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Ji H, Cheon KS, Shin Y, Lee C, Son S, Oh H, Yoon DK, Lee S, Cho M, Jun S, Lee GS, Baek J, Kim SL, Ahn IP, Oh JH, Yoon HJ, Cha YS, Kim KH. Map-Based Cloning and Characterization of a Major QTL Gene, FfR1, Which Confers Resistance to Rice Bakanae Disease. Int J Mol Sci 2024; 25:6214. [PMID: 38892403 PMCID: PMC11172731 DOI: 10.3390/ijms25116214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, is a serious threat to rice production worldwide. Breeding elite rice varieties resistant to BD requires the identification of resistance genes. Previously, we discovered a resistant quantitative trait locus (QTL), qFfR1, in a Korean japonica rice variety, Nampyeong. In this study, we fine-mapped qFfR1 with a Junam*4/Nampyeong BC3F3 population and delimited its location to a 37.1 kb region on chromosome 1. Complementation experiments with seven candidate genes in this region revealed that OsI_02728 is the gene for qFfR1. This gene encodes a protein with a typical leucine-rich repeat (LRR) receptor-like protein structure. RNA-sequencing-based transcriptomic analysis revealed that FfR1 induces the transcription of defense genes, including lignin and terpenoid biosynthesis genes, pathogenesis-related genes, and thionin genes. These results may facilitate investigations into the molecular mechanisms underlying BD resistance, including molecular patterns of Fusarium fujikuroi interacting with FfR1 and players working in signal transduction pathways downstream of FfR1, and the breeding of new BD-resistant varieties by providing a BD resistance gene with its precise selection marker. This will contribute to efficient control of BD, which is becoming more prevalent according to temperature rises due to climate change.
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Affiliation(s)
- Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Kyeong-Seong Cheon
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Chaewon Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Republic of Korea
| | - Seungmin Son
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Dong-Kyung Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Miryang 50424, Republic of Korea
| | - Seoyeon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Mihyun Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Soojin Jun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Il-Pyung Ahn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Jae-Hyeon Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Hye-Jin Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
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Yang X, Yu S, Yan S, Wang H, Fang W, Chen Y, Ma X, Han L. Progress in Rice Breeding Based on Genomic Research. Genes (Basel) 2024; 15:564. [PMID: 38790193 PMCID: PMC11121554 DOI: 10.3390/genes15050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.
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Affiliation(s)
- Xingye Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Shicong Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Shen Yan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Hao Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Wei Fang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Yanqing Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.Y.); (S.Y.); (H.W.); (W.F.); (Y.C.)
| | - Longzhi Han
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Dipta B, Sood S, Mangal V, Bhardwaj V, Thakur AK, Kumar V, Singh B. KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance. Mol Biol Rep 2024; 51:508. [PMID: 38622474 DOI: 10.1007/s11033-024-09455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.
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Affiliation(s)
- Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India.
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, 305206, India
| | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
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Kushwaha AK, Ellur RK, Maurya SK, Krishnan S. G, Bashyal BM, Bhowmick PK, Vinod KK, Bollinedi H, Singh NK, Singh AK. Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1265176. [PMID: 38023939 PMCID: PMC10667430 DOI: 10.3389/fpls.2023.1265176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.
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Affiliation(s)
- Amar Kant Kushwaha
- Division of Crop Improvement and Biotechnology, Indian Council of Agricultural Research (ICAR)-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sarvesh Kumar Maurya
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopala Krishnan S.
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Prolay Kumar Bhowmick
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - K. K. Vinod
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Haritha Bollinedi
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra Kumar Singh
- National Professor B.P. Pal Chair, Indian Council of Agricultural Research (ICAR)-National Institute of Plant Biotechnology, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Karthik C, Shu Q. Current insights on rice ( Oryza sativa L.) bakanae disease and exploration of its management strategies. J Zhejiang Univ Sci B 2023; 24:755-778. [PMID: 37701954 PMCID: PMC10500098 DOI: 10.1631/jzus.b2300085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/16/2023] [Indexed: 09/14/2023]
Abstract
Bakanae is an emerging rice disease caused by the seed- and soil-borne pathogen Fusariumfujikuroi. It is becoming a more serious threat to sustainable rice production throughout rice-growing regions. Bakanae disease infection is responsible for high yield losses ranging from 3% to 95%, and disease incidence varies based on the region and cultivars. Hence, understanding the nature of the pathogen, its pathogenicity, disease epidemiology, symptoms, host-pathogen interaction, and the role of secondary metabolites in the disease cycle will be helpful in the development of effective and sustainable management strategies. However, very few comprehensive studies have described the details of rice bakanae disease. Thus, in this review we summarize and discuss in detail the information available from 1898 to 2023 on various critical facets of bakanae disease, and provide perspectives on future research.
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Affiliation(s)
- Chinnannan Karthik
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA
| | - Qingyao Shu
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China.
- National Key Laboratory of Rice Biology and Breeding / The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, China.
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An YN, Murugesan C, Choi H, Kim KD, Chun SC. Current Studies on Bakanae Disease in Rice: Host Range, Molecular Identification, and Disease Management. MYCOBIOLOGY 2023; 51:195-209. [PMID: 37711983 PMCID: PMC10498795 DOI: 10.1080/12298093.2023.2241247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 09/16/2023]
Abstract
The seed borne disease such as bakanae is difficult to control. Crop yield loss caused by bakanae depending on the regions and varieties grown, ranging from 3.0% to 95.4%. Bakanae is an important disease of rice worldwide and the pathogen was identified as Fusarium fujikuroi Nirenberg (teleomorph: Gibberella fujikuroi Sawada). Currently, four Fusaria (F. fujikuroi, F. proliferatum, F. verticillioides and F. andiyazi) belonging to F. fujikuroi species complex are generally known as the pathogens of bakanae. The infection occurs through both seed and soil-borne transmission. When infection occurs during the heading stage, rice seeds become contaminated. Molecular detection of pathogens of bakanae is important because identification based on morphological and biological characters could lead to incorrect species designation and time-consuming. Seed disinfection has been studied for a long time in Korea for the management of the bakanae disease of rice. As seed disinfectants have been studied to control bakanae, resistance studies to chemicals have been also conducted. Presently biological control and resistant varieties are not widely used. The detection of this pathogen is critical for seed certification and for preventing field infections. In South Korea, bakanae is designated as a regulated pathogen. To provide highly qualified rice seeds to farms, Korea Seed & Variety Service (KSVS) has been producing and distributing certified rice seeds for producing healthy rice in fields. Therefore, the objective of the study is to summarize the recent progress in molecular identification, fungicide resistance, and the management strategy of bakanae.
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Affiliation(s)
- Yu Na An
- Dongbu Branch Office of Korea Seed & Variety Service, Gimcheon-si, South Korea
| | | | - Hyowon Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju, South Korea
| | - Ki Deok Kim
- Division Biotechnology, College of Life Science, Korea University, Seoul, South Korea
| | - Se-Chul Chun
- Department of Environmental and Health Sciences, Konkuk University, Seoul, South Korea
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Chen SY, Lai MH, Chu YL, Wu DH, Tung CW, Chen YJ, Chung CL. Identification of qBK2.1, a novel QTL controlling rice resistance against Fusarium fujikuroi. BOTANICAL STUDIES 2023; 64:11. [PMID: 37079162 PMCID: PMC10119339 DOI: 10.1186/s40529-023-00375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bakanae disease caused by Fusarium fujikuroi is an increasing threat to rice production. The infected plants show symptoms such as elongation, slenderness, chlorosis, a large leaf angle, and even death. Bakanae disease is traditionally managed by seed treatment. However, fungicide-resistant F. fujikuroi isolates have emerged in several Asian areas, including Taiwan. This study aimed to identify new bakanae resistance quantitative trait loci (QTLs) and provide molecular markers to assist future breeding. RESULTS A population of F2:9 recombinant inbred lines (RILs) was derived from the cross between an elite japonica Taiwanese cultivar 'Taikeng 16 (TK16)' and an indica variety 'Budda'. 'Budda' was found highly resistant to all 24 representative isolates of the F. fujikuroi population in Taiwan. For the RIL population, 6,492 polymorphic single nucleotide polymorphisms (SNPs) spanning the rice genome were obtained by genotyping-by-sequencing (GBS) technique, and the disease severity index (DSI) was evaluated by inoculation with a highly virulent F. fujikuroi isolate Ff266. Trait-marker association analysis of 166 RILs identified two QTLs in 'Budda'. qBK2.1 (21.97-30.15 Mb) is a novel and first bakanae resistance QTL identified on chromosome 2. qBK1.8 (5.24-8.66 Mb) partially overlaps with the previously reported qBK1.3 (4.65-8.41 Mb) on chromosome 1. The log of odds (LOD) scores of qBK1.8 and qBK2.1 were 4.75 and 6.13, accounting for 4.9% and 8.1% of the total phenotypic variation, respectively. 64 RILs carrying both qBK1.8 and qBK2.1 showed lower DSI (7%) than the lines carrying only qBK1.8 (15%), only qBK2.1 (13%), or none of the two QTLs (21%). For the future application of identified QTLs, 11 KBioscience competitive allele-specific PCR (KASP) markers and 3 insertion-deletion (InDel) markers were developed. CONCLUSIONS Compared to other important rice diseases, knowledge of bakanae resistance has been insufficient, which limited the development and deployment of resistant cultivars. The discovery of qBK2.1 has provided a new source of bakanae resistance. The resistant RILs inheriting good plant type, good taste, and high yield characteristics from 'TK16' can be used as good resistance donors. Our newly developed markers targeting qBK2.1 and qBK1.8 can also serve as an important basis for future fine-mapping and resistance breeding.
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Affiliation(s)
- Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 413008, Taiwan
| | - Yi-Ling Chu
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 413008, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Yue-Jie Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 106319, Taiwan.
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Shin S, Ryu H, Jung JY, Yoon YJ, Kwon G, Lee N, Kim NH, Lee R, Oh J, Baek M, Choi YS, Lee J, Kim KH. Past and Future Epidemiological Perspectives and Integrated Management of Rice Bakanae in Korea. THE PLANT PATHOLOGY JOURNAL 2023; 39:1-20. [PMID: 36760045 PMCID: PMC9929170 DOI: 10.5423/ppj.rw.08.2022.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/18/2023]
Abstract
In the past, rice bakanae was considered an endemic disease that did not cause significant losses in Korea; however, the disease has recently become a serious threat due to climate change, changes in farming practices, and the emergence of fungicide-resistant strains. Since the bakanae outbreak in 2006, its incidence has gradually decreased due to the application of effective control measures such as hot water immersion methods and seed disinfectants. However, in 2013, a marked increase in bakanae incidence was observed, causing problems for rice farmers. Therefore, in this review, we present the potential risks from climate change based on an epidemiological understanding of the pathogen, host plant, and environment, which are the key elements influencing the incidence of bakanae. In addition, disease management options to reduce the disease pressure of bakanae below the economic threshold level are investigated, with a specific focus on resistant varieties, as well as chemical, biological, cultural, and physical control methods. Lastly, as more effective countermeasures to bakanae, we propose an integrated disease management option that combines different control methods, including advanced imaging technologies such as remote sensing. In this review, we revisit and examine bakanae, a traditional seed-borne fungal disease that has not gained considerable attention in the agricultural history of Korea. Based on the understanding of the present significance and anticipated risks of the disease, the findings of this study are expected to provide useful information for the establishment of an effective response strategy to bakanae in the era of climate change.
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Affiliation(s)
- Soobin Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Hyunjoo Ryu
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju 55365,
Korea
| | - Jin-Yong Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Yoon-Ju Yoon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Gudam Kwon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Nahyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Na Hee Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Rowoon Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Jiseon Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Minju Baek
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Yoon Soo Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Jungho Lee
- Interdisciplinary Program of Agriculture and Forest Meteorology, Seoul National University, Seoul 08826,
Korea
| | - Kwang-Hyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
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Shakeel Q, Mubeen M, Sohail MA, Ali S, Iftikhar Y, Tahir Bajwa R, Aqueel MA, Upadhyay SK, Divvela PK, Zhou L. An explanation of the mystifying bakanae disease narrative for tomorrow's rice. Front Microbiol 2023; 14:1153437. [PMID: 37143531 PMCID: PMC10151534 DOI: 10.3389/fmicb.2023.1153437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023] Open
Abstract
Rice production is severely hampered by the bakanae disease (Fusarium fujikuroi), formerly recognized as Fusarium moniliforme. F. moniliforme was called the F. fujikuroi species complex (FFSC) because it was later discovered that it had some separate species. The FFSC's constituents are also well recognized for producing phytohormones, which include auxins, cytokinin, and gibberellins (GAs). The normal symptoms of bakanae disease in rice are exacerbated by GAs. The members of the FFSC are responsible for the production of fumonisin (FUM), fusarins, fusaric acid, moniliformin, and beauvericin. These are harmful to both human and animal health. This disease is common around the world and causes significant yield losses. Numerous secondary metabolites, including the plant hormone gibberellin, which causes classic bakanae symptoms, are produced by F. fujikuroi. The strategies for managing bakanae, including the utilization of host resistance, chemical compounds, biocontrol agents, natural goods, and physical approaches, have been reviewed in this study. Bakanae disease is still not entirely preventable, despite the adoption of many different tactics that have been used to manage it. The benefits and drawbacks of these diverse approaches are discussed by the authors. The mechanisms of action of the main fungicides as well as the strategies for resistance to them are outlined. The information compiled in this study will contribute to a better understanding of the bakanae disease and the development of a more effective management plan for it.
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Affiliation(s)
- Qaiser Shakeel
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Cholistan Institute of Desert Studies, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sajjad Ali
- Department of Entomology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasir Iftikhar
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
- Yasir Iftikhar
| | - Rabia Tahir Bajwa
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Muhammad Anjum Aqueel
- Department of Entomology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sudhir K. Upadhyay
- Department of Environmental Science, VBS Purvanchal University, Jaunpur, Uttar Pradesh, India
| | | | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Lei Zhou
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Lee C, Cheon KS, Shin Y, Oh H, Jeong YM, Jang H, Park YC, Kim KY, Cho HC, Won YJ, Baek J, Cha YS, Kim SL, Kim KH, Ji H. Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice. Genes (Basel) 2022; 13:genes13050794. [PMID: 35627177 PMCID: PMC9141132 DOI: 10.3390/genes13050794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.
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Affiliation(s)
- Chaewon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyeong-Seong Cheon
- Division of Forest Tree Improvement and Biotechnology, Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea;
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Genecell Biotech Inc., Wanju, 55322, Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Korea Agriculture Technology Promotion Agency (KOAT), Gimje 54324, Korea;
| | - Hoon Jang
- CELEMICS, Seoul 08506, Korea; (H.J.); (Y.-C.P.)
| | | | - Kyung-Yun Kim
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Hang-Chul Cho
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Yong-Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Song-Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Correspondence: ; Tel.: +82-63-238-4657
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Sun Y, Shi H, Mao C, Wu J, Zhang C. Activity of a SDHI fungicide penflufen and the characterization of natural-resistance in Fusarium fujikuroi. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 179:104960. [PMID: 34802512 DOI: 10.1016/j.pestbp.2021.104960] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
The occurrence of bakanae disease of rice caused by the fungus Fusarium fujikuroi in Zhejiang Province has become increasingly aggravated in recent years, concomitant with the development of resistance to the widely applied fungicides, prochloraz and phenamacril. In this study, the activity of a novel succinate dehydrogenase inhibitor (SDHI) fungicide, penflufen, against different fungi was evaluated in addition to the potential of penflufen in controlling F. fujikuroi infections. Penflufen exhibited good bioactivity against F. fujikuroi, but weak activity against Fusarium spp. and other investigated plant-pathogenic fungi including Colletotrichum spp. In addition to inhibiting mycelial growth, penflufen effectively inhibited F. fujikuroi conidium production. For germination, penflufen could effectively inhibit that of small conidia, but only delay the germination of large conidia. In addition, the sensitivity to penflufen among 100 F. fujikuroi isolates that were collected in areas that were never exposed to SDHIs was determined based on mycelium growth. Sensitivities surprisingly exhibited bimodal distributions, indicating the presence of natural resistance. Cross-resistance was not observed between penflufen in F. fujikuroi and two fungicides that have been extensively applied in field including prochloraz (a DMI) and phenamacril (a 2-cyanoacrylate fungicide), nor with the three SDHIs, fluopyram, benzovindiflupyr, and pydiflumetofen. Additional analysis identified five different point mutations in SDH-A (i.e., at residues 46, 225, 283, 430, and 586) of naturally resistant isolates. These results inform the potential application of the new SDHI fungicide penflufen for managing crop diseases and understanding possible resistance mechanisms among pathogens.
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Affiliation(s)
- Yanan Sun
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Haiping Shi
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chenxin Mao
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Jianyan Wu
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chuanqing Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China.
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Ji H, Shin Y, Lee C, Oh H, Yoon IS, Baek J, Cha YS, Lee GS, Kim SL, Kim KH. Genomic Variation in Korean japonica Rice Varieties. Genes (Basel) 2021; 12:genes12111749. [PMID: 34828355 PMCID: PMC8623644 DOI: 10.3390/genes12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022] Open
Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties.
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Bai Y, Gu CY, Pan R, Abid M, Zang HY, Yang X, Tan GJ, Chen Y. Activity of A Novel Succinate Dehydrogenase Inhibitor Fungicide Pydiflumetofen Against Fusarium fujikuroi causing Rice Bakanae Disease. PLANT DISEASE 2021; 105:3208-3217. [PMID: 33560887 DOI: 10.1094/pdis-10-20-2274-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New fungicides are tools to manage fungal diseases and overcome emerging resistance in fungal pathogens. In this study, a total of 121 Fusarium fujikuroi isolates were collected from various geographical regions of China and their sensitivity to a novel succinate dehydrogenase inhibitor (SDHI) fungicide 'pydiflumetofen' was evaluated. The 50% effective concentration (EC50) value of pydiflumetofen for mycelial growth suppression ranged from 0.0101 to 0.1012 μg/ml and for conidial germination inhibition ranged from 0.0051 to 0.1082 μg/ml. Pydiflumetofen-treated hyphae showed contortion and increased branching, cell membrane permeability, and glycerol content significantly. The result of electron microscope transmission indicated that pydiflumetofen damaged the mycelial cell wall and the cell membrane, and almost broke up the cells, which increased the intracellular plasma leakage. There was no cross-resistance between pydiflumetofen and the widely used fungicides such as carbendazim, prochloraz, and phenamacril. Pydiflumetofen was found safe to seeds and rice seedlings of four rice cultivars, used up to 400 μg/ml. Seed treatment significantly decreased the rate of diseased plants in the greenhouse as well as in field trials in 2017 and 2018. Pydiflumetofen showed superb results against the rice bakanae disease (RBD), when used at 10 or 20 g a.i./100 kg of treated seeds, providing over 90% control efficacy (the maximum control efficacy was up to 97%), which was significantly higher than that of 25% phenamacril (SC) at 10 g or carbendazim at 100 g. Pydiflumetofen is highly effective against F. fujikuroi growth and sporulation as well as RBD in the field.
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Affiliation(s)
- Yang Bai
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Rui Pan
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Muhammad Abid
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Gen-Jia Tan
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Integrated Pest Management on crops, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agicultural University, Hefei 230036, China
| | - Yu Chen
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Integrated Pest Management on crops, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agicultural University, Hefei 230036, China
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14
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Lee SB, Kim N, Jo S, Hur YJ, Lee JY, Cho JH, Lee JH, Kang JW, Song YC, Bombay M, Kim SR, Lee J, Seo YS, Ko JM, Park DS. Mapping of a Major QTL, qBK1Z, for Bakanae Disease Resistance in Rice. PLANTS 2021; 10:plants10030434. [PMID: 33668736 PMCID: PMC7996363 DOI: 10.3390/plants10030434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022]
Abstract
Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two RM (Rice Microsatellite) markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.
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Affiliation(s)
- Sais-Beul Lee
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Namgyu Kim
- Department of Microbiology, Pusan National University, Pusan 46241, Korea; (N.K.); (Y.-S.S.)
| | - Sumin Jo
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Yeon-Jae Hur
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Ji-Youn Lee
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Jun-Hyeon Cho
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Jong-Hee Lee
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Ju-Won Kang
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - You-Chun Song
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Maurene Bombay
- International Rice Research Institute, Pili Drive, Los Baños 4031, Laguna, Philippines; (M.B.); (S.-R.K.)
| | - Sung-Ryul Kim
- International Rice Research Institute, Pili Drive, Los Baños 4031, Laguna, Philippines; (M.B.); (S.-R.K.)
| | - Jungkwan Lee
- College of Natural Resources and Life Science, Dong-A University, Pusan 49135, Korea;
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Pusan 46241, Korea; (N.K.); (Y.-S.S.)
| | - Jong-Min Ko
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
| | - Dong-Soo Park
- National Institute of Crop Science, Milyang 50424, Korea; (S.-B.L.); (S.J.); (Y.-J.H.); (J.-Y.L.); (J.-H.C.); (J.-H.L.); (J.-W.K.); (Y.-C.S.); (J.-M.K.)
- International Rice Research Institute, Pili Drive, Los Baños 4031, Laguna, Philippines; (M.B.); (S.-R.K.)
- Correspondence: ; Tel.: +82-55-530-1184
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15
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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16
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Cheon KS, Jeong YM, Oh H, Oh J, Kang DY, Kim N, Lee E, Baek J, Kim SL, Choi I, Yoon IS, Kim KH, Won YJ, Cho YI, Han JH, Ji H. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties. PLANTS 2020; 9:plants9111531. [PMID: 33182649 PMCID: PMC7698039 DOI: 10.3390/plants9111531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 12/02/2022]
Abstract
Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.
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Affiliation(s)
- Kyeong-Seong Cheon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje 54324, Korea;
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Jun Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Do-Yu Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Nyunhee Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Eungyeong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Inchan Choi
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - In Sun Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Young-il Cho
- Seed Business Team, Department of Seed Services, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Iksan 54667, Korea;
| | - Jung-Heon Han
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
- Correspondence:
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Cheng AP, Chen SY, Lai MH, Wu DH, Lin SS, Chen CY, Chung CL. Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi. RICE (NEW YORK, N.Y.) 2020; 13:65. [PMID: 32910281 PMCID: PMC7483690 DOI: 10.1186/s12284-020-00426-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/02/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. RESULTS This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK. CONCLUSIONS Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi-colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.
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Affiliation(s)
- An-Po Cheng
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 10617 Taiwan
| | - Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 10617 Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 41362 Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist, Taichung City, 41362 Taiwan
- Department of Agronomy, National Chung Hsing University, No. 145, Xingda Rd., South Dist, Taichung City, 40227 Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 10617 Taiwan
| | - Chieh-Yi Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 10617 Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei City, 10617 Taiwan
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Monitoring Phenolic Compounds in Rice during the Growing Season in Relation to Fungal and Mycotoxin Contamination. Toxins (Basel) 2020; 12:toxins12050341. [PMID: 32455855 PMCID: PMC7291125 DOI: 10.3390/toxins12050341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
Total phenolic content (TPC) and several phenolic acids present in rice grains were compared with fungal infection and mycotoxin presence throughout the growing season. Samples of 4 rice varieties were collected in 2018 and 2019 at 3 different plant phenological stages. Total fungal and main mycotoxigenic fungi incidence were checked and mycotoxin content was analysed. On the same samples, TPC and the concentration of 8 main phenolic acids (chlorogenic acid, caffeic acid, syringic acid, 4-hydroxybenzoic acid (4-HBA), p-coumaric acid, ferulic acid, protocatecuic acid and gallic acid) were measured. The results showed significant differences between years for both fungal incidence and mycotoxin presence. In 2018 there was a lower fungal presence (42%) than in 2019 (57%) while, regarding mycotoxins, sterigmatocystin (STC) was found in almost all the samples and at all growing stages while deoxynivalenol (DON) was found particularly during ripening. An interesting relationship was found between fungal incidence and TPC, and some phenolic acids seemed to be more involved than others in the plant defense system. Ferulic acid and protocatecuic acid showed a different trend during the growing season depending on fungal incidence and resulted to be positively correlated with p-coumaric acid and 4-HBA that seem involved in mycotoxin containment in field.
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Chromosomal Distribution of Genes Conferring Tolerance to Abiotic Stresses Versus That of Genes Controlling Resistance to Biotic Stresses in Plants. Int J Mol Sci 2020; 21:ijms21051820. [PMID: 32155784 PMCID: PMC7084258 DOI: 10.3390/ijms21051820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
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