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Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing

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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 (28 February 2021) | Viewed by 67311

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Special Issue Editors

Prof. Dr. Ki-Hong Jung

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Guest Editor

Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
Interests: rice; root hair development; pollen genetics; ROS process; abiotic stress tolerance; transcirptome analysis; network analysis; genome editing; phylogenomics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jae-Yean Kim

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Guest Editor

Division of Life Science, Gyeongsang National University, 27-306, 501 Jinju-Daero, Jinju, Gyeongnam 660-701, Republic of Korea
Interests: plasmodesmata; phloem; cell-to-cell communication; intercellular protein and RNA trafficking; genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Functional redundancy is the concept that is proposed to explain no or little phenotype of the null mutant due to genetic compensation by duplicate genes of the target gene. This phenomenon is a universal feature across higher organisms and produces genetic robustness against various environmental conditions and accidental mutation. Crop plants provide calorie and nutrient uptake for humankind, and improvement of agricultural traits is a major focus of fucntional genomic studies. However, despite a variety of mutant population and omics data being generated, functional identification of target genes to enhance the agronomic traits has reached a bottleneck due to functional redundancy in the genome. Less than 10% of genes in the Arabidiopsis genome have been functionally characterized through loss of function study of a single gene, which is one of major methods used to improve agronomic traits using gene editing technology, including the clustered regularly interspaced short palindromic repeats associated system (CRISPR/Cas). Application of multiple genes-editing methods will improve crops by repressing negative regulators of agronomic traits and provide new insight into functional genomics. On the other hand, single gene mutations can lead to changes in various phenotypes or traits. It will be great to have genes of which mutations improve multiple agricultural/commercial traits.

Papers submitted to this Special Issue must report novel results and/or plausible and testable new models. This Special Issue includes studies relating to diverse agnromic tratis through single gene editing or multiple targets-editing in model plant and crop plant species, and covers methods or webtools to predict suitable targets for single gene- or multiple-genes-editing in various plant species

Prof. Ki-Hong Jung
Prof. Jae-Yean Kim
Guest Editors

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Keywords

agronomic traits
CRISPR/Cas9
crop plant
gene editing
functional genomics
functional redundancy

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Published Papers (9 papers)

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Research

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12 pages, 1380 KiB

Open AccessCommunication

The Functional Association of ACQOS/VICTR with Salt Stress Resistance in Arabidopsis thaliana Was Confirmed by CRISPR-Mediated Mutagenesis

by Sang-Tae Kim, Minkyung Choi, Su-Ji Bae and Jin-Soo Kim

Int. J. Mol. Sci. 2021, 22(21), 11389; https://doi.org/10.3390/ijms222111389 - 21 Oct 2021

Cited by 21 | Viewed by 2715

Abstract

Clustered regularly interspaced palindromic repeat (CRISPR)-mediated mutagenesis has become an important tool in plant research, enabling the characterization of genes via gene knock-out. CRISPR genome editing tools can be applied to generate multi-gene knockout lines. Typically, multiple single-stranded, single guide RNAs (gRNAs) must be expressed in an organism to target multiple genes simultaneously; however, a single gRNA can target multiple genes if the target genes share similar sequences. A gene cluster comprising ACQUIRED OSMOTOLERANCE (ACQOS; AT5G46520) and neighboring nucleotide-binding leucine-rich repeats (NLRs; AT5G46510) is associated with osmotic tolerance. To investigate the role of ACQOS and the tandemly arranged NLR in osmotic tolerance, we introduced small insertion/deletion mutations into two target genes using a single gRNA and obtained transformant plant lines with three different combinations of mutant alleles. We then tested our mutant lines for osmotic tolerance after a salt-stress acclimation period by determining the chlorophyll contents of the mutant seedlings. Our results strongly suggest that ACQOS is directly associated with salt resistance, while the neighboring NLR is not. Here, we confirmed previous findings suggesting the involvement of ACQOS in salt tolerance and demonstrated the usefulness of CRISPR-mediated mutagenesis in validating the functions of genes in a single genetic background. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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18 pages, 19525 KiB

Open AccessArticle

Conserved Opposite Functions in Plant Resistance to Biotrophic and Necrotrophic Pathogens of the Immune Regulator SRFR1

by Geon Hui Son, Jiyun Moon, Rahul Mahadev Shelake, Uyen Thi Vuong, Robert A. Ingle, Walter Gassmann, Jae-Yean Kim and Sang Hee Kim

Int. J. Mol. Sci. 2021, 22(12), 6427; https://doi.org/10.3390/ijms22126427 - 15 Jun 2021

Cited by 7 | Viewed by 4593

Abstract

Plant immunity is mediated in large part by specific interactions between a host resistance protein and a pathogen effector protein, named effector-triggered immunity (ETI). ETI needs to be tightly controlled both positively and negatively to enable normal plant growth because constitutively activated defense responses are detrimental to the host. In previous work, we reported that mutations in SUPPRESSOR OF rps4-RLD1 (SRFR1), identified in a suppressor screen, reactivated EDS1-dependent ETI to Pseudomonas syringae pv. tomato (Pto) DC3000. Besides, mutations in SRFR1 boosted defense responses to the generalist chewing insect Spodoptera exigua and the sugar beet cyst nematode Heterodera schachtii. Here, we show that mutations in SRFR1 enhance susceptibility to the fungal necrotrophs Fusarium oxysporum f. sp. lycopersici (FOL) and Botrytis cinerea in Arabidopsis. To translate knowledge obtained in AtSRFR1 research to crops, we generated SlSRFR1 alleles in tomato using a CRISPR/Cas9 system. Interestingly, slsrfr1 mutants increased expression of SA-pathway defense genes and enhanced resistance to Pto DC3000. In contrast, slsrfr1 mutants elevated susceptibility to FOL. Together, these data suggest that SRFR1 is functionally conserved in both Arabidopsis and tomato and functions antagonistically as a negative regulator to (hemi-) biotrophic pathogens and a positive regulator to necrotrophic pathogens. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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20 pages, 3078 KiB

Open AccessArticle

Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage (Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs

by Haemyeong Jung, Areum Lee, Seung Hee Jo, Hyun Ji Park, Won Yong Jung, Hyun-Soon Kim, Hyo-Jun Lee, Seon-Geum Jeong, Youn-Sung Kim and Hye Sun Cho

Int. J. Mol. Sci. 2021, 22(9), 4631; https://doi.org/10.3390/ijms22094631 - 28 Apr 2021

Cited by 10 | Viewed by 3060

Abstract

Precise flowering timing is critical for the plant life cycle. Here, we examined the molecular mechanisms and regulatory network associated with flowering in Chinese cabbage (Brassica rapa L.) by comparative transcriptome profiling of two Chinese cabbage inbred lines, “4004” (early bolting) and “50” (late bolting). RNA-Seq and quantitative reverse transcription PCR (qPCR) analyses showed that two positive nitric oxide (NO) signaling regulator genes, nitrite reductase (BrNIR) and nitrate reductase (BrNIA), were up-regulated in line “50” with or without vernalization. In agreement with the transcription analysis, the shoots in line “50” had substantially higher nitrogen levels than those in “4004”. Upon vernalization, the flowering repressor gene Circadian 1 (BrCIR1) was significantly up-regulated in line “50”, whereas the flowering enhancer genes named SUPPRESSOR OF OVEREXPRESSION OF CONSTANCE 1 homologs (BrSOC1s) were substantially up-regulated in line “4004”. CRISPR/Cas9-mediated mutagenesis in Chinese cabbage demonstrated that the BrSOC1-1/1-2/1-3 genes were involved in late flowering, and their expression was mutually exclusive with that of the nitrogen signaling genes. Thus, we identified two flowering mechanisms in Chinese cabbage: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrSOC1s to control flowering time and positive feedback control of the expression of BrSOC1s. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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12 pages, 2460 KiB

Open AccessArticle

Agrobacterium-Mediated Capsicum annuum Gene Editing in Two Cultivars, Hot Pepper CM334 and Bell Pepper Dempsey

by Sung-il Park, Hyun-Bin Kim, Hyun-Ji Jeon and Hyeran Kim

Int. J. Mol. Sci. 2021, 22(8), 3921; https://doi.org/10.3390/ijms22083921 - 10 Apr 2021

Cited by 19 | Viewed by 5740

Abstract

Peppers (Capsicum annuum L.) are the most widespread and cultivated species of Solanaceae in subtropical and temperate countries. These vegetables are economically attractive worldwide. Although whole-genome sequences of peppers and genome-editing tools are currently available, the precision editing of peppers is still in its infancy because of the lack of a stable pepper transformation method. Here, we employed three Agrobacterium tumefaciens strains—AGL1, EHA101, and GV3101—to investigate which Agrobacterium strain could be used for pepper transformation. Hot pepper CM334 and bell pepper Dempsey were chosen in this study. Agrobacterium tumefaciens GV3101 induced the highest number of calli in cv. Dempsey. All three strains generated similar numbers of calli for cv. CM334. We optimized a suitable concentration of phosphinothricin (PPT) to select a CRISPR/Cas9 binary vector (pBAtC) for both pepper types. Finally, we screened transformed calli for PPT resistance (1 and 5 mg/L PPT for cv. CM334 and Dempsey, respectively). These selected calli showed different indel frequencies from the non-transformed calli. However, the primary indel pattern was consistent with a 1-bp deletion at the target locus of the C. annuumMLO gene (CaMLO2). These results demonstrate the different sensitivity between cv. CM334 and Dempsey to A. tumefaciens-mediated callus induction, and a differential selection pressure of PPT via pBAtC binary vector. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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18 pages, 4443 KiB

Open AccessArticle

CRISPR/Cas9-Mediated Generation of Pathogen-Resistant Tomato against Tomato Yellow Leaf Curl Virus and Powdery Mildew

by Dibyajyoti Pramanik, Rahul Mahadev Shelake, Jiyeon Park, Mi Jung Kim, Indeok Hwang, Younghoon Park and Jae-Yean Kim

Int. J. Mol. Sci. 2021, 22(4), 1878; https://doi.org/10.3390/ijms22041878 - 13 Feb 2021

Cited by 87 | Viewed by 10237

Abstract

Tomato is one of the major vegetable crops consumed worldwide. Tomato yellow leaf curl virus (TYLCV) and fungal Oidium sp. are devastating pathogens causing yellow leaf curl disease and powdery mildew. Such viral and fungal pathogens reduce tomato crop yields and cause substantial economic losses every year. Several commercial tomato varieties include Ty-5 (SlPelo) and Mildew resistance locus o 1 (SlMlo1) locus that carries the susceptibility (S-gene) factors for TYLCV and powdery mildew, respectively. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a valuable genome editing tool to develop disease-resistant crop varieties. In this regard, targeting susceptibility factors encoded by the host plant genome instead of the viral genome is a promising approach to achieve pathogen resistance without the need for stable inheritance of CRISPR components. In this study, the CRISPR/Cas9 system was employed to target the SlPelo and SlMlo1 for trait introgression in elite tomato cultivar BN-86 to confer host-mediated immunity against pathogens. SlPelo-knockout lines were successfully generated, carrying the biallelic indel mutations. The pathogen resistance assays in SlPelo mutant lines confirmed the suppressed accumulation of TYLCV and restricted the spread to non-inoculated plant parts. Generated knockout lines for the SlMlo1 showed complete resistance to powdery mildew fungus. Overall, our results demonstrate the efficiency of the CRISPR/Cas9 system to introduce targeted mutagenesis for the rapid development of pathogen-resistant varieties in tomato. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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Review

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17 pages, 909 KiB

Open AccessReview

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

by Lei Liu, Penelope L. Lindsay and David Jackson

Int. J. Mol. Sci. 2021, 22(10), 5167; https://doi.org/10.3390/ijms22105167 - 13 May 2021

Cited by 12 | Viewed by 4512

Abstract

Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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17 pages, 1795 KiB

Open AccessReview

Recent Advances in Effector-Triggered Immunity in Plants: New Pieces in the Puzzle Create a Different Paradigm

by Quang-Minh Nguyen, Arya Bagus Boedi Iswanto, Geon Hui Son and Sang Hee Kim

Int. J. Mol. Sci. 2021, 22(9), 4709; https://doi.org/10.3390/ijms22094709 - 29 Apr 2021

Cited by 74 | Viewed by 15138

Abstract

Plants rely on multiple immune systems to protect themselves from pathogens. When pattern-triggered immunity (PTI)—the first layer of the immune response—is no longer effective as a result of pathogenic effectors, effector-triggered immunity (ETI) often provides resistance. In ETI, host plants directly or indirectly perceive pathogen effectors via resistance proteins and launch a more robust and rapid defense response. Resistance proteins are typically found in the form of nucleotide-binding and leucine-rich-repeat-containing receptors (NLRs). Upon effector recognition, an NLR undergoes structural change and associates with other NLRs. The dimerization or oligomerization of NLRs signals to downstream components, activates “helper” NLRs, and culminates in the ETI response. Originally, PTI was thought to contribute little to ETI. However, most recent studies revealed crosstalk and cooperation between ETI and PTI. Here, we summarize recent advancements in our understanding of the ETI response and its components, as well as how these components cooperate in the innate immune signaling pathways. Based on up-to-date accumulated knowledge, this review provides our current perspective of potential engineering strategies for crop protection. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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13 pages, 1858 KiB

Open AccessReview

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops

by Taeyoung Um, Taehyeon Park, Jae Sung Shim, Youn Shic Kim, Gang-Seob Lee, Ik-Young Choi, Ju-Kon Kim, Jun Sung Seo and Soo Chul Park

Int. J. Mol. Sci. 2021, 22(7), 3743; https://doi.org/10.3390/ijms22073743 - 3 Apr 2021

Cited by 12 | Viewed by 5044

Abstract

Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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28 pages, 3965 KiB

Open AccessReview

A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement

by Sunny Ahmar, Sumbul Saeed, Muhammad Hafeez Ullah Khan, Shahid Ullah Khan, Freddy Mora-Poblete, Muhammad Kamran, Aroosha Faheem, Ambreen Maqsood, Muhammad Rauf, Saba Saleem, Woo-Jong Hong and Ki-Hong Jung

Int. J. Mol. Sci. 2020, 21(16), 5665; https://doi.org/10.3390/ijms21165665 - 7 Aug 2020

Cited by 69 | Viewed by 14779

Abstract

Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist’s mind, as it allows genome editing in multiple biological systems. Full article

(This article belongs to the Special Issue Crop Improvement through Multi-Trait Gene Editing or Multiple Genes-Editing)

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