Genetic Engineering in Agriculture

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	3.3	4.9	2011	19.2 Days	CHF 2600
Bioengineering bioengineering	3.8	4.0	2014	16.4 Days	CHF 2700
Genes genes	2.8	5.2	2010	14.9 Days	CHF 2600
International Journal of Molecular Sciences ijms	4.9	8.1	2000	16.8 Days	CHF 2900
Plants plants	4.0	6.5	2012	18.9 Days	CHF 2700
DNA dna	-	-	2021	23.3 Days	CHF 1000

24 pages, 2898 KiB

Open AccessReview

Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology

by Abel Lucido, Oriol Basallo, Alberto Marin-Sanguino, Abderrahmane Eleiwa, Emilce Soledad Martinez, Ester Vilaprinyo, Albert Sorribas and Rui Alves

Plants 2025, 14(3), 470; https://doi.org/10.3390/plants14030470 - 5 Feb 2025

Viewed by 1120

Abstract

Global food insecurity and environmental degradation highlight the urgent need for more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology offers the potential for enhanced crop traits, it also entails risks [...] Read more.

Global food insecurity and environmental degradation highlight the urgent need for more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology offers the potential for enhanced crop traits, it also entails risks of extensive environmental damage. This review highlights the complexities and risks associated with plant synthetic biology, while presenting the potential of multiscale mathematical modeling to assess and mitigate those risks effectively. Despite its potential, applying multiscale mathematical models in plants remains underutilized. Here, we advocate for integrating technological advancements in agricultural data analysis to develop a comprehensive understanding of crops across biological scales. By reviewing common modeling approaches and methodologies applicable to plants, the paper establishes a foundation for creating and utilizing integrated multiscale mathematical models. Through modeling techniques such as parameter estimation, bifurcation analysis, and sensitivity analysis, researchers can identify mutational targets and anticipate pleiotropic effects, thereby enhancing the safety of genetically engineered species. To demonstrate the potential of this approach, ongoing efforts are highlighted to develop an integrated multiscale mathematical model for maize (Zea mays L.), engineered through synthetic biology to enhance resilience against Striga (Striga spp.) and drought. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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28 pages, 1072 KiB

Open AccessEditor’s ChoiceReview

Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR

by Piao Yang, Abraham Condrich, Ling Lu, Sean Scranton, Camina Hebner, Mohsen Sheykhhasan and Muhammad Azam Ali

DNA 2024, 4(4), 427-454; https://doi.org/10.3390/dna4040030 - 14 Nov 2024

Cited by 4 | Viewed by 6633

Abstract

Genetic engineering has revolutionized our ability to modify microorganisms for various applications in agriculture, medicine, and industry. This review examines recent advances in genetic engineering techniques for bacteria, fungi, and oomycetes, with a focus on CRISPR-Cas systems. In bacteria, CRISPR-Cas9 has enabled precise [...] Read more.

Genetic engineering has revolutionized our ability to modify microorganisms for various applications in agriculture, medicine, and industry. This review examines recent advances in genetic engineering techniques for bacteria, fungi, and oomycetes, with a focus on CRISPR-Cas systems. In bacteria, CRISPR-Cas9 has enabled precise genome editing, enhancing applications in antibiotic production and metabolic engineering. For fungi, despite challenges associated with their complex cell structures, CRISPR/Cas9 has advanced the production of enzymes and secondary metabolites. In oomycetes, significant plant pathogens, modified Agrobacterium-mediated transformation, and CRISPR/Cas12a have contributed to developing disease-resistant crops. This review provides a comparative analysis of genetic engineering efficiencies across these microorganisms and addresses ethical and regulatory considerations. Future research directions include refining genetic tools to improve efficiency and expand applicability in non-model organisms. This comprehensive overview highlights the transformative potential of genetic engineering in microbiology and its implications for addressing global challenges in agriculture, medicine, and biotechnology. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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16 pages, 2299 KiB

Open AccessArticle

Comparison Between Electroporation at Different Voltage Levels and Microinjection to Generate Porcine Embryos with Multiple Xenoantigen Knock-Outs

by Juan Pablo Fernández, Björn Petersen, Petra Hassel, Andrea Lucas Hahn, Paul Kielau, Johannes Geibel and Wilfried A. Kues

Int. J. Mol. Sci. 2024, 25(22), 11894; https://doi.org/10.3390/ijms252211894 - 5 Nov 2024

Cited by 1 | Viewed by 1261

Abstract

In the context of xenotransplantation, the production of genetically modified pigs is essential. For several years, knock-out pigs were generated through somatic cell nuclear transfer employing donor cells with the desired genetic modifications, which resulted in a lengthy and cumbersome procedure. The CRISPR/Cas9 [...] Read more.

In the context of xenotransplantation, the production of genetically modified pigs is essential. For several years, knock-out pigs were generated through somatic cell nuclear transfer employing donor cells with the desired genetic modifications, which resulted in a lengthy and cumbersome procedure. The CRISPR/Cas9 system enables direct targeting of specific genes in zygotes directly through microinjection or electroporation. However, these techniques require improvement to minimize mosaicism and low mutation rates without compromising embryo survival. This study aimed to determine the gene editing potential of these two techniques to deliver multiplexed ribonucleotide proteins (RNPs) to generate triple-knock-out porcine embryos with a multi-transgenic background. We designed RNP complexes targeting the major porcine xenoantigens GGTA1, CMAH, and B4GALNT2. We then compared the development of mosaicism and gene editing efficiencies between electroporation and microinjection. Our results indicated a significant effect of voltage increase on molecule intake in electroporated embryos, without it notably affecting the blastocyst formation rate. Our gene editing analysis revealed differences among delivery approaches and gene loci. Notably, employing electroporation at 35 V yielded the highest frequency of biallelic disruptions. However, mosaicism was the predominant genetic variant in all RNP delivery methods, underscoring the need for further research to optimize multiplex genome editing in porcine zygotes. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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13 pages, 3986 KiB

Open AccessArticle

Refinement and Enhancement of Agrobacterium-Mediated Transient Transformation for Functional Gene Examination in Mulberry (Morus L.)

by Rongli Mo, Na Zhang, Changyu Qiu, Sheng Huang, Wei Wei, Chaohua Zhang, Dan Liu and Qiang Lin

Genes 2024, 15(10), 1277; https://doi.org/10.3390/genes15101277 - 28 Sep 2024

Cited by 1 | Viewed by 1492

Abstract

Background: Mulberry (Morus L.), a vital perennial woody plant with significant economic importance, is utilized for silkworm rearing, human consumption and medicinal use. The availability of mulberry’s whole-genome sequencing data has underscored the demand for an effective, user-friendly, and high-throughput protocol to [...] Read more.

Background: Mulberry (Morus L.), a vital perennial woody plant with significant economic importance, is utilized for silkworm rearing, human consumption and medicinal use. The availability of mulberry’s whole-genome sequencing data has underscored the demand for an effective, user-friendly, and high-throughput protocol to facilitate the elucidation of gene functions. Methods and Results: In this investigation, we established a transient transformation approach using Agrobacterium tumefaciens-mediated sonication followed by vacuum infiltration in mulberry tissue culture seedlings. Simultaneously, we optimized the transformation conditions, including mulberry genotypes, A. tumefaciens strain, acetosyringone concentration, bacterial density, sonication time, and days after agroinfiltration. These optimizations aimed to achieve heightened transformation efficiency, employing GFP as a reporter gene to monitor transformation events. The optimized method included the use of an infiltration medium (10 mM MgCl₂, 10 mM MES (2-(N-morpholino)ethanesulfonic acid sodium salt), 150 μM acetosyringone, and OD600 0.5 of A. tumefaciens LBA4404) supplemented with the surfactant 0.02% Silwet L-77, with 20 s sonication followed by 20 min vacuum infiltration (0.07 MPa). Among the four mulberry genotypes, ‘Taiguo’ was the most responsive genotype and produced the highest levels of GFP expression at 7 d after infiltration. Furthermore, the optimized transient transformation approach has been proven to be successfully applicable for transiently overexpressing MaANS and MaDFR in mulberry fruits of ‘Taiguo’, in vitro, which distinctly enhanced fruit coloring and significantly increased anthocyanin accumulation, respectively. Conclusions: In summary, we devised a dependable, stable and highly efficient transient transformation approach suitable for rapid gene function examination in mulberry leaves and fruits, in vitro. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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16 pages, 2372 KiB

Open AccessEditor’s ChoiceArticle

Transgenic Soybean for Production of Thermostable α-Amylase

by Zhenyan Cao, Ye Jiang, Jiajie Li, Ting Zheng, Chaoyang Lin and Zhicheng Shen

Plants 2024, 13(11), 1539; https://doi.org/10.3390/plants13111539 - 2 Jun 2024

Viewed by 2523

Abstract

Alpha-amylases are crucial hydrolase enzymes which have been widely used in food, feed, fermentation, and pharmaceutical industries. Methods for low-cost production of α-amylases are highly desirable. Soybean seed, functioning as a bioreactor, offers an excellent platform for the mass production of recombinant proteins [...] Read more.

Alpha-amylases are crucial hydrolase enzymes which have been widely used in food, feed, fermentation, and pharmaceutical industries. Methods for low-cost production of α-amylases are highly desirable. Soybean seed, functioning as a bioreactor, offers an excellent platform for the mass production of recombinant proteins for its ability to synthesize substantial quantities of proteins. In this study, we generated and characterized transgenic soybeans expressing the α-amylase AmyS from Bacillus stearothermophilus. The α-amylase expression cassettes were constructed for seed specific expression by utilizing the promoters of three different soybean storage peptides and transformed into soybean via Agrobacterium-mediated transformation. The event with the highest amylase activity reached 601 U/mg of seed flour (one unit is defined as the amount of enzyme that generates 1 micromole reducing ends per min from starch at 65 °C in pH 5.5 sodium acetate buffer). The optimum pH, optimum temperature, and the enzymatic kinetics of the soybean expressed enzyme are similar to that of the E. coli expressed enzyme. However, the soybean expressed α-amylase is glycosylated, exhibiting enhanced thermostability and storage stability. Soybean AmyS retains over 80% activity after 100 min at 75 °C, and the transgenic seeds exhibit no significant activity loss after one year of storage at room temperature. The accumulated AmyS in the transgenic seeds represents approximately 15% of the total seed protein, or about 4% of the dry seed weight. The specific activity of the transgenic soybean seed flour is comparable to many commercial α-amylase enzyme products in current markets, suggesting that the soybean flour may be directly used for various applications without the need for extraction and purification. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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14 pages, 1137 KiB

Open AccessReview

Application of Nanotechnology in Plant Genetic Engineering

by Kexin Wu, Changbin Xu, Tong Li, Haijie Ma, Jinli Gong, Xiaolong Li, Xuepeng Sun and Xiaoli Hu

Int. J. Mol. Sci. 2023, 24(19), 14836; https://doi.org/10.3390/ijms241914836 - 2 Oct 2023

Cited by 13 | Viewed by 6087

Abstract

The ever-increasing food requirement with globally growing population demands advanced agricultural practices to improve grain yield, to gain crop resilience under unpredictable extreme weather, and to reduce production loss caused by insects and pathogens. To fulfill such requests, genome engineering technology has been [...] Read more.

The ever-increasing food requirement with globally growing population demands advanced agricultural practices to improve grain yield, to gain crop resilience under unpredictable extreme weather, and to reduce production loss caused by insects and pathogens. To fulfill such requests, genome engineering technology has been applied to various plant species. To date, several generations of genome engineering methods have been developed. Among these methods, the new mainstream technology is clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases. One of the most important processes in genome engineering is to deliver gene cassettes into plant cells. Conventionally used systems have several shortcomings, such as being labor- and time-consuming procedures, potential tissue damage, and low transformation efficiency. Taking advantage of nanotechnology, the nanoparticle-mediated gene delivery method presents technical superiority over conventional approaches due to its high efficiency and adaptability in different plant species. In this review, we summarize the evolution of plant biomolecular delivery methods and discussed their characteristics as well as limitations. We focused on the cutting-edge nanotechnology-based delivery system, and reviewed different types of nanoparticles, preparation of nanomaterials, mechanism of nanoparticle transport, and advanced application in plant genome engineering. On the basis of established methods, we concluded that the combination of genome editing, nanoparticle-mediated gene transformation and de novo regeneration technologies can accelerate crop improvement efficiently in the future. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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15 pages, 6409 KiB

Open AccessEditor’s ChoiceArticle

Stacking Multiple Genes Improves Resistance to Chilo suppressalis, Magnaporthe oryzae, and Nilaparvata lugens in Transgenic Rice

by Bai Li, Zhongkai Chen, Huizhen Chen, Chunlei Wang, Liyan Song, Yue Sun, Yicong Cai, Dahu Zhou, Linjuan Ouyang, Changlan Zhu, Haohua He and Xiaosong Peng

Genes 2023, 14(5), 1070; https://doi.org/10.3390/genes14051070 - 12 May 2023

Cited by 1 | Viewed by 2293

Abstract

The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains [...] Read more.

The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains with broad-spectrum resistance to multiple pathogens. Here, we produced resistance rice lines with multiple, stacked resistance genes by stacking breeding and comprehensively evaluated their resistance to Chilo suppressalis (striped rice stemborer), Magnaporthe oryzae (rice blast), and Nilaparvata lugens (brown planthopper) in a pesticide-free environment. CRY1C and CRY2A are exogenous genes from Bacillus thuringiensis. Pib, Pikm, and Bph29 are natural genes in rice. CH121TJH was introduced into CRY 1C, Pib, Pikm, and Bph29. CH891TJH and R205XTJH were introduced into CRY 2A, Pib, Pikm, and Bph29. Compared with those observed in their recurrent parents, CH121TJH significantly increased the mortality of borers. The other two lines CH891TJH and R205XTJH are the same result. Three lines introduction of Pib and Pikm significantly reduced the area of rice blast lesions, and introduction of Bph29 significantly reduced seedling mortality from N. lugens. Introduction of the exogenous genes had relatively few effects on agronomic and yield traits of the original parents. These findings suggest that stacking of rice resistance genes through molecular marker-assisted backcross breeding can confer broad spectrum and multiple resistance in differently genetic backgrounds. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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15 pages, 9305 KiB

Open AccessArticle

DoMYB5 and DobHLH24, Transcription Factors Involved in Regulating Anthocyanin Accumulation in Dendrobium officinale

by Kun Yang, Yibin Hou, Mei Wu, Qiuyu Pan, Yilong Xie, Yusen Zhang, Fenghang Sun, Zhizhong Zhang and Jinghua Wu

Int. J. Mol. Sci. 2023, 24(8), 7552; https://doi.org/10.3390/ijms24087552 - 20 Apr 2023

Cited by 12 | Viewed by 3107

Abstract

As a kind of orchid plant with both medicinal and ornamental value, Dendrobium officinale has garnered increasing research attention in recent years. The MYB and bHLH transcription factors play important roles in the synthesis and accumulation of anthocyanin. However, how MYB and bHLH [...] Read more.

As a kind of orchid plant with both medicinal and ornamental value, Dendrobium officinale has garnered increasing research attention in recent years. The MYB and bHLH transcription factors play important roles in the synthesis and accumulation of anthocyanin. However, how MYB and bHLH transcription factors work in the synthesis and accumulation of anthocyanin in D. officinale is still unclear. In this study, we cloned and characterized one MYB and one bHLH transcription factor, namely, D. officinale MYB5 (DoMYB5) and D. officinaleb bHLH24 (DobHLH24), respectively. Their expression levels were positively correlated with the anthocyanin content in the flowers, stems, and leaves of D. officinale varieties with different colors. The transient expression of DoMYB5 and DobHLH24 in D. officinale leaf and their stable expression in tobacco significantly promoted the accumulation of anthocyanin. Both DoMYB5 and DobHLH24 could directly bind to the promoters of D. officinale CHS (DoCHS) and D. officinale DFR (DoDFR) and regulate DoCHS and DoDFR expression. The co-transformation of the two transcription factors significantly enhanced the expression levels of DoCHS and DoDFR. DoMYB5 and DobHLH24 may enhance the regulatory effect by forming heterodimers. Drawing on the results of our experiments, we propose that DobHLH24 may function as a regulatory partner by interacting directly with DoMYB5 to stimulate anthocyanin accumulation in D. officinale. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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16 pages, 4328 KiB

Open AccessArticle

Genome-Wide Analysis of the LATERAL ORGAN BOUNDARIES Domain (LBD) Members in Alfalfa and the Involvement of MsLBD48 in Nitrogen Assimilation

by Xu Jiang, Huiting Cui, Zhen Wang, Junmei Kang, Qingchuan Yang and Changhong Guo

Int. J. Mol. Sci. 2023, 24(5), 4644; https://doi.org/10.3390/ijms24054644 - 28 Feb 2023

Cited by 8 | Viewed by 2542

Abstract

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a transcription factor family specific to the land plants, have been implicated in multiple biological processes including organ development, pathogen response and the uptake of inorganic nitrogen. The study focused on LBDs in legume forage [...] Read more.

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a transcription factor family specific to the land plants, have been implicated in multiple biological processes including organ development, pathogen response and the uptake of inorganic nitrogen. The study focused on LBDs in legume forage Alfalfa. The genome-wide analysis revealed that in Alfalfa 178 loci across 31 allelic chromosomes encoded 48 unique LBDs (MsLBDs), and the genome of its diploid progenitor M. sativa spp. Caerulea encoded 46 LBDs. Synteny analysis indicated that the expansion of AlfalfaLBDs was attributed to the whole genome duplication event. The MsLBDs were divided into two major phylogenetic classes, and the LOB domain of the Class I members was highly conserved relative to that of the Class II. The transcriptomic data demonstrated that 87.5% of MsLBDs were expressed in at least one of the six test tissues, and Class II members were preferentially expressed in nodules. Moreover, the expression of Class II LBDs in roots was upregulated by the treatment of inorganic nitrogen such as KNO₃ and NH₄Cl (0.3 mM). The overexpression of MsLBD48, a Class II member, in Arabidopsis resulted in growth retardance with significantly declined biomass compared with the non-transgenic plants, and the transcription level of the genes involved in nitrogen uptake or assimilation, including NRT1.1, NRT2.1, NIA1 and NIA2 was repressed. Therefore, the LBDs in Alfalfa are highly conserved with their orthologs in embryophytes. Our observations that ectopic expression of MsLBD48 inhibited Arabidopsis growth by repressing nitrogen adaption suggest the negative role of the transcription factor in plant uptake of inorganic nitrogen. The findings imply the potential application of MsLBD48 in Alfalfa yield improvement via gene editing. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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15 pages, 5988 KiB

Open AccessArticle

Gonadal Transcriptome Analysis and Sequence Characterization of Sex-Related Genes in Cranoglanis bouderius

by Dongjie Wang, Zhengkun Pan, Guoxia Wang, Bin Ye, Qiujie Wang, Zhiheng Zuo, Jixing Zou and Shaolin Xie

Int. J. Mol. Sci. 2022, 23(24), 15840; https://doi.org/10.3390/ijms232415840 - 13 Dec 2022

Cited by 4 | Viewed by 2092

Abstract

In China, the Cranoglanis bouderius is classified as a national class II-protected animal. The development of C. bouderius populations has been affected by a variety of factors over the past few decades, with severe declines occurring. Considering the likelihood of continued population declines [...] Read more.

In China, the Cranoglanis bouderius is classified as a national class II-protected animal. The development of C. bouderius populations has been affected by a variety of factors over the past few decades, with severe declines occurring. Considering the likelihood of continued population declines of the C. bouderius in the future, it is critical to investigate the currently unknown characteristics of gonadal differentiation and sex-related genes for C. bouderius conservation. In this study, the Illumina sequencing platform was used to sequence the gonadal transcriptome of the C. bouderius to identify the pathways and genes related to gonadal development and analyze the expression differences in the gonads. A total of 12,002 DEGs were identified, with 7220 being significantly expressed in the ovary and 4782 being significantly expressed in the testis. According to the functional enrichment results, the cell cycle, RNA transport, apoptosis, Wnt signaling pathway, p53 signaling pathway, and prolactin signaling pathway play important roles in sex development in the C. bouderius. Furthermore, the sequence characterization and evolutionary analysis revealed that AMH, DAX1, NANOS1, and AR of the C. bouderius are highly conserved. Specifically, the qRT-PCR results from various tissues showed significant differences in AMH, DAX1, NANOS1, and AR expression levels in the gonads of both sexes of C. bouderius. These analyses indicated that AMH, DAX1, NANOS1, and AR may play important roles in the differentiation and development of C. bouderius gonads. To our best knowledge, this study is the first to analyze the C. bouderius gonadal transcriptome and identify the structures of sex-related genes, laying the foundation for future research. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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18 pages, 2998 KiB

Open AccessArticle

Identification of Alkaline Salt Tolerance Genes in Brassica napus L. by Transcriptome Analysis

by Yu Xu, Shunxian Tao, Yunlin Zhu, Qi Zhang, Ping Li, Han Wang, Yan Zhang, Aldiyar Bakirov, Hanming Cao, Mengfan Qin, Kai Wang, Yiji Shi, Xiang Liu, Lin Zheng, Aixia Xu and Zhen Huang

Genes 2022, 13(8), 1493; https://doi.org/10.3390/genes13081493 - 21 Aug 2022

Cited by 3 | Viewed by 3039

Abstract

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) [...] Read more.

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) line 2205 exhibited more tolerance to alkaline salt than line 1423 did. In line 2205, the lesser plasma membrane damage index, the accumulated osmotic solute, and higher antioxidant enzyme activities contributed to alkaline tolerance. A more integrated mesophyll-cell structure was revealed under alkali salt stress by ultrastructure observation in line 2205, which also implied a lesser injury. Transcriptome analysis showed that more genes responded to alkaline salt in line 2205. The expression of specific-response genes in line 1423 was lower than in line 2205. However, most of the specific-response genes in line 2205 had higher expression, which was mainly enriched in carbohydrate metabolism, photosynthetic processes, ROS regulating, and response to salt stress. It can be seen that the tolerance to alkaline salt is attributed to the high expression of some genes in these pathways. Based on these, twelve cross-differentially expressed genes were proposed as candidates. They provide clues for further analysis of the resistance mechanism of rapeseed. Full article

(This article belongs to the Topic Genetic Engineering in Agriculture)

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