 2022
Cited by 2 | Viewed by 2083
Abstract
The CRISPR/Cas9 system is an efficient tool for reverse genetics validation, and the application of this system in the cell lines provides a new perspective on target gene analysis for the development of biotechnology tools. However, in the cell lines of diamondback moth, [...] Read more.
The CRISPR/Cas9 system is an efficient tool for reverse genetics validation, and the application of this system in the cell lines provides a new perspective on target gene analysis for the development of biotechnology tools. However, in the cell lines of diamondback moth, Plutella xylostella, the integrity of the CRISPR/Cas9 system and the utilization of this cell lines still need to be improved to ensure the application of the system. Here, we stabilize the transfection efficiency of the P. xylostella cell lines at different passages at about 60% by trying different transfection reagents and adjusting the transfection method. For Cas9 expression in the CRIPSPR/Cas9 system, we identified a strong endogenous promoter: the 217–2 promoter. The dual-luciferase and EGFP reporter assay demonstrated that it has a driving efficiency close to that of the IE1 promoter. We constructed pB-Cas9-Neo plasmid and pU6-sgRNA plasmid for CRISPR/Cas9 system and subsequent cell screening. The feasibility of the CRISPR/Cas9 system in P. xylostella cell lines was verified by knocking out endogenous and exogenous genes. Finally, we generated a transgenic Cas9 cell line of P. xylostella that would benefit future exploitation, such as knock-in and multi-threaded editing. Our works provides the validity of the CRISPR/Cas9 system in the P. xylostella cell lines and lays the foundation for further genetic and molecular studies on insects, particularly favoring gene function analysis. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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20 pages, 3199 KiB  
Article
The Potential Role of the Methionine Aminopeptidase Gene PxMetAP1 in a Cosmopolitan Pest for Bacillus thuringiensis Toxin Tolerance
by Min Ye, Lei Xiong, Yi Dong, Chao Xie, Zhen Zhang, Lingling Shen, Zeyun Li, Zhen Yue, Puzi Jiang, Zhiguang Yuchi, Minsheng You and Shijun You
Int. J. Mol. Sci. 2022, 23(21), 13005; https://doi.org/10.3390/ijms232113005 - 27 Oct 2022
Viewed by 1691
Abstract
Methionine aminopeptidases (MetAPs) catalyze the cleavage of the N-terminal initiator methionine (iMet) in new peptide chains and arylamides, which is essential for protein and peptide synthesis. MetAP is differentially expressed in two diamondback moth (DBM; Plutella xylostella) strains: the G88 susceptible strain [...] Read more.
Methionine aminopeptidases (MetAPs) catalyze the cleavage of the N-terminal initiator methionine (iMet) in new peptide chains and arylamides, which is essential for protein and peptide synthesis. MetAP is differentially expressed in two diamondback moth (DBM; Plutella xylostella) strains: the G88 susceptible strain and the Cry1S1000 strain, which are resistant to the Bt toxin Cry1Ac, implicating that MetAP expression might be associated with Bt resistance. In this study, we identified and cloned a MetAP gene from DBMs, named PxMetAP1, which has a CDS of 1140 bp and encodes a 379 amino acid protein. The relative expression of PxMetAP1 was found to be ~2.2-fold lower in the Cry1S1000 strain compared to that in the G88 strain. PxMetAP1 presents a stage- and tissue-specific expression pattern, with higher levels in the eggs, adults, integument, and fatbody of DBMs. The linkage between PxMetAP1 and Cry1Ac resistance is verified by genetic linkage analysis. The knockout of PxMetAP1 in G88 by CRISPR/Cas9 leads to a ~5.6-fold decrease in sensitivity to the Cry1Ac toxin, further supporting the association between the PxMetAP1 gene and Bt tolerance. Our research sheds light on the role of MetAP genes in the development of Bt tolerance in P. xylostella and enriches the knowledge for the management of such a cosmopolitan pest. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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15 pages, 4902 KiB  
Article
Genome-Wide Characterization of Chrysanthemum indicum Nuclear Factor Y, Subunit C Gene Family Reveals the Roles of CiNF-YCs in Flowering Regulation
by Xueting Wang, Yao Yao, Shiyun Wen, Jing Bin, Qinghua Tan, Jinpeng Lou, Li Xie, Ruizhen Zeng, Herong Guo, Zhisheng Zhang and Qian Wei
Int. J. Mol. Sci. 2022, 23(21), 12812; https://doi.org/10.3390/ijms232112812 - 24 Oct 2022
Cited by 1 | Viewed by 1399
Abstract
Nuclear Factor Y, Subunit C (NF-YC) transcription factors are conserved in most plants, and play essential roles in plant growth and development, especially in flowering regulation. Chrysanthemums are important commercial plants, and their market value is strongly impacted by flowering time. Until now, [...] Read more.
Nuclear Factor Y, Subunit C (NF-YC) transcription factors are conserved in most plants, and play essential roles in plant growth and development, especially in flowering regulation. Chrysanthemums are important commercial plants, and their market value is strongly impacted by flowering time. Until now, no details regarding the NF-YC family in the Chrysanthemum genus have been available. In this study, five NF-YC genes were cloned from Chrysanthemum indicum. Multiple alignments showed that CiNF-YCs had the highly conserved characteristic regions. Phylogenetic analyses identified a pair of paralogue NF-YC proteins in chrysanthemums. Gene structure and conserved motifs were also analyzed for functional understanding. According to the results of the expression experiments, CiNF-YC1 and CiNF-YC5 were mainly expressed in leaves or flowers, and their expression levels varied greatly from the seedling to flower bud differentiation stage. Arabidopsis overexpressing CiNF-YC1 and CiNF-YC3 showed significantly delayed flowering, accompanied by other morphological alterations. RT-qPCR analysis revealed that genes associated with photoperiod, vernalization, aging, and gibberellin pathways were downregulated in CiNF-YC1-OX lines, relative to the wild type, whereas in CiNF-YC3-OX lines, only SHORT VEGETATIVE PHASE (AtSVP), the key factor in the ambient temperature pathway, was upregulated. Taken together, these findings suggest that CiNF-YC1 and CiNF-YC3 negatively regulate flowering in Arabidopsis via different flowering pathways. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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16 pages, 4115 KiB  
Article
Comparative Physiological and Transcriptomic Analyses of Improved Heat Stress Tolerance in Celery (Apium Graveolens L.) Caused by Exogenous Melatonin
by Mengyao Li, Jin Zhou, Jiageng Du, Xiaoyan Li, Yue Sun, Zhuo Wang, Yuanxiu Lin, Yunting Zhang, Yan Wang, Wen He, Xiaorong Wang, Qing Chen, Yong Zhang, Ya Luo and Haoru Tang
Int. J. Mol. Sci. 2022, 23(19), 11382; https://doi.org/10.3390/ijms231911382 - 27 Sep 2022
Cited by 11 | Viewed by 1981
Abstract
Melatonin (MT) is crucial in plant growth, development, and response to stress. Celery is a vegetable that grows in a cool climate, and a hot climate can deteriorate its growth, yield, and quality. This study investigates the effect of exogenous melatonin on celery [...] Read more.
Melatonin (MT) is crucial in plant growth, development, and response to stress. Celery is a vegetable that grows in a cool climate, and a hot climate can deteriorate its growth, yield, and quality. This study investigates the effect of exogenous melatonin on celery physiology. Transcriptional levels were analyzed by spraying celery with exogenous MT before exposing it to high temperatures. The regulatory mechanism of exogenous MT-mediated heat tolerance was examined. The results show that the exogenous MT reduced the thermal damage state of celery seedlings, as well as the malondialdehyde (MDA) content and relative conductivity (REC), increasing the oxidase activity, the osmotic regulatory substances, and chlorophyll, enhancing the leaf transpiration and the light energy utilization efficiency. We examined the mechanism of exogenous MT in mitigating high-temperature damage using the transcriptome sequencing method. A total of 134 genes were expressed differently at high temperature in the celery treated with MT compared with the untreated celery. Functional annotation analysis revealed that the differentially expressed genes were abundant in the “pyruvate metabolism” pathway and the “peroxidase activity” pathway. According to the pathway-based gene expression analysis, exogenous MT can inhibit the upregulation of pyruvate synthesis genes and the downregulation of pyruvate consumption genes, preventing the accumulated pyruvate from rapidly upregulating the expression of peroxidase genes, and thereby enhancing peroxidase activity. RT-qPCR verification showed a rising encoding peroxidase gene expression under MT treatment. The gene expression pattern involved in pyruvate anabolism and metabolism agreed with the abundant transcriptome expression, validating the physiological index results. These results indicate that the application of exogenous MT to celery significantly enhances the ability of plant to remove reactive oxygen species (ROS) in response to heat stress, thereby improving the ability of plant to resist heat stress. The results of this study provide a theoretical basis for the use of MT to alleviate the damage caused by heat stress in plant growth and development. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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20 pages, 8410 KiB  
Article
Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought
by Shicong Wang, Jieqiang He, Mengting Deng, Caixia Wang, Ruifeng Wang, Jinjiao Yan, Minrong Luo, Fengwang Ma, Qingmei Guan and Jidi Xu
Int. J. Mol. Sci. 2022, 23(19), 11191; https://doi.org/10.3390/ijms231911191 - 23 Sep 2022
Cited by 9 | Viewed by 5024
Abstract
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes [...] Read more.
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes in chromatin accessibility can play an important role in abiotic stress in plants by affecting RNA polymerase binding and various regulatory factors. However, the changes in chromatin accessibility during drought in apples are not well understood. In this study, the landscape of chromatin accessibility associated with the gene expression of apple (GL3) under drought conditions was analyzed by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq. Differential analysis between drought treatment and control identified 23,466 peaks of upregulated chromatin accessibility and 2447 peaks of downregulated accessibility. The drought-induced chromatin accessibility changed genes were mainly enriched in metabolism, stimulus, and binding pathways. By combining results from differential analysis of RNA-seq and ATAC-seq, we identified 240 genes with higher chromatin accessibility and increased gene expression under drought conditions that may play important functions in the drought response process. Among them, a total of nine transcription factor genes were identified, including ATHB7, HAT5, and WRKY26. These transcription factor genes are differentially expressed with different chromatin accessibility motif binding loci that may participate in apple response to drought by regulating downstream genes. Our study provides a reference for chromatin accessibility under drought stress in apples and the results will facilitate subsequent studies on chromatin remodelers and transcription factors. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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8 pages, 1460 KiB  
Article
Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale
by Jakob Petereit, Cassandria Tay Fernandez, Jacob I. Marsh, Philipp E. Bayer, William J. W. Thomas, Aybeniz Javad Aliyeva, Miroslava Karafiátová, Jaroslav Doležel, Jacqueline Batley and David Edwards
Int. J. Mol. Sci. 2022, 23(19), 11106; https://doi.org/10.3390/ijms231911106 - 21 Sep 2022
Cited by 1 | Viewed by 1383
Abstract
Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield [...] Read more.
Rye (Secale cereale) is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic diversity of rye will assist both the improvement of this crop and facilitate the introgression of more valuable traits into wheat. Here, we isolated and sequenced the short arm of rye chromosome 7 (7RS) from Triticale 380SD using flow cytometry and compared it to the public Lo7 rye whole genome reference assembly. We identify 2747 Lo7 genes present on the isolated chromosome arm and two clusters containing seven and sixty-five genes that are present on Triticale 380SD 7RS, but absent from Lo7 7RS. We identified 29 genes that are not assigned to chromosomal locations in the Lo7 assembly but are present on Triticale 380SD 7RS, suggesting a chromosome arm location for these genes. Our study supports the Lo7 reference assembly and provides a repertoire of genes on Triticale 7RS. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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18 pages, 8445 KiB  
Article
Identification of Chilling-Responsive Genes in Litchi chinensis by Transcriptomic Analysis Underlying Phytohormones and Antioxidant Systems
by Xiaoting Zhang, Hao Liu, Lijie Huang and Biyan Zhou
Int. J. Mol. Sci. 2022, 23(15), 8424; https://doi.org/10.3390/ijms23158424 - 29 Jul 2022
Viewed by 1579
Abstract
Litchi (Litchi chinensis Sonn.) is an important subtropical and tropical evergreen fruit tree that is seriously affected by chilling stress. In order to identify genes that may be involved in the response to chilling in litchi, we investigate the physiological and biochemical [...] Read more.
Litchi (Litchi chinensis Sonn.) is an important subtropical and tropical evergreen fruit tree that is seriously affected by chilling stress. In order to identify genes that may be involved in the response to chilling in litchi, we investigate the physiological and biochemical changes under chilling stress and construct 12 RNA-Seq libraries of leaf samples at 0, 4, 8, and 12 days of chilling. The results show that antioxidant enzymes are activated by chilling treatments. Comparing the transcriptome data of the four time points, we screen 2496 chilling-responsive genes (CRGs), from which we identify 63 genes related to the antioxidant system (AO-CRGs) and 54 ABA, 40 IAA, 37 CTK, 27 ETH, 21 BR, 13 GA, 35 JA, 29 SA, and 4 SL signal transduction-related genes. Expression pattern analysis shows that the expression trends of the 28 candidate genes detected by qRT-PCR are similar to those detected by RNA-Seq, indicating the reliability of our RNA-Seq data. Partial Least Squares Structural Equation Modeling (PLS-SEM) analysis of the RNA-Seq data suggests a model for the litchi plants in response to chilling stress that alters the expression of the plant hormone signaling-related genes, the transcription factor-encoding genes LcICE1, LcCBFs, and LcbZIPs, and the antioxidant system-related genes. This study provides candidate genes for the future breeding of litchi cultivars with high chilling resistance, and elucidates possible pathways for litchi in response to chilling using transcriptomic data. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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25 pages, 78608 KiB  
Article
Transcriptomic and Metabolomic Analysis of Quality Changes during Sweet Cherry Fruit Development and Mining of Related Genes
by Chaoqun Chen, Hongxu Chen, Wenlong Yang, Jie Li, Wenjing Tang and Ronggao Gong
Int. J. Mol. Sci. 2022, 23(13), 7402; https://doi.org/10.3390/ijms23137402 - 03 Jul 2022
Cited by 19 | Viewed by 2865
Abstract
Sweet cherries are economically important fruit trees, and their quality changes during development need to be determined. The mechanism of fruit quality changes in sweet cherries were determined by analyzing sweet cherry fruits at 12 developmental stages. The results showed that the soluble [...] Read more.
Sweet cherries are economically important fruit trees, and their quality changes during development need to be determined. The mechanism of fruit quality changes in sweet cherries were determined by analyzing sweet cherry fruits at 12 developmental stages. The results showed that the soluble sugar, anthocyanin content, and hormones of sweet cherries all changed drastically during the color transition. Therefore, the fruits at the beginning of color conversion, at the end of color conversion, and at the ripening state were selected for the comprehensive analysis of their metabolome and transcriptome. Different sugars, such as D-glucose, sucrose, and trehalose, were identified in the metabolome. Dihydroquercetin, delphinidin-3-glucoside, cyanidin-3-rutincoside, and other flavonoid species were also identified. D-glucose and cyanidin-3-rutinoside were among the most important components of sweet cherry soluble sugars and anthocyanins, respectively. The transcriptional analysis identified key structural genes and nine transcription factors involved in the ABA, sugar, organic acid, and anthocyanin synthesis pathways, with the following specific regulatory patterns. NAC71, WRKY57, and WRKY3 regulate fruit sugar accumulation mainly by acting on INV, SPS, and SUS. MYC2 is involved in the synthesis of anthocyanin precursors by activating PAL and C4H, whereas TCP7 mainly regulates CHI and F3H. WRKY3, NAC71, and WRKY57 have important positive regulatory significance on anthocyanin accumulation, mainly by activating the expression of DFR, ANS, and 3GT. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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19 pages, 11308 KiB  
Article
Genome-Wide Identification of the Ginkgo (Ginkgo biloba L.) LBD Transcription Factor Gene and Characterization of Its Expression
by Yating Tian, Xin Han, Yanshu Qu, Yifan Zhang, Hao Rong, Kai Wu and Li’an Xu
Int. J. Mol. Sci. 2022, 23(10), 5474; https://doi.org/10.3390/ijms23105474 - 13 May 2022
Cited by 10 | Viewed by 2234
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors involved in various transcriptional regulation processes. We identified a total of 37 GbLBD genes in ginkgo, and based on gene structure and phylogenetic analysis, the GbLBD gene family was classified into class I [...] Read more.
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors involved in various transcriptional regulation processes. We identified a total of 37 GbLBD genes in ginkgo, and based on gene structure and phylogenetic analysis, the GbLBD gene family was classified into class I (33, with the largest number of Id genes (16)) and class II (4). The ginkgo LBD gene was also analyzed regarding its chromosomal distributions, gene duplications, promoters, and introns/exons. In addition, gene expression profiling and real-time quantitative PCR analysis showed that the expression of 14 GbLBD genes differed in six different tissues and three developmental stages. The GbLBD gene of class II were highly expressed relative to the class I gene in all tissues and developmental stages, while class Id gene were generally at low levels or were not expressed, especially in seed developmental stages. The expression pattern analysis of cold/drought treatment and IAA/ABA hormone treatment showed that abiotic stress treatment could significantly induce the expression of GbLBD gene, of which class II genes played a key role in stress treatment. Our study provides a solid foundation for further evolutionary and functional analysis of the ginkgo LBD gene family. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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20 pages, 3562 KiB  
Article
Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Quinoa Seedlings to Different Phosphorus Stresses
by Qianchao Wang, Yirui Guo, Tingzhi Huang, Xuesong Zhang, Ping Zhang, Heng Xie, Junna Liu, Li Li, Zhiyou Kong and Peng Qin
Int. J. Mol. Sci. 2022, 23(9), 4704; https://doi.org/10.3390/ijms23094704 - 24 Apr 2022
Cited by 5 | Viewed by 2430
Abstract
Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We [...] Read more.
Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli–1299 and Dianli–71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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Review

Jump to: Research

27 pages, 1554 KiB  
Review
CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future
by Fangning Zhang, Ting Xiang Neik, William J. W. Thomas and Jacqueline Batley
Int. J. Mol. Sci. 2023, 24(10), 8623; https://doi.org/10.3390/ijms24108623 - 11 May 2023
Cited by 2 | Viewed by 3313
Abstract
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline [...] Read more.
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops. Full article
(This article belongs to the Special Issue Plant Genomics and Genome Editing 2.0)
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