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Sung YW, Kim J, Yang JW, Shim D, Kim YH. Transcriptome-Based Comparative Expression Profiling of Sweet Potato during a Compatible Response with Root-Knot Nematode Meloidogyne incognita Infection. Genes (Basel) 2023; 14:2074. [PMID: 38003017 PMCID: PMC10671793 DOI: 10.3390/genes14112074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
M. incognita, a root-knot nematode (RKN), infects the roots of several important food crops, including sweet potato (Ipomoea batatas Lam.), and severely reduces yields. However, the molecular mechanisms underlying infection remain unclear. Previously, we investigated differential responses to RKN invasion in susceptible and resistant sweet potato cultivars through RNA-seq-based transcriptome analysis. In this study, gene expression similarities and differences were examined in RKN-susceptible sweet potato cultivars during the compatible response to RKN infection. Three susceptible cultivars investigated in previous research were used: Dahomi (DHM), Shinhwangmi (SHM), and Yulmi (YM). Of the three cultivars, YM had the highest number of genes with altered expression in response to infection. YM was also the cultivar with the highest susceptibility to RKN. Comparisons among cultivars identified genes that were regulated in more than one cultivar upon infection. Pairwise comparisons revealed that YM and DHM shared the most regulated genes, whereas YM and SHM shared the lowest number of regulated genes. Five genes were up-regulated, and two were down-regulated, in all three cultivars. Among these, four genes were highly up-regulated in all cultivars: germin-like protein, anthranilate synthase α subunit, isocitrate lyase, and uncharacterized protein. Genes were also identified that were uniquely regulated in each cultivar in response to infection, suggesting that susceptible cultivars respond to infection through shared and cultivar-specific pathways. Our findings expand the understanding of the compatible response to RKN invasion in sweet potato roots and provide useful information for further research on RKN defense mechanisms.
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Affiliation(s)
- Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jung-Wook Yang
- Department of Crop Cultivation & Environment, Research National Institute of Crop Science, RDA, Suwon 16429, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
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Tran MT, Son GH, Song YJ, Nguyen NT, Park S, Thach TV, Kim J, Sung YW, Das S, Pramanik D, Lee J, Son KH, Kim SH, Vu TV, Kim JY. CRISPR-Cas9-based precise engineering of SlHyPRP1 protein towards multi-stress tolerance in tomato. Front Plant Sci 2023; 14:1186932. [PMID: 37255559 PMCID: PMC10225705 DOI: 10.3389/fpls.2023.1186932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023]
Abstract
Recently, CRISPR-Cas9-based genome editing has been widely used for plant breeding. In our previous report, a tomato gene encoding hybrid proline-rich protein 1 (HyPRP1), a negative regulator of salt stress responses, has been edited using a CRISPR-Cas9 multiplexing approach that resulted in precise eliminations of its functional domains, proline-rich domain (PRD) and eight cysteine-motif (8CM). We subsequently demonstrated that eliminating the PRD domain of HyPRP1 in tomatoes conferred the highest level of salinity tolerance. In this study, we characterized the edited lines under several abiotic and biotic stresses to examine the possibility of multiple stress tolerance. Our data reveal that the 8CM removal variants of HK and the KO alleles of both HK and 15T01 cultivars exhibited moderate heat stress tolerance. Similarly, plants carrying either the domains of the PRD removal variant (PR1v1) or 8CM removal variants (PR2v2 and PR2v3) showed better germination under osmosis stress (up to 200 mM mannitol) compared to the WT control. Moreover, the PR1v1 line continuously grew after 5 days of water cutoff. When the edited lines were challenged with pathogenic bacteria of Pseudomonas syringae pv. tomato (Pto) DC3000, the growth of the bacterium was significantly reduced by 2.0- to 2.5-fold compared to that in WT plants. However, the edited alleles enhanced susceptibility against Fusarium oxysporum f. sp. lycopersici, which causes fusarium wilt. CRISPR-Cas9-based precise domain editing of the SlHyPRP1 gene generated multi-stress-tolerant alleles that could be used as genetic materials for tomato breeding.
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Affiliation(s)
- Mil Thi Tran
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
- Crop Science and Rural Development Division, College of Agriculture, Bac Lieu University, Bac Lieu, Vietnam
- Division of Horticultural Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Geon Hui Son
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Seonyeong Park
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Thanh Vu Thach
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jinsu Lee
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki-Ho Son
- Division of Horticultural Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
- Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Hanoi, Vietnam
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
- Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
- Nulla Bio R&D Center, Nulla Bio Inc., Jinju, Republic of Korea
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Vu TV, Doan DTH, Tran MT, Sung YW, Song YJ, Kim JY. Improvement of the LbCas12a-crRNA System for Efficient Gene Targeting in Tomato. Front Plant Sci 2021; 12:722552. [PMID: 34447405 PMCID: PMC8383147 DOI: 10.3389/fpls.2021.722552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/16/2021] [Indexed: 05/03/2023]
Abstract
Plant gene targeting (GT) can be utilized to precisely replace up to several kilobases of a plant genome. Recent studies using the powerful clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nucleases significantly improved plant GT efficiency. However, GT for loci without associated selection markers is still inefficient. We previously utilized Lachnospiraceae bacterium Cas12a (LbCas12a) in combination with a replicon for tomato GT and obtained high GT efficiency with some selection markers. In this study, we advance our GT system by inhibiting the cNHEJ pathway with small chemical molecules such as NU7441. Further optimization of the GT is also possible with the treatment of silver nitrate possibly via its pronounced actions in ethylene inhibition and polyamine production. Importantly, the GT efficiency is significantly enhanced with the use of a temperature-tolerant LbCas12a (ttLbCas12a) that is capable of performing target cleavage even at low temperatures. Targeted deep sequencing, as well as conventional methods, are used for the assessment of the editing efficiency at both cell and plant levels. Our work demonstrates the significance of the selection of gene scissors, the appropriate design and number of LbCas12a crRNAs, the use of chemical treatments, and the establishment of favorable experimental conditions for further enhancement of plant HDR to enable efficient GT in tomato.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Hanoi, Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Crop Science and Rural Development Division, College of Agriculture, Bac Lieu University, Bạc Liêu, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Life Science, Gyeongsang National University, Jinju, South Korea
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Tran MT, Doan DTH, Kim J, Song YJ, Sung YW, Das S, Kim EJ, Son GH, Kim SH, Van Vu T, Kim JY. CRISPR/Cas9-based precise excision of SlHyPRP1 domain(s) to obtain salt stress-tolerant tomato. Plant Cell Rep 2021; 40:999-1011. [PMID: 33074435 DOI: 10.1007/s00299-020-02622-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/03/2020] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE CRISPR/Cas9-based multiplexed editing of SlHyPRP1 resulted in precise deletions of its functional motif(s), thereby resulting in salt stress-tolerant events in cultivated tomato. Crop genetic improvement to address environmental stresses for sustainable food production has been in high demand, especially given the current situation of global climate changes and reduction of the global food production rate/population rate. Recently, the emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-based targeted mutagenesis has provided a revolutionary approach to crop improvement. The major application of CRISPR/Cas in plant genome editing has been the generation of indel mutations via error-prone nonhomologous end joining (NHEJ) repair of DNA DSBs. In this study, we examined the power of the CRISPR/Cas9-based novel approach in the precise manipulation of protein domains of tomato hybrid proline-rich protein 1 (HyPRP1), which is a negative regulator of salt stress responses. We revealed that the precise elimination of SlHyPRP1 negative-response domain(s) led to high salinity tolerance at the germination and vegetative stages in our experimental conditions. CRISPR/Cas9-based domain editing may be an efficient tool to engineer multidomain proteins of important food crops to cope with global climate changes for sustainable agriculture and future food security.
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Affiliation(s)
- Mil Thi Tran
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- Crop Science and Rural Development Division, College of Agriculture, Bac Lieu University, Bac Lieu, 97000, Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Eun-Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Geon Hui Son
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam.
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. Plant Biotechnol J 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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Vu TV, Sivankalyani V, Kim E, Doan DTH, Tran MT, Kim J, Sung YW, Park M, Kang YJ, Kim J. Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato. Plant Biotechnol J 2020; 18:2133-2143. [PMID: 32176419 PMCID: PMC7540044 DOI: 10.1111/pbi.13373] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/08/2020] [Accepted: 02/23/2020] [Indexed: 05/04/2023]
Abstract
Genome editing via the homology-directed repair (HDR) pathway in somatic plant cells is very inefficient compared with error-prone repair by nonhomologous end joining (NHEJ). Here, we increased HDR-based genome editing efficiency approximately threefold compared with a Cas9-based single-replicon system via the use of de novo multi-replicon systems equipped with CRISPR/LbCpf1 in tomato and obtained replicon-free but stable HDR alleles. The efficiency of CRISPR/LbCpf1-based HDR was significantly modulated by physical culture conditions such as temperature and light. Ten days of incubation at 31 °C under a light/dark cycle after Agrobacterium-mediated transformation resulted in the best performance among the tested conditions. Furthermore, we developed our single-replicon system into a multi-replicon system that effectively increased HDR efficiency. Although this approach is still challenging, we showed the feasibility of HDR-based genome editing of a salt-tolerant SlHKT1;2 allele without genomic integration of antibiotic markers or any phenotypic selection. Self-pollinated offspring plants carrying the HKT1;2 HDR allele showed stable inheritance and germination tolerance in the presence of 100 mm NaCl. Our work may pave the way for transgene-free editing of alleles of interest in asexually and sexually reproducing plants.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteBac Tu LiemVietnam
| | - Velu Sivankalyani
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Eun‐Jung Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | | | - Yang Jae Kang
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
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Van Vu T, Sung YW, Kim J, Doan DTH, Tran MT, Kim JY. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. Rice (N Y) 2019; 12:95. [PMID: 31858277 PMCID: PMC6923311 DOI: 10.1186/s12284-019-0355-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/04/2019] [Indexed: 05/18/2023]
Abstract
Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Sung YW, Lee IH, Shim D, Lee KL, Nam KJ, Yang JW, Lee JJ, Kwak SS, Kim YH. Transcriptomic changes in sweetpotato peroxidases in response to infection with the root-knot nematode Meloidogyne incognita. Mol Biol Rep 2019; 46:4555-4564. [PMID: 31222458 DOI: 10.1007/s11033-019-04911-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/13/2022]
Abstract
A previous transcriptomic analysis of the roots of susceptible and resistant cultivars of sweetpotato (Ipomoea batatas) identified genes that were likely to contribute to protection against infection with the root-knot nematode Meloidogyne incognita. The current study examined the roles of peroxidase genes in sweetpotato defense responses during root-knot nematode infection, using the susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) cultivars. Differentially expressed genes were assigned to gene ontology categories to predict their functional roles and associated biological processes. Comparison with Arabidopsis peroxidases identified a group of genes orthologous to Arabidopsis PEROXIDASE 52 (AtPrx52). An analysis of sweetpotato peroxidase genes determined their roles in protecting plants against root-knot nematode infection and enabled identification of important peroxidases. The interactions involved in sweetpotato resistance to nematode infection are discussed.
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Affiliation(s)
- Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.,Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, Republic of Korea
| | - Il Hwan Lee
- Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Kang-Lok Lee
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Ki Jung Nam
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jung-Wook Yang
- National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jeung Joo Lee
- Department of Plant Medicine, IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
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Lee IH, Shim D, Jeong JC, Sung YW, Nam KJ, Yang JW, Ha J, Lee JJ, Kim YH. Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-resistant and susceptible sweetpotato cultivars. Planta 2019; 249:431-444. [PMID: 30232599 DOI: 10.1007/s00425-018-3001-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/29/2018] [Indexed: 05/17/2023]
Abstract
Transcriptome analysis was performed on the roots of susceptible and resistant sweetpotato cultivars infected with the major root-knot nematode species Meloidogyne incognita. In addition, we identified a transcription factor-mediated defense signaling pathway that might function in sweetpotato-nematode interactions. Root-knot nematodes (RKNs, Meloidogyne spp.) are important sedentary endoparasites of many agricultural crop plants that significantly reduce production in field-grown sweetpotato. To date, no studies involving gene expression profiling in sweetpotato during RKN infection have been reported. Therefore, in the present study, transcriptome analysis was performed on the roots of susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) sweetpotato cultivars infected with the widespread, major RKN species Meloidogyne incognita. Using the Illumina HiSeq 2000 platform, we generated 455,295,628 pair-end reads from the fibrous roots of both cultivars, which were assembled into 74,733 transcripts. A number of common and unique genes were differentially expressed in susceptible vs. resistant cultivars as a result of RKN infection. We assigned the differentially expressed genes into gene ontology categories and used MapMan annotation to predict their functional roles and associated biological processes. The candidate genes including hormonal signaling-related transcription factors and pathogenesis-related genes that could contribute to protection against RKN infection in sweetpotato roots were identified and sweetpotato-nematode interactions involved in resistance are discussed.
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Affiliation(s)
- Il Hwan Lee
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Jea Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Ki Jung Nam
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jung-Wook Yang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Joon Ha
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, Republic of Korea
| | - Jeung Joo Lee
- Department of Plant Medicine, IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
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Sung-Chan P, Sung YW, Zhao X, Brownson RC. Family-based models for childhood-obesity intervention: a systematic review of randomized controlled trials. Obes Rev 2013; 14:265-78. [PMID: 23136914 DOI: 10.1111/obr.12000] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 09/19/2012] [Accepted: 09/26/2012] [Indexed: 11/26/2022]
Abstract
Effective interventions are needed to address the growing epidemic of childhood obesity. In the past 35 years, family-based approach has gradually developed as a preferred intervention. This review aimed to examine the methodological rigour and treatment effectiveness of family-based interventions according to intervention types and theoretical orientations. A total of 15 randomized controlled trials (RCTs) of family-based lifestyle interventions for children and adolescents aged 2-19 years were included. The adapted Methodological Quality Rating Scales (MQRS) and a four-grade qualitative scoring scheme were adopted to evaluate the methodological rigour and the effectiveness of treatment, respectively. The average MQRS score was 7.93 out of 14 points. Ten of the 15 RCTs had well aligned their research questions with appropriate research methods. The overall short-term outcome of the15 RCTs were satisfactory with an average score of 3.1. Family-based interventions rooted in behaviour theory achieved better results than those theoretically connected to family systems theory in terms of treatment effectiveness. Results suggest future studies to improve the methodological design and continue to explore the potential of the family systems approach.
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Affiliation(s)
- P Sung-Chan
- Department of Applied Social Sciences, The Hong Kong Polytechnic University, Hong Kong, China.
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11
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Abstract
The nasal cycle in patients with septal deviation was studied by acoustic rhinometric techniques. This study included 24 patients with anteriorly located septal deviations (mean age = 23.5), and 26 normal controls (mean age = 24.7). Data of MCA (minimum cross-sectional area) and NV (nasal volume), collected in 20-minute intervals, were plotted for each subject during 8 hours. Twenty of 24 patients (83%) with septal deviation and 20 of 26 normal subjects (77%) showed at least one complete cycle. Duration of the nasal cycle, which ranged from 100 minutes to 400 minutes, had no statistical difference between the septal deviation group (mean duration of 216 minutes) and the normal control group (mean duration of 227 minutes). The degrees of variation of MCA and NV, defined as Degree of Variation of MCA (%) = 100 (MCAmax - MCAmin)/MCAmax, Degree of Variation of NV (%) = 100 (NVmax - NVmin)/NVmax, which represent the percent change of MCA and NV throughout the study, showed no difference between the wide side and the narrow side, or between the septal deviation group and the normal control group. These findings suggest that the nasal cycle is relatively independent of peripheral anatomic factors for its generation. However, the amplitude of changes of MCA was greater in the wide side, and the sum of both MCAs tended to fluctuate in accordance with the fluctuation of MCA of the wide side. Thus, the nasal cycle seemed to be affected by septal deviation.
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Affiliation(s)
- Y W Sung
- Department of Otolaryngology, College of Medicine, Chung-Nam National University, Taejon, Republic of Korea
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12
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Sung YW. [An experimental study on Korean sounds by palatal thickness by patient with full denture (author's transl)]. Taehan Chikkwa Uisa Hyophoe Chi 1973; 11:801-9. [PMID: 4523387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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