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Chen S, Lu X, Fang H, Perumal AB, Li R, Feng L, Wang M, Liu Y. Early surveillance of rice bakanae disease using deep learning and hyperspectral imaging. ABIOTECH 2024; 5:281-297. [PMID: 39279856 PMCID: PMC11399517 DOI: 10.1007/s42994-024-00169-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/04/2024] [Indexed: 09/18/2024]
Abstract
Bakanae disease, caused by Fusarium fujikuroi, poses a significant threat to rice production and has been observed in most rice-growing regions. The disease symptoms caused by different pathogens may vary, including elongated and weak stems, slender and yellow leaves, and dwarfism, as example. Bakanae disease is likely to cause necrosis of diseased seedlings, and it may cause a large area of infection in the field through the transmission of conidia. Therefore, early disease surveillance plays a crucial role in securing rice production. Traditional monitoring methods are both time-consuming and labor-intensive and cannot be broadly applied. In this study, a combination of hyperspectral imaging technology and deep learning algorithms were used to achieve in situ detection of rice seedlings infected with bakanae disease. Phenotypic data were obtained on the 9th, 15th, and 21st day after rice infection to explore the physiological and biochemical performance, which helps to deepen the research on the disease mechanism. Hyperspectral data were obtained over these same periods of infection, and a deep learning model, named Rice Bakanae Disease-Visual Geometry Group (RBD-VGG), was established by leveraging hyperspectral imaging technology and deep learning algorithms. Based on this model, an average accuracy of 92.2% was achieved on the 21st day of infection. It also achieved an accuracy of 79.4% as early as the 9th day. Universal characteristic wavelengths were extracted to increase the feasibility of using portable spectral equipment for field surveillance. Collectively, the model offers an efficient and non-destructive surveillance methodology for monitoring bakanae disease, thereby providing an efficient avenue for disease prevention and control. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00169-1.
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Affiliation(s)
- Sishi Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
| | - Xuqi Lu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
| | - Hongda Fang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058 China
| | - Anand Babu Perumal
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
- Computational Modeling and Nanoscale Processing Unit, National Institute of Food Technology, Entrepreneurship and Management - Thanjavur, Ministry of Food Processing Industries, Thanjavur, 613005 India
| | - Ruyue Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Lei Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058 China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
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Zhang C, Zhao T, Li J, Liu X, Wang W, Huang X, Liu Y, Sun Y, Wei P. Ultrasensitive and on-site diagnosis of rice bakanae disease based on CRISPR-LbCas12a coupled with LAMP. PEST MANAGEMENT SCIENCE 2024. [PMID: 39183634 DOI: 10.1002/ps.8390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/20/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Rice bakanae disease (RBD) has longstanding challenges impacted rice production, which is predominantly induced by Fusarium fujikuroi Nirenberg. Early diagnosis of F. fujikuroi is important to control RBD and improve quality and quantity of rice production. This study presents a novel on-site diagnosis platform combined with CRISPR/LbCas12a and LAMP to detect F. fujikuroi. RESULTS LAMP amplification of TEF1-α, a characteristic gene of F. fujikuroi were performed, followed with trans-cleavage reaction of LbCas12a, cleaving the single-stranded DNA reporter, which is modified by the terminal fluorophore and quencher groups, producing fluorescence signal. The platform was confirmed with high specificity and sensitivity (LOD <1 aM). Furthermore, we designed a lateral flow strip experiment based on the trans-cleavage activity of LbCas12a, which was identified with similar sensitivity and specificity to the fluorescence detection method. CONCLUSION In summary, this study achieved a platform with remarkable sensitivity and specificity for F. fujikuroi detection and provide potential for on-site and ultrasensitive diagnostic tools for RBD. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chao Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Tianyue Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Jianhang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xiaoshuang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Wenting Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xuanda Huang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Yu Liu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Yang Sun
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Pengcheng Wei
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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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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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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Peringottillam M, Sundaram KT, Manickavelu A. Genetic potential of grain-related traits in rice landraces: phenomics and multi-locus association analyses. Mol Biol Rep 2023; 50:9323-9334. [PMID: 37815669 DOI: 10.1007/s11033-023-08807-5] [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: 06/23/2023] [Accepted: 09/07/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Grain length, width, weight, and the number of grains per panicle are crucial determinants contributing to yield in cereal crops. Understanding the genetic basis of grain-related traits has been the main research object in crop science. METHODS AND RESULTS Kerala has a collection of different rice landraces. Characterization of these valuable genetic resources for 39 distinct agro-morphological traits was carried out in two seasons from 2017 to 2019 directly in farmers field. Most characteristics were polymorphic except ligule shape, leaf angle, and panicle axis. The results of principal component analysis implied that leaf length, plant height, culm length, flag leaf length, and grain-related traits were the principal discriminatory characteristics of rice landraces. For identifying the genetic basis of key grain traits of rice, three multi locus GWAS models were performed based on 1,47,994 SNPs in 73 rice accessions. As a result, 48 quantitative trait nucleotides (QTNs) were identified to be associated with these traits. After characterization of their function and expression, 15 significant candidate genes involved in regulating grain width, number of grains per panicle, and yield were identified. CONCLUSIONS The detected QTNs and candidate genes in this study could be further used for marker-assisted high-quality breeding of rice.
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Affiliation(s)
- Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod, 671316, Kerala, India
| | - Krishna T Sundaram
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod, 671316, Kerala, India
- International Rice Research Institute (IRRI), South Asia hub, Patancheru, India
| | - Alagu Manickavelu
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod, 671316, Kerala, 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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Song G, Son S, Nam S, Suh EJ, Lee SI, Park SR. OsWRKY114 Is a Player in Rice Immunity against Fusarium fujikuroi. Int J Mol Sci 2023; 24:ijms24076604. [PMID: 37047576 PMCID: PMC10094899 DOI: 10.3390/ijms24076604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Every year, invasive pathogens cause significant damage to crops. Thus, identifying genes conferring broad-spectrum resistance to invading pathogens is critical for plant breeding. We previously demonstrated that OsWRKY114 contributes to rice (Oryza sativa L.) immunity against the bacterial pathovar Xanthomonas oryzae pv. oryzae (Xoo). However, it is not known whether OsWRKY114 is involved in defense responses to other pathogens. In this study, we revealed that OsWRKY114 enhances innate immunity in rice against the fungal pathogen Fusarium fujikuroi, which is the causal agent of bakanae disease. Transcript levels of various gibberellin-related genes that are required for plant susceptibility to F. fujikuroi were reduced in rice plants overexpressing OsWRKY114. Analysis of disease symptoms revealed increased innate immunity against F. fujikuroi in OsWRKY114-overexpressing rice plants. Moreover, the expression levels of OsJAZ genes, which encode negative regulators of jasmonic acid signaling that confer immunity against F. fujikuroi, were reduced in OsWRKY114-overexpressing rice plants. These results indicate that OsWRKY114 confers broad-spectrum resistance not only to Xoo but also to F. fujikuroi. Our findings provide a basis for developing strategies to mitigate pathogen attack and improve crop resilience to biotic stress.
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Affiliation(s)
- Giha Song
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Seungmin Son
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Suhyeon Nam
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
- Department of Crop Science & Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Eun-Jung Suh
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Soo In Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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11
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Genetic analysis for detection of genes associated to drought tolerance in rice accessions belonging to north east India. Mol Biol Rep 2023; 50:1993-2006. [PMID: 36536186 DOI: 10.1007/s11033-022-08145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The North East (NE) India is rich in biodiversity and also considered as the secondary centre for origin of rice. The NE rice accessions was characterized previously using genetic markers and morphological traits. Simultaneously, genome-wide association studies (GWAS) reveal significant marker-trait associations for the drought tolerance traits. METHODS AND RESULTS The genetic diversity and population structure of 296 NE rice accessions were studied using 96,712 single nucleotide polymorphism (SNP) markers distributed across 12 chromosomes. The accessions were clustered into two major sub-groups (SG). A total of 91 accessions were assembled as SG1 and 114 accessions as SG2, while the remaining 91 were admixture genotypes. A total of 200 genotypes belonging to different groups were phenotyped for yield component traits under drought and control conditions. The GWAS was performed to identify significant marker-trait associations (MTAs). Consequently, 47 MTAs were detected under drought, exhibiting 0.02-9.95% of phenotypic variance (P.V.). Whereas 58 MTAs were discovered under control conditions, showing a 0.01-9.74% contribution to the phenotype. Through in-silico mining of QTLs, 2999 genes were identified. Among these; only 22 genes were directly associated with stress response. CONCLUSION These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in popular drought susceptible rice varieties.
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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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13
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Bashyal BM, Rawat K, Parmar P, Gupta AK, Gupta S, Krishnan SG, Choudhary R, Ercisli S, Kovacevic A, Aggarwal R. Transcriptomic analysis of bakanae disease resistant and susceptible rice genotypes in response to infection by Fusarium fujikuroi. Mol Biol Rep 2022; 49:11959-11972. [PMID: 36271308 DOI: 10.1007/s11033-022-07877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/21/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Fusarium fujikuroi causing bakanae is one of the most significant pathogens of rice and much responsible for yield losses thereby emerging as a major risk to food security. METHODS In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs. C101A51 inoculated (CI); Rasi control (RC) vs. Rasi inoculated (RI) and C101A51 inoculated (CI) vs. Rasi inoculated (RI). RESULTS In CC vs. CI commonly expressed genes were 12,764. Out of them 567 (4%) were significantly upregulated and 1399 (9%) genes were downregulated. For the RC vs. RI 14, 333 (79%) genes were commonly expressed. For CI vs. RI 13,662 (72%) genes were commonly expressed. Genes related to cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme were upregulated in resistant genotype C101A51. Whereas, genes related to GDSL esterase/lipase, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1-related protein, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and β-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions. CONCLUSION Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the first transcriptomic study against bakanae disease of rice in Indian genotypes. Further, functional studies on identified genes and their utilization through different methodology will be helpful for the development of bakanae disease management strategies.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India.
| | - Kirti Rawat
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Ashish Kumar Gupta
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Sangeeta Gupta
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Ravish Choudhary
- Division of Seed Science and Technology, Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey
| | - Antonija Kovacevic
- BIOTECH - Center for Biotechnological Research and Development, Ivana Cankara 76, 35 000, Slavonski Brod, Croatia
| | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
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14
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Veisi S, Sabouri A, Abedi A. Meta-analysis of QTLs and candidate genes associated with seed germination in rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1587-1605. [PMID: 36389095 PMCID: PMC9530108 DOI: 10.1007/s12298-022-01232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/18/2022] [Accepted: 09/16/2022] [Indexed: 06/12/2023]
Abstract
Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01232-1.
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Affiliation(s)
- Sheida Veisi
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran
| | - Atefeh Sabouri
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P.O. Box: 41635-1314, Rasht, Iran
| | - Amin Abedi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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15
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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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16
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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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Al-Tamimi N, Oakey H, Tester M, Negrão S. Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods Mol Biol 2021; 2238:339-375. [PMID: 33471343 DOI: 10.1007/978-1-0716-1068-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.
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Affiliation(s)
- Nadia Al-Tamimi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Oakey
- School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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18
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Son S, Kim H, Lee KS, Kim S, Park SR. Rice glutaredoxin GRXS15 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae and Fusarium fujikuroi. Biochem Biophys Res Commun 2020; 533:1385-1392. [DOI: 10.1016/j.bbrc.2020.10.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/04/2023]
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19
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Chen CY, Chen SY, Liu CW, Wu DH, Kuo CC, Lin CC, Chou HP, Wang YY, Tsai YC, Lai MH, Chung CL. Invasion and Colonization Pattern of Fusarium fujikuroi in Rice. PHYTOPATHOLOGY 2020; 110:1934-1945. [PMID: 32689901 DOI: 10.1094/phyto-03-20-0068-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bakanae disease in rice can cause abnormal elongation of the stem and leaves, development of adventitious roots, a larger leaf angle, and even death. Little is known about the infection, colonization, and distribution of Fusarium fujikuroi in rice plants across different growth stages. In this study, microscopic observation and quantitative real-time PCR were combined to investigate the pathogenesis of bakanae, using artificially inoculated seedlings of a susceptible rice cultivar, Zerawchanica karatals (ZK), a resistant cultivar, Tainung 67 (TNG67), naturally infected adult field plants (cultivars Kaohsiung 139, Taikeng 2, and Tainan 11), and an F. fujikuroi isolate expressing green fluorescent protein. In rice seedlings, F. fujikuroi hyphae were found to directly penetrate the epidermis of basal stems and roots, then extend inter- and intracellularly to invade the vascular bundles. Occlusion of vascular bundles and radial hyphal expansion from vascular bundles to surrounding parenchyma were observed in adult plants. Analysis of consecutive 3-cm segments of the whole plant revealed that F. fujikuroi was largely confined to the embryo, basal stem, and basal roots in seedlings, and distributed unevenly in the lower aerial parts (including nodes and internodes) of adult plants. The elongation and development of adventitious roots did not necessarily correlate with the amount of F. fujikuroi in diseased plants. Treatment of rice seeds with gibberellic acid-3 (GA3) at 0.5 mg/liter resulted in significantly more elongation of ZK than TNG67 seedlings, suggesting that the susceptibility of ZK to bakanae is associated with its higher sensitivity to GA3.
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Affiliation(s)
- Chieh-Yi Chen
- 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
| | - Chun-Wei Liu
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, No. 189, Chung-Cheng Road, Wufeng, Taichung City 41203, Taiwan
- Department of Agronomy, National Chung Hsing University, No. 145, Xingda Rd., South District, Taichung City 40227, Taiwan
| | - Chien-Chih Kuo
- Crop Environment Section, Taichung District Agricultural Research and Extension Station, Council of Agriculture, No. 370, Song Hwai Road, Tatsuen Hsiang, Changhua County 51544, Taiwan
| | - Chun-Chi Lin
- Crop Environment Section, Taitung District Agricultural Research and Extension Station, Council of Agriculture, No. 675, Chunghua Rd., Sec. 1, Taitung City 95055, Taiwan
| | - Hau-Ping Chou
- Crop Environment Section, Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 2-6 Dehe Rd., Dehe Village, Changjhih Township, Pingtung County 90846, Taiwan
| | - Yu-Yao Wang
- Crop Environment Section, Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 2-6 Dehe Rd., Dehe Village, Changjhih Township, Pingtung County 90846, Taiwan
| | - Yi-Chen Tsai
- Crop Environment Section, Hualien District Agricultural Research and Extension Station, Council of Agriculture, No. 150, Sec. 2, Ji'an Rd., Ji'an Township, Hualien County 97365, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, No. 189, Chung-Cheng Road, Wufeng, Taichung City 41203, 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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Volante A, Tondelli A, Desiderio F, Abbruscato P, Menin B, Biselli C, Casella L, Singh N, McCouch SR, Tharreau D, Zampieri E, Cattivelli L, Valè G. Genome wide association studies for japonica rice resistance to blast in field and controlled conditions. RICE (NEW YORK, N.Y.) 2020; 13:71. [PMID: 33030605 PMCID: PMC7544789 DOI: 10.1186/s12284-020-00431-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/24/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. RESULTS The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11-2 and BRGC11-3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. CONCLUSIONS We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
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Affiliation(s)
- Andrea Volante
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Present Address: CREA Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038, Sanremo, IM, Italy.
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Pamela Abbruscato
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
| | - Barbara Menin
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Via Livorno 60, 10144, Torino, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Laura Casella
- SA.PI.SE. Coop. Agricola, via G. Mameli 7, 13100, Vercelli, Italy
| | - Namrata Singh
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Didier Tharreau
- UMR BGPI, CIRAD, TA A54/K, F 34398, Montpellier, France
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Elisa Zampieri
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Present Address: Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Dipartimento di Scienze e Innovazione Tecnologica, Complesso Universitario S. Giuseppe, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy.
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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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Chen SY, Lai MH, Tung CW, Wu DH, Chang FY, Lin TC, Chung CL. Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem. RICE (NEW YORK, N.Y.) 2019; 12:85. [PMID: 31754813 PMCID: PMC6872702 DOI: 10.1186/s12284-019-0337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/15/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties. RESULTS A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance. CONCLUSIONS This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.
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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, 10617 Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City, 41362 Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City, 10617 Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City, 41362 Taiwan
| | - Fang-Yu Chang
- Kaohsiung District Agricultural Research and Extension Station, No.2-6, Dehe Rd., Changzhi Township, Pingtung County, 90846 Taiwan
| | - Tsung-Chun Lin
- Plant Pathology Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City, 41362 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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GWAS for Starch-Related Parameters in Japonica Rice ( Oryza sativa L.). PLANTS 2019; 8:plants8080292. [PMID: 31430915 PMCID: PMC6724095 DOI: 10.3390/plants8080292] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/28/2022]
Abstract
Rice quality is mainly related to the following two starch components, apparent amylose content (AAC) and resistant starch (RS). The former affects grain cooking properties, while RS acts as a prebiotic. In the present study, a Genome Wide Association Scan (GWAS) was performed using 115 rice japonica accessions, including tropical and temperate genotypes, with the purpose of expanding the knowledge of the genetic bases affecting RS and AAC. High phenotypic variation was recorded for the two traits, which positively correlated. Moreover, both the parameters correlated with seed length (positive correlation) and seed width (negative correlation). A correlational selection according to human preferences has been hypothesized for the two starch traits and grain size. In addition, human selection has been proposed as the causal agent even for the different phenotypes related to starch and grain size showed by the tropical and temperate japonica accessions utilized in this study. The present GWAS led to the identification of 11 associations for RS on seven chromosomes and five associations for AAC on chromosome 6. Candidate genes and co-positional relationships with quantitative trait loci (QTLs) previously identified as affecting RS and AAC were identified for 6 associations. The candidate genes and the new RS- and/or AAC-associated regions detected provide valuable sources for future functional characterizations and for breeding programs aimed at improving rice grain quality.
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Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi. Int J Mol Sci 2019; 20:ijms20102598. [PMID: 31137840 PMCID: PMC6566380 DOI: 10.3390/ijms20102598] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, ‘Samgwang’ and ‘Junam’, respectively. Resequencing of ‘Junam’ and ‘Samgwang’ genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24–7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the ‘Junam’ and ‘Samgwang’ genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.
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25
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Lee SB, Kim N, Hur YJ, Cho SM, Kim TH, Lee JY, Cho JH, Lee JH, Song YC, Seo YS, Ko JM, Park DS. Fine mapping of qBK1, a major QTL for bakanae disease resistance in rice. RICE (NEW YORK, N.Y.) 2019; 12:36. [PMID: 31089902 PMCID: PMC6517470 DOI: 10.1186/s12284-019-0295-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/26/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. Incidence of rice bakanae disease creates serious problems in the foremost rice growing countries, and no rice variety has been found to be completely resistant to this disease. However, breeding rice varieties resistant to bakanae disease may be a cost-saving solution preferable to the application of fungicides. In this study, we aimed to determine the exact position and the candidate gene for qBK1, a major resistant quantitative trait locus (QTLs) for bakanae disease. RESULTS The genotypes/phenotypes of recombinants selected from backcrossed recombinant inbred lines of two rice varieties, Shingwang (resistant) and Ilpum (susceptible), indicated that the locus qBK1, conferring resistance to bakanae disease in Shingwang, was delimited to a 35-kb interval delimited by InDel 18 (23.637 Mbp) and InDel 19-14 (23.672 Mbp). Sequence analysis of this 35-kb region revealed four candidate genes, LOC_Os01g41770, LOC_Os01g41780, LOC_Os01g41790, and LOC_Os01g41800. There were many non-synonymous SNPs in LOC_Os01g41770 and the transcript of LOC_Os01g41790 was early terminated in Shingwang, whereas there were no differences in both LOC_Os01g41780 and LOC_Os01g41800 sequences between Ilpum and Shingwang. Expression profiling of the four candidate genes showed the up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790 in Ilpum and of LOC_Os01g41800 in Shingwang after inoculation of G. fujikuroi. CONCLUSION Utilization of marker-assisted selection (MAS) with a precise molecular marker on qBK1 could provide an effective tool for breeding rice varieties resistant to bakanae disease. To our knowledge, this is the first report on fine mapping and candidate gene approaches for identifying the gene for qBK1.
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Affiliation(s)
- Sais-Beul Lee
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Namgyu Kim
- Department of Microbiology, Pusan National University, Pusan, 46241 Republic of Korea
| | - Yeon-Jae Hur
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Su-Min Cho
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Tae-Heon Kim
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Ji-youn Lee
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Jun-Hyeon Cho
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Jong-Hee Lee
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - You-Chun Song
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Pusan, 46241 Republic of Korea
| | - Jong-Min Ko
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
| | - Dong-Soo Park
- National Institute of Crop Science, Milyang, 50424 Republic of Korea
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Ji Z, Zeng Y, Liang Y, Qian Q, Yang C. Proteomic dissection of the rice-Fusarium fujikuroi interaction and the correlation between the proteome and transcriptome under disease stress. BMC Genomics 2019; 20:91. [PMID: 30691406 PMCID: PMC6350333 DOI: 10.1186/s12864-019-5435-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/07/2019] [Indexed: 02/08/2023] Open
Abstract
Background Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated this disease. To gain a better understanding of the molecular mechanisms of rice bakanae disease resistance, we employed a 6-plex tandem mass tag approach for relative quantitative proteomic comparison of infected and uninfected rice seedlings 7 days post-inoculation with two genotypes: the resistant genotype 93–11 and the susceptible genotype Nipponbare. Results In total, 123 (77.2% up-regulated, 22.8% down-regulated) and 91 (94.5% up-regulated, 5.5% down-regulated) differentially expressed proteins (DEPs) accumulated in 93–11 and Nipponbare, respectively. Only 11 DEPs were both shared by the two genotypes. Clustering results showed that the protein regulation trends for the two genotypes were highly contrasting, which suggested obviously different interaction mechanisms of the host and the pathogen between 93 and 11 and Nipponbare. Further analysis showed that a noticeable aquaporin, PIP2–2, was sharply upregulated with a fold change (FC) of 109.2 in 93–11, which might be related to pathogen defense and the execution of bakanae disease resistance. Certain antifungal proteins were regulated in both 93–11 and Nipponbare with moderate FCs. These proteins might participate in protecting the cellular integrity required for basic growth of the susceptible genotype. Correlation analysis between the transcriptome and proteome revealed that Pearson correlation coefficients of R = 0.677 (P = 0.0005) and R = − 0.097 (P = 0.702) were obtained for 93–11 and Nipponbare, respectively. Our findings raised an intriguing result that a significant positive correlation only in the resistant genotype, while no correlation was found in the susceptible genotype. The differences in codon usage was hypothesized for the cause of the result. Conclusions Quantitative proteomic analysis of the rice genotypes 93-11and Nipponbare after F. fujikuroi infection revealed that the aquaporin protein PIP2–2 might execute bakanae disease resistance. The difference in the correlation between the transcriptome and proteome might be due to the differences in codon usage between 93-11and Nipponbare. Overall, the protein regulation trends observed under bakanae disease stress are highly contrasting, and the molecular mechanisms of disease defense are obviously different between 93 and 11 and Nipponbare. In summary, these findings deepen our understanding of the functions of proteins induced by bakanae disease and the mechanisms of rice bakanae disease resistance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5435-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhijuan Ji
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Yuxiang Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Yan Liang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China.
| | - Changdeng Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, No.359 Tiyuchang Road, Hangzhou, 310006, People's Republic of China.
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Singh PK, Nag A, Arya P, Kapoor R, Singh A, Jaswal R, Sharma TR. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice. Int J Mol Sci 2018; 19:E1141. [PMID: 29642631 PMCID: PMC5979409 DOI: 10.3390/ijms19041141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.
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Affiliation(s)
- Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Nag
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
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Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing. Mol Genet Genomics 2017; 293:579-586. [PMID: 29230584 DOI: 10.1007/s00438-017-1407-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 12/07/2017] [Indexed: 01/25/2023]
Abstract
Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties. Using these SNPs, 161 cleaved amplified polymorphic sequence (CAPS) markers and six derived CAPS markers were developed; then, a genetic map was constructed from the genotypes of 180 plants from the DongjinAD/Nampyeong F2 plants. The total length of the constructed genetic map was 1386 cM, with an average interval of 8.9 cM between markers. The BD mortality rates of each F3 family were measured by testing 40 F3 progenies using in vitro seedling screening method. QTL analysis based on the genetic map and mortality rate data revealed a major QTL, qFfR1, on rice chromosome 1. qFfR1 was located at 89.8 cM with a logarithm of the odds (LOD) score of 22.7. Further, there were three markers at this point: JNS01033, JNS01037, and JNS01041. A total of 15 genes were identified with annotations related to defense against plant diseases among the 179 genes in the qFfR1 interval at 95% probability, thereby providing potential candidate genes for qFfR1. qFfR1 and its closely linked markers will be useful in breeding rice varieties resistant to BD.
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29
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Volante A, Desiderio F, Tondelli A, Perrini R, Orasen G, Biselli C, Riccardi P, Vattari A, Cavalluzzo D, Urso S, Ben Hassen M, Fricano A, Piffanelli P, Cozzi P, Biscarini F, Sacchi GA, Cattivelli L, Valè G. Genome-Wide Analysis of japonica Rice Performance under Limited Water and Permanent Flooding Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1862. [PMID: 29163588 PMCID: PMC5670151 DOI: 10.3389/fpls.2017.01862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/12/2017] [Indexed: 05/02/2023]
Abstract
A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering. Significant MTAs were detected across all the 12 rice chromosomes, while clusters of effects influencing different traits under LW or in both watering conditions were, respectively, observed on chromosomes 4, 8, and 12 and on chromosomes 1, 3, 4, 5, and 8. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to traits related to plant morphology, grain yield, and physiological parameters allowed the identification of genes that were demonstrated to affect the respective traits. Among these, three (OsOFP2, Dlf1, OsMADS56) and seven (SUI1, Sd1, OsCOL4, Nal1, OsphyB, GW5, Ehd1) candidate genes were, respectively, identified to co-localize with LW-specific associations and associations in common between the two water treatments. For several LW-specific MTAs, or in common among the two treatments, positional co-localizations with previously identified QTLs for rice adaptation to water shortages were observed, a result that further supports the role of the loci identified in this work in conferring adaptation to LW. The most robust associations identified here could represent suitable targets for genomic selection approaches to improve yield-related traits under LW.
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Affiliation(s)
- Andrea Volante
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Francesca Desiderio
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | - Alessandro Tondelli
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | - Rosaria Perrini
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Gabriele Orasen
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Biselli
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | | | | | - Daniela Cavalluzzo
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Simona Urso
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | - Manel Ben Hassen
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Agostino Fricano
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | | | | | | | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Luigi Cattivelli
- Research Centre for Genomics and Bioinformatics, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Fiorenzuola d’Arda, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
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