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New Advance on Functional Genomics and Genome Editing in Plant

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

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 27512

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Special Issue Editors

Prof. Dr. Baohong Zhang

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Guest Editor

Department of Biology, East Carolina University, Greenville, NC 27858, USA
Interests: genome editing; small regulatory RNAs; molecular genetics; plant biotechnology; abiotic stress; gene expression and regulation
Special Issues, Collections and Topics in MDPI journals

Dr. Anshu Alok

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Guest Editor

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
Interests: plant genetic engineering; transgenic technology; CRISPR/Cas-mediated editing; metabolic pathway engineering

Dr. Praveen Awasthi

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Guest Editor

Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre ASCR, 37005 České Budějovice, Czech Republic
Interests: plant genetic engineering; transgenic technology; crispr/cas mediated editing; metabolic pathway engineering

Special Issue Information

Dear Colleagues,

Exponential growth in whole-genome sequence data availability in plants, including model and fruit crops, has accelerated functional genomic research. Transcriptomics and small RNA sequencing data repositories of various tissues in different plants are an imperative resource towards underpinning the goal to identify potential candidate genes for trait development in crops. The genome-wide analysis of several important genes and transcription factors at the DNA, RNA, and protein levels conclude a few important genes for trait improvements. The potential genes, promoter, long noncoding, and miRNA need to validate their functional role. For this, various genetic engineering tools, such as overexpression and RNAi, and genome editing tools, such as ZNF, TALENS, and CRISPR/Cas, have been utilized in various plants. However, the development of CRISPR/Cas technology and its variants has become a powerful, efficient, and versatile tool for gene editing, transcriptional activation, suppression, etc. Functional genomics and genome editing technology is widely used in various plants to improve key traits in plant systems, such as high levels of desirable secondary metabolites, excellent flavor, higher yield, disease resistance, high resin content, good storage stability, and improved nutritional and medicinal value. In the present Special Issue, reviews and research articles related to functional genomics and genome editing in plants are welcomed.

Prof. Dr. Baohong Zhang
Dr. Anshu Alok
Dr. Praveen Awasthi
Guest Editors

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Keywords

genome
genome-wide
transcriptome, miRNA
long non-coding RNA
genetic engineering
transgenic
CRISPR/Cas
editing
mutation
crops

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Published Papers (8 papers)

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Research

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17 pages, 12121 KiB

Open AccessArticle

Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport

by Jiujun Du, Changjian Du, Xiaolan Ge, Shuangshuang Wen, Xinglu Zhou, Lei Zhang and Jianjun Hu

Int. J. Mol. Sci. 2023, 24(1), 624; https://doi.org/10.3390/ijms24010624 - 30 Dec 2022

Cited by 2 | Viewed by 2108

Abstract

The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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14 pages, 4241 KiB

Open AccessArticle

Tropaeolum majus R2R3 MYB Transcription Factor TmPAP2 Functions as a Positive Regulator of Anthocyanin Biosynthesis

by Xiaoping Wang, Wei Wang, Siyu Chen, Yuji Lian and Shucai Wang

Int. J. Mol. Sci. 2022, 23(20), 12395; https://doi.org/10.3390/ijms232012395 - 17 Oct 2022

Cited by 6 | Viewed by 1897

Abstract

Anthocyanins are an important group of water-soluble and non-toxic natural pigments with antioxidant and anti-inflammatory properties that can be found in flowers, vegetables, and fruits. Anthocyanin biosynthesis is regulated by several different types of transcription factors, including the WD40-repeat protein Transparent Testa Glabra 1 (TTG1), the bHLH transcription factor Transparent Testa 8 (TT8), Glabra3 (GL3), Enhancer of GL3 (EGL3), and the R2R3 MYB transcription factor Production of Anthocyanin Pigment 1 (PAP1), PAP2, MYB113, and MYB114, which are able to form MYB-bHLH-WD40 (MBW) complexes to regulate the expression of late biosynthesis genes (LBGs) in the anthocyanin biosynthesis pathway. Nasturtium (Tropaeolum majus) is an edible flower plant that offers many health benefits, as it contains numerous medicinally important ingredients, including anthocyanins. By a comparative examination of the possible anthocyanin biosynthesis regulator genes in nasturtium varieties with different anthocyanin contents, we found that TmPAP2, an R2R3 MYB transcription factor gene, is highly expressed in “Empress of India”, a nasturtium variety with high anthocyanin content, while the expression of TmPAP2 in Arabidopsis led to the overproduction of anthocyanins. Protoplast transfection shows that TmPAP2 functions as a transcription activator; consistent with this finding, some of the biosynthesis genes in the general phenylpropanoid pathway and anthocyanin biosynthesis pathway were highly expressed in “Empress of India” and the 35S:TmPAP2 transgenic Arabidopsis plants. However, protoplast transfection indicates that TmPAP2 may not be able to form an MBW complex with TmGL3 and TmTTG1. These results suggest that TmPAP2 may function alone as a key regulator of anthocyanin biosynthesis in nasturtiums. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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20 pages, 4434 KiB

Open AccessArticle

An Integrative Transcriptional Network Revealed Spatial Molecular Interplay Underlying Alantolactone and Inulin Biosynthesis in Inula racemosa Hook f.

by Romit Seth, Amna Devi, Balraj Sharma, Mamta Masand, Gopal Singh, Poonam Pal, Ashlesha Holkar, Shikha Sharma, Vishal Sharma, Shivanti Negi and Ram Kumar Sharma

Int. J. Mol. Sci. 2022, 23(19), 11213; https://doi.org/10.3390/ijms231911213 - 23 Sep 2022

Cited by 3 | Viewed by 2688

Abstract

Inula racemosa Hook. f. (Pushkarmula), a perennial Himalayan herb known for its aromatic and phytopharmaceutical attributes, is not yet explored at genomic/transcriptomic scale. In this study, efforts were made to unveil the global transcriptional atlas underlying organ-specific specialized metabolite biosynthesis by integrating RNA-Seq analysis of 433 million sequenced reads with the phytochemical analysis of leaf, stem, and root tissues. Overall, 7242 of 83,772 assembled nonredundant unigenes were identified exhibiting spatial expression in leaf (3761), root (2748), and stem (733). Subsequently, integration of the predicted transcriptional interactome network of 2541 unigenes (71,841 edges) with gene ontology and KEGG pathway enrichment analysis revealed isoprenoid, terpenoid, diterpenoid, and gibberellin biosynthesis with antimicrobial activities in root tissue. Interestingly, the root-specific expression of germacrene-mediated alantolactone biosynthesis (GAS, GAO, G8H, IPP, DMAP, and KAO) and antimicrobial activities (BZR1, DEFL, LTP) well-supported with both quantitative expression profiling and phytochemical accumulation of alantolactones (726.08 μg/10 mg) and isoalantolactones (988.59 μg/10 mg), which suggests “roots” as the site of alantolactone biosynthesis. A significant interaction of leaf-specific carbohydrate metabolism with root-specific inulin biosynthesis indicates source (leaf) to sink (root) regulation of inulin. Our findings comprehensively demonstrate the source-sink transcriptional regulation of alantolactone and inulin biosynthesis, which can be further extended for upscaling the targeted specialized metabolites. Nevertheless, the genomic resource created in this study can also be utilized for development of genome-wide functionally relevant molecular markers to expedite the breeding strategies for genetic improvement of I. racemosa. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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20 pages, 3128 KiB

Open AccessArticle

Genome-Wide Identification of WRKY Gene Family in Pitaya Reveals the Involvement of HmoWRKY42 in Betalain Biosynthesis

by Canbin Chen, Fangfang Xie, Kamran Shah, Qingzhu Hua, Jiayi Chen, Zhike Zhang, Jietang Zhao, Guibing Hu and Yonghua Qin

Int. J. Mol. Sci. 2022, 23(18), 10568; https://doi.org/10.3390/ijms231810568 - 12 Sep 2022

Cited by 18 | Viewed by 2533

Abstract

The WRKY gene family is a plant-specific transcription factor (TF) that regulates many physiological processes and (a) biotic stress responses. Despite this, little is known about the molecular properties and roles of WRKY TFs in pitaya betalain biosynthesis. Here we report the identification of 70 WRKY in Hylocereus undatus, their gene structure, locations on each chromosome, systematic phylogenetic analysis, conserved motif analysis, and synteny of HuWRKY genes. HmoWRKY42 is a Group IIb WRKY protein and contains a coiled-coil motif, a WRKY domain and a C₂H₂ zinc-finger motif (CX₅CX₂₃HXH). Results from yeast one-hybrid and transient dual-luciferase assays showed that HmoWRKY42 was a transcriptional repressor and could repress HmocDOPA5GT1 expression by binding to its promoter. Yeast two-hybrid assays showed that HmoWRKY42 could interact with itself to form homodimers. Knocking out the coiled-coil motif of HmoWRKY42 prevented its self-interaction and prevented it from binding to the HmocDOPA5GT1 promoter. Knocking out the WRKY domain and C₂H₂ zinc-finger motif sequence of HmoWRKY42 also prevented it from binding to the HmocDOPA5GT1 promoter. The coiled-coil motif, the WRKY domain and the C₂H₂ zinc finger motif are key motifs for the binding of HmoWRKY42 to the HmocDOPA5GT1 promoter. HmoWRKY42 is localized in the nucleus and possesses trans-activation ability responsible for pitaya betalain biosynthesis by repressing the transcription of HmocDOPA5GT1. As far as we know, no reports are available on the role of HmoWRKY42 in pitaya betalain biosynthesis. The results provide an important foundation for future analyses of the regulation and functions of the HuWRKY gene family. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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16 pages, 3498 KiB

Open AccessArticle

Global Identification of White Lupin lncRNAs Reveals Their Role in Cluster Roots under Phosphorus Deficiency

by Mehtab Muhammad Aslam, Muhammad Waseem, Weifeng Xu, Li Ying, Jianhua Zhang and Wei Yuan

Int. J. Mol. Sci. 2022, 23(16), 9012; https://doi.org/10.3390/ijms23169012 - 12 Aug 2022

Cited by 7 | Viewed by 2116

Abstract

Phosphorus (P) deficiency heterogeneously affected plant nutritional status and physiological performance, ultimately leading to a severe yield reduction. A few putative long non-coding RNAs (lncRNAs) responding to P-starvation in the model crops Arabidopsis thaliana and Oryza sativa have been characterized. White lupin (Lupinus albus) is of prime importance, and is a legume with increasing agronomic value as a protein crop as it exhibits extreme tolerance to nutrient deficiency, particularly P deficiency. Despite its adapted nature to P deficiency, nothing is known about low P-induced lncRNAs in white lupin roots. To address this issue, we identified 39,840 mRNA and 2028 lncRNAs in the eight developmental stages of white lupin root (S0–S7 and lateral root, LR) grown under P deficiency. From these 2028 lncRNAs, 1564 were intergenic and 464 natural antisense intergenic transcript (NAT) lncRNAs. We further predicted six potential targets of miRNAs with twelve lncRNAs, which may regulate P-deficiency-related processes. Moreover, the weighted gene co-expression network analysis (WGCNA) revealed seven modules that were correlated with the expression pattern of lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 606 GO terms and 27 different pathways including signal transduction, energy synthesis, detoxification, and Pi transport. In addition, we screened 13 putative lncRNAs that showed a distinct expression pattern in each root, indicating their role in the P deficiency regulatory network. Therefore, white lupin may be a reference legume to characterize P-deficiency-responsive novel lncRNAs, which would highlight the role of lncRNAs in the regulation of plant responses to P deficiency. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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18 pages, 4055 KiB

Open AccessArticle

Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton

by Qiankun Liu, Pengtao Li, Shuang Cheng, Zilin Zhao, Yuling Liu, Yangyang Wei, Quanwei Lu, Jiangping Han, Xiaoyan Cai, Zhongli Zhou, Muhammad Jawad Umer, Renhai Peng, Baohong Zhang and Fang Liu

Int. J. Mol. Sci. 2022, 23(5), 2845; https://doi.org/10.3390/ijms23052845 - 5 Mar 2022

Cited by 17 | Viewed by 3878

Abstract

As one of the pioneer crops widely planted in saline-alkaline areas, Gossypium provides daily necessities, including natural fiber, vegetable proteins, and edible oils. However, cotton fiber yield and quality are highly influenced by salt stress. Therefore, elucidating the molecular mechanisms of cotton in response to salinity stress is importance to breed new cultivars with high tolerance. In this study, we first developed a method for single-cell RNA-seq based on isolating protoplast from cotton root tips; then, we studied the impact of salinity stress on gene expression profiling and their dynamic changes using the developed high-efficiency method for protoplast dissociation suitable for single-cell RNA-seq. A total of 3391 and 2826 differentially expressed genes (DEGs) were identified in salt-treated samples before and after protoplast dissociation, respectively, which were enriched into several molecular components, including response to stimulus, response to stress, and cellular macromolecule metabolic process by gene ontology (GO) analysis. Plant hormone signal transduction, phenylpropanoid biosynthesis, and MAPK signaling pathway were found to be enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Twenty-two and nine salinity-responsive DEGs participated in plant hormone signaling and MAPK signaling in roots, before and after protoplast dissociation, respectively; six upregulated DEGs were involved in ABA signaling transduction, namely, Ga04G2111, Ga07G0142, Ga09G2061, Ga10G0262, Ga01G0063, and Ga08G1915 which indicates their potential functions on plants adapting to salt stress. Additionally, 384 and 257 transcription factors (TFs) were differentially expressed in salt-stress roots before and after protoplast dissociation, respectively, of which significantly up-regulated TFs mainly belonged to the AP2/ERF-ERF family, which implied their potential roles responding to salt stress. These results not only provide novel insights to reveal the regulatory networks in plant’s root response to salt stress, but also lay the solid foundation for further exploration on cellular heterogeneity by single-cell transcriptome sequencing. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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Review

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13 pages, 828 KiB

Open AccessReview

Virus-Induced Gene Editing and Its Applications in Plants

by Chao Zhang, Shanhe Liu, Xuan Li, Ruixuan Zhang and Jun Li

Int. J. Mol. Sci. 2022, 23(18), 10202; https://doi.org/10.3390/ijms231810202 - 6 Sep 2022

Cited by 24 | Viewed by 5604

Abstract

CRISPR/Cas-based genome editing technologies, which allow the precise manipulation of plant genomes, have revolutionized plant science and enabled the creation of germplasms with beneficial traits. In order to apply these technologies, CRISPR/Cas reagents must be delivered into plant cells; however, this is limited by tissue culture challenges. Recently, viral vectors have been used to deliver CRISPR/Cas reagents into plant cells. Virus-induced genome editing (VIGE) has emerged as a powerful method with several advantages, including high editing efficiency and a simplified process for generating gene-edited DNA-free plants. Here, we briefly describe CRISPR/Cas-based genome editing. We then focus on VIGE systems and the types of viruses used currently for CRISPR/Cas9 cassette delivery and genome editing. We also highlight recent applications of and advances in VIGE in plants. Finally, we discuss the challenges and potential for VIGE in plants. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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17 pages, 1853 KiB

Open AccessReview

CRISPR-Based Genome Editing and Its Applications in Woody Plants

by Tian Min, Delight Hwarari, Dong’ao Li, Ali Movahedi and Liming Yang

Int. J. Mol. Sci. 2022, 23(17), 10175; https://doi.org/10.3390/ijms231710175 - 5 Sep 2022

Cited by 14 | Viewed by 4472

Abstract

CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants. Full article

(This article belongs to the Special Issue New Advance on Functional Genomics and Genome Editing in Plant)

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