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Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L, Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li C, He X, Zhu Y, Friml J, Du Y. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nat Commun 2024; 15:3437. [PMID: 38653755 DOI: 10.1038/s41467-024-47746-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.
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Affiliation(s)
- Lihui Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiaoyan Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Yiting Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- Shanxi Agricultural University/Shanxi Academy of Agricultural Sciences. The Industrial Crop Institute, Fenyang, 032200, China
| | - Haiyan Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Xinqi Lu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Wuying Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Xinyue Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan Zhou
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Ao Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Xie He
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Man Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Ziai Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Liwei Guo
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jiancheng Wen
- Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yong Xie
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Shusheng Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Chengyun Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiahong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Youyong Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China.
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Wei YY, Liang S, Zhu XM, Liu XH, Lin FC. Recent Advances in Effector Research of Magnaporthe oryzae. Biomolecules 2023; 13:1650. [PMID: 38002332 PMCID: PMC10669146 DOI: 10.3390/biom13111650] [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: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Recalcitrant rice blast disease is caused by Magnaporthe oryzae, which has a significant negative economic reverberation on crop productivity. In order to induce the disease onto the host, M. oryzae positively generates many types of small secreted proteins, here named as effectors, to manipulate the host cell for the purpose of stimulating pathogenic infection. In M. oryzae, by engaging with specific receptors on the cell surface, effectors activate signaling channels which control an array of cellular activities, such as proliferation, differentiation and apoptosis. The most recent research on effector identification, classification, function, secretion, and control mechanism has been compiled in this review. In addition, the article also discusses directions and challenges for future research into an effector in M. oryzae.
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Affiliation(s)
- Yun-Yun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China;
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xiao-Hong Liu
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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3
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Biswas B, Thakur K, Pote TD, Sharma KD, Krishnan SG, Singh AK, Sharma TR, Rathour R. Genetic and molecular analysis of leaf blast resistance in Tetep derived line RIL4 and its relationship to genes at Pita/Pita 2 locus. Sci Rep 2023; 13:18683. [PMID: 37907574 PMCID: PMC10618204 DOI: 10.1038/s41598-023-46070-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023] Open
Abstract
The Vietnamese indica landrace 'Tetep' is known worldwide for its durable and broad spectrum-resistance to blast. We performed genetic and molecular analyses of leaf blast resistance in a Tetep derived recombinant inbred line 'RIL4' which is resistant to both leaf and neck blast. Phenotypic analysis of segregating F2 progenies suggested that leaf blast resistance in RIL4 was controlled by a dominant gene tentatively designated as Pi-l(t). The gene was mapped to a 2.4 cm region close to the centromere of chromosome 12. The search for the gene content in the equivalent genomic region of reference cv. Nipponbare revealed the presence of five NBS-LRR genes, two of which corresponded to the alleles of Pita and Pi67 genes previously identified from Tetep. The two other genes, LOC_Os12g17090, and LOC_Os12g17490 represented the homologs of stripe rust resistance gene Yr10. The allelic tests with Pita2 and Pi67 lines suggested that the leaf blast resistance gene in RIL4 is either allelic or tightly linked to these genes. The genomic position of the leaf blast resistance gene in RIL4 perfectly coincided with the genomic position of a neck blast resistance gene Pb2 previously identified from this line suggesting that the same gene confers resistance to leaf and neck blast. The present results were discussed in juxtaposition with past studies on the genes of Pita/Pita2 resistance gene complex.
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Affiliation(s)
- B Biswas
- CSK Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - K Thakur
- College of Horticulture and Forestry, Dr YSP University of Horticulture and Forestry, Thunag, 175048, India
| | - T D Pote
- CSK Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - K D Sharma
- CSK Himachal Pradesh Agricultural University, Palampur, 176062, India
| | - S Gopala Krishnan
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A K Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - T R Sharma
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - R Rathour
- CSK Himachal Pradesh Agricultural University, Palampur, 176062, India.
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4
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Chen P, Gao G, Lou G, Hu J, Wang Y, Liu R, Zhao D, Liu Q, Sun B, Mao X, Jiang L, Zhang J, Lv S, Yu H, Chen W, Fan Z, Li C, He Y. Improvement of Rice Blast Resistance in TGMS Line HD9802S through Optimized Anther Culture and Molecular Marker-Assisted Selection. Int J Mol Sci 2023; 24:14446. [PMID: 37833893 PMCID: PMC10572977 DOI: 10.3390/ijms241914446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/12/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Rice blast caused by Magnaporthe oryzae is one of the most serious rice diseases worldwide. The early indica rice thermosensitive genic male sterile (TGMS) line HD9802S has the characteristics of stable fertility, reproducibility, a high outcrossing rate, excellent rice quality, and strong combining ability. However, this line exhibits poor blast resistance and is highly susceptible to leaf and neck blasts. In this study, backcross introduction, molecular marker-assisted selection, gene chipping, anther culture, and resistance identification in the field were used to introduce the broad-spectrum blast-resistance gene R6 into HD9802S to improve its rice blast resistance. Six induction media were prepared by varying the content of each component in the culture medium. Murashige and Skoog's medium with 3 mg/L 2,4-dichlorophenoxyacetic acid, 2 mg/L 1-naphthaleneacetic acid, and 1 mg/L kinetin and N6 medium with 800 mg/L casein hydrolysate, 600 mg/L proline, and 500 mg/L glutamine could improve the callus induction rate and have a higher green seedling rate and a lower white seedling rate. Compared to HD9802S, two doubled haploid lines containing R6 with stable fertility showed significantly enhanced resistance to rice blast and no significant difference in spikelet number per panicle, 1000-grain weight, or grain shape. Our findings highlight a rapid and effective method for improving rice blast resistance in TGMS lines.
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Affiliation(s)
- Pingli Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Hu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufu Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Da Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Joshi A, Song HG, Yang SY, Lee JH. Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2454. [PMID: 37447014 DOI: 10.3390/plants12132454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Hyung-Geun Song
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Shafi A, Khan RS, Mir S, Khan GH, Masoodi KZ, Sofi NR, Mohidin FA, Lone JA, Shikari AB. Gene expression of near-isogenic lines (NILs) carrying blast resistance genes Pi9 and Pi54 in the background of rice cultivar Mushk Budji. Mol Biol Rep 2023:10.1007/s11033-023-08475-5. [PMID: 37245171 DOI: 10.1007/s11033-023-08475-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/19/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Kashmir valley, India is a homeland to rice landraces like Zag, Nunbeoul, Qadirbeigh, Kawkadur, Kamad, Mushk Budji, etc., generally characterized by short grains, aroma, earliness and cold tolerance. Mushk Budji is a commercially important speciality rice known for its taste and aroma, nonetheless, is extremely vulnerable to blast disease. Through the use of the marker-assisted backcrossing (MABC) approach, a set of 24 Near-isogenic lines (NILs) was created, and the lines with the highest background genome recovery were chosen. The expression analysis was carried out for the component genes and other eight pathway genes related to blast resistance. RESULTS The major blast resistance genes Pi9 (from IRBL-9W) and Pi54 (from DHMAS 70Q 164-1b) were incorporated following simultaneous-but-step-wise MABC. The NILs harbouring genes Pi9 + Pi54, Pi9 and Pi54 expressed resistance to isolate (Mo-nwi-kash-32) under controlled and natural field conditions. The loci controlling ETI (effector triggered immunity) included the gene Pi9 and showed 61.18 and 60.27 fold change in relative gene expression in Pi54 + Pi9 and Pi9 carrying NILs against RP Mushk Budji. Pi54 was up regulated and showed 41 and 21 fold change in relative gene expression for NIL-Pi54 + Pi9 and NIL-Pi54, respectively. Among the pathway genes, LOC_Os01g60600 (WRKY 108) recorded 8 and 7.5 fold up regulation in Pi9 and Pi54 NILs. CONCLUSION The NILs showed recurrent parent genome recovery (RPG) per cent of 81.67 to 92.54 and were on par in performance to recurrent parent Mushk Budji. The lines were utilized to study the expression of the loci controlling WRKYs, peroxidases and chitinases that confer overall ETI response.
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Affiliation(s)
- Afshana Shafi
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, J&K, 190 025, India
| | - Raheel Shafeeq Khan
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Wadura, J&K, 193 201, India
| | - Saba Mir
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Khudwani, J&K, 192 102, India
| | - Gazala H Khan
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Khudwani, J&K, 192 102, India
| | - K Z Masoodi
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, J&K, 190 025, India
| | - Najeebul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Khudwani, J&K, 192 102, India
| | - F A Mohidin
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Khudwani, J&K, 192 102, India
| | - Javeed A Lone
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Khudwani, J&K, 192 102, India
| | - Asif Bashir Shikari
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Wadura, J&K, 193 201, India.
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7
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B J, Hosahatti R, Koti PS, Devappa VH, Ngangkham U, Devanna P, Yadav MK, Mishra KK, Aditya JP, Boraiah PK, Gaber A, Hossain A. Phenotypic and Genotypic screening of fifty-two rice (Oryza sativa L.) genotypes for desirable cultivars against blast disease. PLoS One 2023; 18:e0280762. [PMID: 36897889 PMCID: PMC10004593 DOI: 10.1371/journal.pone.0280762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/08/2023] [Indexed: 03/11/2023] Open
Abstract
Magnaporthe oryzae, the rice blast fungus, is one of the most dangerous rice pathogens, causing considerable crop losses around the world. In order to explore the rice blast-resistant sources, initially performed a large-scale screening of 277 rice accessions. In parallel with field evaluations, fifty-two rice accessions were genotyped for 25 major blast resistance genes utilizing functional/gene-based markers based on their reactivity against rice blast disease. According to the phenotypic examination, 29 (58%) and 22 (42%) entries were found to be highly resistant, 18 (36%) and 29 (57%) showed moderate resistance, and 05 (6%) and 01 (1%), respectively, were highly susceptible to leaf and neck blast. The genetic frequency of 25 major blast resistance genes ranged from 32 to 60%, with two genotypes having a maximum of 16 R-genes each. The 52 rice accessions were divided into two groups based on cluster and population structure analysis. The highly resistant and moderately resistant accessions are divided into different groups using the principal coordinate analysis. According to the analysis of molecular variance, the maximum diversity was found within the population, while the minimum diversity was found between the populations. Two markers (RM5647 and K39512), which correspond to the blast-resistant genes Pi36 and Pik, respectively, showed a significant association to the neck blast disease, whereas three markers (Pi2-i, Pita3, and k2167), which correspond to the blast-resistant genes Pi2, Pita/Pita2, and Pikm, respectively, showed a significant association to the leaf blast disease. The associated R-genes might be utilized in rice breeding programmes through marker-assisted breeding, and the identified resistant rice accessions could be used as prospective donors for the production of new resistant varieties in India and around the world.
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Affiliation(s)
- Jeevan B
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | | | - Prasanna S Koti
- The University of Trans-Disciplinary Health Sciences and Technology, Jarakabande Kaval, Bengaluru, Karnataka, India
| | | | - Umakanta Ngangkham
- ICAR- Research Complex for North- Eastern Hill Region, Manipur centre, Imphal, Manipur, India
| | - Pramesh Devanna
- Rice Pathology Laboratory, AICRIP, Gangavathi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Manoj Kumar Yadav
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India
| | - Krishna Kant Mishra
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Jay Prakash Aditya
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Palanna Kaki Boraiah
- Project Coordinating Unit, ICAR-AICRP on Small Millets, UAS, GKVK, Bengaluru, Karnataka, India
| | - Ahmed Gaber
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
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Sahu PK, Sao R, Choudhary DK, Thada A, Kumar V, Mondal S, Das BK, Jankuloski L, Sharma D. Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease. PLANTS 2022; 11:plants11182386. [PMID: 36145787 PMCID: PMC9504543 DOI: 10.3390/plants11182386] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 01/02/2023]
Abstract
Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | | | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
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9
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Navia-Urrutia M, Mosquera G, Ellsworth R, Farman M, Trick HN, Valent B. Effector Genes in Magnaporthe oryzae Triticum as Potential Targets for Incorporating Blast Resistance in Wheat. PLANT DISEASE 2022; 106:1700-1712. [PMID: 34931892 DOI: 10.1094/pdis-10-21-2209-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Wheat blast (WB), caused by Magnaporthe oryzae Triticum pathotype, recently emerged as a destructive disease that threatens global wheat production. Because few sources of genetic resistance have been identified in wheat, genetic transformation of wheat with rice blast resistance genes could expand resistance to WB. We evaluated the presence/absence of homologs of rice blast effector genes in Triticum isolates with the aim of identifying avirulence genes in field populations whose cognate rice resistance genes could potentially confer resistance to WB. We also assessed presence of the wheat pathogen AVR-Rmg8 gene and identified new alleles. A total of 102 isolates collected in Brazil, Bolivia, and Paraguay from 1986 to 2018 were evaluated by PCR using 21 pairs of gene-specific primers. Effector gene composition was highly variable, with homologs to AvrPiz-t, AVR-Pi9, AVR-Pi54, and ACE1 showing the highest amplification frequencies (>94%). We identified Triticum isolates with a functional AvrPiz-t homolog that triggers Piz-t-mediated resistance in the rice pathosystem and produced transgenic wheat plants expressing the rice Piz-t gene. Seedlings and heads of the transgenic lines were challenged with isolate T25 carrying functional AvrPiz-t. Although slight decreases in the percentage of diseased spikelets and leaf area infected were observed in two transgenic lines, our results indicated that Piz-t did not confer useful WB resistance. Monitoring of avirulence genes in populations is fundamental to identifying effective resistance genes for incorporation into wheat by conventional breeding or transgenesis. Based on avirulence gene distributions, rice resistance genes Pi9 and Pi54 might be candidates for future studies.
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Affiliation(s)
- Monica Navia-Urrutia
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Gloria Mosquera
- Rice Pathology, International Center for Tropical Agriculture, Palmira, 763537, Colombia
| | - Rebekah Ellsworth
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
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10
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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11
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Panibe JP, Wang L, Lee YC, Wang CS, Li WH. Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution. BOTANICAL STUDIES 2022; 63:9. [PMID: 35347474 PMCID: PMC8960516 DOI: 10.1186/s40529-022-00336-x] [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: 11/25/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. RESULTS Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. CONCLUSIONS We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
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Affiliation(s)
- Jerome P. Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 China
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung, 40227 Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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12
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Tian T, Chen L, Ai Y, He H. Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq. Genes (Basel) 2022; 13:genes13020224. [PMID: 35205268 PMCID: PMC8871662 DOI: 10.3390/genes13020224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.
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Affiliation(s)
| | | | - Yufang Ai
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
| | - Huaqin He
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
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Yu S, Ali J, Zhou S, Ren G, Xie H, Xu J, Yu X, Zhou F, Peng S, Ma L, Yuan D, Li Z, Chen D, Zheng R, Zhao Z, Chu C, You A, Wei Y, Zhu S, Gu Q, He G, Li S, Liu G, Liu C, Zhang C, Xiao J, Luo L, Li Z, Zhang Q. From Green Super Rice to green agriculture: Reaping the promise of functional genomics research. MOLECULAR PLANT 2022; 15:9-26. [PMID: 34883279 DOI: 10.1016/j.molp.2021.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.
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Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shaochuan Zhou
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guangjun Ren
- Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Huaan Xie
- Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Fasong Zhou
- China National Seed Group Co., Ltd, Beijing, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangyong Ma
- China National Rice Research Institute, Hangzhou, China
| | | | - Zefu Li
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dazhou Chen
- Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | | | | | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aiqing You
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yu Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Susong Zhu
- Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Qiongyao Gu
- Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Shigui Li
- Sichuan Agricultural University, Chengdu, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changhua Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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Evaluation of indigenous aromatic rice cultivars from sub-Himalayan Terai region of India for nutritional attributes and blast resistance. Sci Rep 2021; 11:4786. [PMID: 33637778 PMCID: PMC7910543 DOI: 10.1038/s41598-021-83921-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/03/2021] [Indexed: 01/12/2023] Open
Abstract
Indigenous folk rice cultivars often possess remarkable but unrevealed potential in terms of nutritional attributes and biotic stress tolerance. The unique cooking qualities and blissful aroma of many of these landraces make it an attractive low-cost alternative to high priced Basmati rice. Sub-Himalayan Terai region is bestowed with great agrobiodiversity in traditional heirloom rice cultivars. In the present study, ninety-nine folk rice cultivars from these regions were collected, purified and characterized for morphological and yield traits. Based on traditional importance and presence of aroma, thirty-five genotypes were selected and analyzed for genetic diversity using micro-satellite marker system. The genotypes were found to be genetically distinct and of high nutritive value. The resistant starch content, amylose content, glycemic index and antioxidant potential of these genotypes represented wide variability and 'Kataribhog', 'Sadanunia', 'Chakhao' etc. were identified as promising genotypes in terms of different nutritional attributes. These cultivars were screened further for resistance against blast disease in field trials and cultivars like 'Sadanunia', 'T4M-3-5', 'Chakhao Sampark' were found to be highly resistant to the blast disease whereas 'Kalonunia', 'Gobindabhog', 'Konkanijoha' were found to be highly susceptible. Principal Component analysis divided the genotypes in distinct groups for nutritional potential and blast tolerance. The resistant and susceptible genotypes were screened for the presence of the blast resistant pi genes and association analysis was performed with disease tolerance. Finally, a logistic model based on phenotypic traits for prediction of the blast susceptibility of the genotypes is proposed with more than 80% accuracy.
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15
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Understanding Rice- Magnaporthe Oryzae Interaction in Resistant and Susceptible Cultivars of Rice under Panicle Blast Infection Using a Time-Course Transcriptome Analysis. Genes (Basel) 2021; 12:genes12020301. [PMID: 33672641 PMCID: PMC7924189 DOI: 10.3390/genes12020301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/21/2023] Open
Abstract
Rice blast is a global threat to food security with up to 50% yield losses. Panicle blast is a more severe form of rice blast and the response of rice plant to leaf and panicle blast is distinct in different genotypes. To understand the specific response of rice in panicle blast, transcriptome analysis of blast resistant cultivar Tetep, and susceptible cultivar HP2216 was carried out using RNA-Seq approach after 48, 72 and 96 h of infection with Magnaporthe oryzae along with mock inoculation. Transcriptome data analysis of infected panicle tissues revealed that 3553 genes differentially expressed in HP2216 and 2491 genes in Tetep, which must be the responsible factor behind the differential disease response. The defense responsive genes are involved mainly in defense pathways namely, hormonal regulation, synthesis of reactive oxygen species, secondary metabolites and cell wall modification. The common differentially expressed genes in both the cultivars were defense responsive transcription factors, NBS-LRR genes, kinases, pathogenesis related genes and peroxidases. In Tetep, cell wall strengthening pathway represented by PMR5, dirigent, tubulin, cell wall proteins, chitinases, and proteases was found to be specifically enriched. Additionally, many novel genes having DOMON, VWF, and PCaP1 domains which are specific to cell membrane were highly expressed only in Tetep post infection, suggesting their role in panicle blast resistance. Thus, our study shows that panicle blast resistance is a complex phenomenon contributed by early defense response through ROS production and detoxification, MAPK and LRR signaling, accumulation of antimicrobial compounds and secondary metabolites, and cell wall strengthening to prevent the entry and spread of the fungi. The present investigation provided valuable candidate genes that can unravel the mechanisms of panicle blast resistance and help in the rice blast breeding program.
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Khanna A, Ellur RK, Gopala Krishnan S, Vinod KK, Bhowmick PK, Nagarajan M, Haritha B, Singh AK. Utilizing Host-Plant Resistance to Circumvent Blast Disease in Rice. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Advances in Genetics and Genomics for Management of Blast Disease in Cereal Crops. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Sharma SK, Sharma D, Meena RP, Yadav MK, Hosahatti R, Dubey AK, Sharma P, Kumar S, Pramesh D, Nabi SU, Bhuvaneshwari S, Anand YR, Dubey SK, Singh TS. Recent Insights in Rice Blast Disease Resistance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Zhou Y, Lei F, Wang Q, He W, Yuan B, Yuan W. Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining. RICE (NEW YORK, N.Y.) 2020; 13:80. [PMID: 33284383 PMCID: PMC7721961 DOI: 10.1186/s12284-020-00442-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND As rice (Oryza sativa) is the staple food of more than half the world's population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. RESULTS We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast. CONCLUSIONS The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.
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Affiliation(s)
- Ying Zhou
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Fang Lei
- Institute of Model Animal of Wuhan University, Basic Medical School of Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Qiong Wang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Weicong He
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Bin Yuan
- Key Laboratory of Integrated Management of Crops of Central China, Ministry of Agriculture, Wuhan, 430064 People’s Republic of China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, 430064 People’s Republic of China
| | - Wenya Yuan
- College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
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Ramalingam J, Raveendra C, Savitha P, Vidya V, Chaithra TL, Velprabakaran S, Saraswathi R, Ramanathan A, Arumugam Pillai MP, Arumugachamy S, Vanniarajan C. Gene Pyramiding for Achieving Enhanced Resistance to Bacterial Blight, Blast, and Sheath Blight Diseases in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:591457. [PMID: 33329656 PMCID: PMC7711134 DOI: 10.3389/fpls.2020.591457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/06/2020] [Indexed: 05/27/2023]
Abstract
Bacterial blight, blast, and sheath blight are the commonest diseases causing substantial yield loss in rice around the world. Stacking of broad-spectrum resistance genes/QTLs into popular cultivars is becoming a major objective of any disease resistance breeding program. The varieties ASD 16 and ADT 43 are the two popular, high yielding, and widely grown rice cultivars of South India, which are susceptible to bacterial blight (BB), blast, and sheath blight diseases. The present study was carried out to improve the cultivars (ASD 16 and ADT 43) through introgression of bacterial blight (xa5, xa13, and Xa21), blast (Pi54), and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance genes/QTLs by MABB (marker-assisted backcross breeding). IRBB60 (xa5, xa13, and Xa21) and Tetep (Pi54; qSBR7-1, qSBR11-1, and qSBR11-2) were used as donors to introgress BB, blast, and sheath blight resistance into the recurrent parents (ASD 16 and ADT 43). Homozygous (BC3F3 generation), three-gene bacterial blight pyramided (xa5 + xa13 + Xa21) lines were developed, and these lines were crossed with Tetep to combine blast (Pi54) and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance. In BC3F3 generation, the improved pyramided lines carrying a total of seven genes/QTLs (xa5 + xa13 + Xa21 + Pi54 + qSBR7-1 + qSBR11-1 + qSBR11-2) were selected through molecular and phenotypic assay, and these were evaluated for resistance against bacterial blight, blast, and sheath blight pathogens under greenhouse conditions. We have selected nine lines in ASD 16 background and 15 lines in ADT 43 background, exhibiting a high degree of resistance to BB, blast, and sheath blight diseases and also possessing phenotypes of recurrent parents. The improved pyramided lines are expected to be used as improved varieties or used as a potential donor in breeding programs. The present study successfully introgressed Pi54, and qSBR QTLs (qSBR7-1, qSBR11-1, and qSBR11-2) from Tetep and major effective BB-resistant genes (xa5, xa13, and Xa21) from IRBB60 into the commercial varieties for durable resistance to multiple diseases.
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Affiliation(s)
- Jegadeesan Ramalingam
- Centre of Excellence for Innovations, Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chandavarapu Raveendra
- Centre of Excellence for Innovations, Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Palanisamy Savitha
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Venugopal Vidya
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Senthilvel Velprabakaran
- Centre of Excellence for Innovations, Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Ramasamy Saraswathi
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ayyasamy Ramanathan
- Tamil Nadu Rice Research Institute, Tamil Nadu Agricultural University, Aduthurai, India
| | | | | | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
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Ramalingam J, Palanisamy S, Alagarasan G, Renganathan VG, Ramanathan A, Saraswathi R. Improvement of Stable Restorer Lines for Blast Resistance through Functional Marker in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11111266. [PMID: 33121205 PMCID: PMC7692511 DOI: 10.3390/genes11111266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022] Open
Abstract
Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly susceptible to blast disease. To improve the restorer lines for resistance against blasts, we introgressed the broad-spectrum dominant gene Pi54 into these elite restorer lines through two independent crosses. Foreground selection for Pi54 was done by using gene-specific functional marker, Pi54 MAS, at each back-cross generation. Back-crossing was continued until BC3 and background analysis with seventy polymorphic SSRs covering all the twelve chromosomes to recover the maximum recurrent parent genome was done. At BC3F2, closely linked gene-specific/SSR markers, DRRM-RF3-10, DRCG-RF4-8, and RM 6100, were used for the identification of fertility restoration genes, Rf3 and Rf4, along with target gene (Pi54), respectively, in the segregating population. Subsequently, at BC3F3, plants, homozygous for the Pi54 and fertility restorer genes (Rf3 and Rf4), were evaluated for blast disease resistance under uniform blast nursery (UBN) and pollen fertility status. Stringent phenotypic selection resulted in the identification of nine near-isogenic lines in CB 87 R × B 95 and thirteen in CB 174 R × B 95 as the promising restorer lines possessing blast disease resistance along with restoration ability. The improved lines also showed significant improvement in agronomic traits compared to the recurrent parents. The improved restorer lines developed through the present study are now being utilized in our hybrid development program.
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Affiliation(s)
- Jegadeesan Ramalingam
- Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai 625104, India;
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
- Correspondence:
| | - Savitha Palanisamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
| | - Ganesh Alagarasan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
| | | | - Ayyasamy Ramanathan
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.R.); (R.S.)
| | - Ramasamy Saraswathi
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.R.); (R.S.)
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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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Singh J, Gupta SK, Devanna BN, Singh S, Upadhyay A, Sharma TR. Blast resistance gene Pi54 over-expressed in rice to understand its cellular and sub-cellular localization and response to different pathogens. Sci Rep 2020; 10:5243. [PMID: 32251298 PMCID: PMC7090074 DOI: 10.1038/s41598-020-59027-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/31/2019] [Indexed: 11/26/2022] Open
Abstract
Rice blast resistance gene, Pi54 provides broad-spectrum resistance against different strains of Magnaporthe oryzae. Understanding the cellular localization of Pi54 protein is an essential step towards deciphering its place of interaction with the cognate Avr-gene. In this study, we investigated the sub-cellular localization of Pi54 with Green Fluorescent Protein (GFP) as a molecular tag through transient and stable expression in onion epidermal cells (Allium cepa) and susceptible japonica cultivar rice Taipei 309 (TP309), respectively. Confocal microscopy based observations of the onion epidermal cells revealed nucleus and cytoplasm specific GFP signals. In the stable transformed rice plants, GFP signal was recorded in the stomata, upper epidermal cells, mesophyll cells, vascular bundle, and walls of bundle sheath and bulliform cells of leaf tissues. These observations were further confirmed by Immunocytochemical studies. Using GFP specific antibodies, it was found that there was sufficient aggregation of GFP::Pi54protein in the cytoplasm of the leaf mesophyll cells and periphery of the epidermal cells. Interestingly, the transgenic lines developed in this study could show a moderate level of resistance to Xanthomonas oryzae and Rhizoctonia solani, the causal agents of the rice bacterial blight and sheath blight diseases, respectively. This study is a first detailed report, which emphasizes the cellular and subcellular distribution of the broad spectrum blast resistance gene Pi54 in rice and the impact of its constitutive expression towards resistance against other fungal and bacterial pathogens of rice.
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Affiliation(s)
- Jyoti Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.,Hislop College, R.T.M Nagpur University, Nagpur, India
| | | | - B N Devanna
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.,ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Sunil Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - Tilak R Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India. .,National Agri-Food Biotechnology Institute, Mohali, Punjab, India.
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24
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Hu X, Cui Y, Dong G, Feng A, Wang D, Zhao C, Zhang Y, Hu J, Zeng D, Guo L, Qian Q. Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces. Sci Rep 2019; 9:19096. [PMID: 31836812 PMCID: PMC6910903 DOI: 10.1038/s41598-019-55757-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/28/2019] [Indexed: 11/09/2022] Open
Abstract
Genetic erosion refers to the loss of genetic variation in a crop. In China, only a few original landraces of rice (Oryza sativa) were used in breeding and these became the primary genetic background of modern varieties. Expanding the genetic diversity among Chinese rice varieties and cultivating high-yielding and high-quality varieties with resistance to different biotic and abiotic stresses is critical. Here, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9(Cas9) genome editing system to edit Semi-Dwarf1 (SD1) in the elite landraces Kasalath and TeTePu (TTP), which contain many desired agronomic traits such as tolerance to low phosphorous and broad-spectrum resistance to several diseases and insects. Mutations of SD1 confer shorter plant height for better resistance to lodging. Field trials demonstrated that the yield of the new Kasalath and TTP mutant lines was better than that of the wild type under modern cultivation and that the lines maintained the same desirable agronomic characteristics as their wild-type progenitors. Our results showed that breeding using available landraces in combination with genomic data of different landraces and gene-editing techniques is an effective way to relieve genetic erosion in modern rice varieties.
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Affiliation(s)
- Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yongtao Cui
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Anhui Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Danying Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Chunyan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yu Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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GAVHANE DNYANESHWARB, KULWAL PAWANL, KUMBHAR SHAILESHD, JADHAV ASHOKS, SARAWATE CHANDRAKANTD. Cataloguing of blast resistance genes in landraces and breeding lines of rice from India. J Genet 2019. [DOI: 10.1007/s12041-019-1148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Deciphering signalling network in broad spectrum Near Isogenic Lines of rice resistant to Magnaporthe oryzae. Sci Rep 2019; 9:16939. [PMID: 31729398 PMCID: PMC6858299 DOI: 10.1038/s41598-019-50990-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023] Open
Abstract
Disease resistance (R) genes like Pi9, Pita, Pi21, Pi54 are playing important role for broad spectrum blast resistance in rice. Development of near isogenic lines (NILs) using these type of broad spectrum genes and understanding their signalling networks is essential to cope up with highly evolving Magnaporthe oryzae strains for longer duration. Here, transcriptional-level changes were studied in three near-isogenic lines (PB1 + Pi1, PB1 + Pi9 and PB1 + Pi54) of rice resistant to blast infection, to find the loci that are unique to resistant lines developed in the background of Pusa Basmati 1 (PB1). The pathway analysis of loci, unique to resistant NILs compared to susceptible control revealed that plant secondary metabolite synthesis was the common mechanism among all NILs to counter against M. oryzae infection. Comparative transcriptome analysis helped to find out common clusters of co-expressed significant differentially expressed loci (SDEL) in both PB1 + Pi9 and PB1 + Pi54 NILs. SDELs from these clusters were involved in the synthesis and degradation of starch; synthesis and elongation of fatty acids; hydrolysis of phospholipids; synthesis of phenylpropanoid; and metabolism of ethylene and jasmonic acid. Through detailed analysis of loci specific to each resistant NIL, we identified a network of signalling pathways mediated by each blast resistance gene. The study also offers insights into transcriptomic dynamics, points to a set of important candidate genes that serve as module to regulate the changes in resistant NILs. We suggest that pyramiding of the blast resistance gene Pi9 with Pi54 will lead to maximum broad spectrum resistance to M. oryzae.
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Sarkar C, Saklani BK, Singh PK, Asthana RK, Sharma TR. Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis. PLoS One 2019; 14:e0224088. [PMID: 31689303 PMCID: PMC6830779 DOI: 10.1371/journal.pone.0224088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/05/2019] [Indexed: 11/18/2022] Open
Abstract
Rice blast, caused by the ascomycete fungus Magnaporthe oryzae is a destructive disease of rice and responsible for causing extensive damage to the crop. Pi54, a dominant blast resistance gene cloned from rice line Tetep, imparts a broad spectrum resistance against various M. oryzae isolates. Many of its alleles have been explored from wild Oryza species and landraces whose sequences are available in the public domain. Its cognate effector gene AvrPi54 has also been cloned from M. oryzae. Complying with the Flor’s gene-for-gene system, Pi54 protein interacts with AvrPi54 protein following fungal invasion leading to the resistance responses in rice cell that prevents the disease development. In the present study Pi54 alleles from 72 rice lines were used to understand the interaction of Pi54 (R) proteins with AvrPi54 (Avr) protein. The physiochemical properties of these proteins varied due to the nucleotide level polymorphism. The ab initio tertiary structures of these R- and Avr- proteins were generated and subjected to the in silico interaction. In this interaction, the residues in the LRR region of R- proteins were shown to interact with the Avr protein. These R proteins were found to have variable strengths of binding due to the differential spatial arrangements of their amino acid residues. Additionally, molecular dynamic simulations were performed for the protein pairs that showed stronger interaction than Pi54tetep (original Pi54 from Tetep) protein. We found these proteins were forming h-bond during simulation which indicated an effective binding. The root mean square deviation values and potential energy values were stable during simulation which validated the docking results. From the interaction studies and the molecular dynamics simulations, we concluded that the AvrPi54 protein interacts directly with the resistant Pi54 proteins through the LRR region of Pi54 proteins. Some of the Pi54 proteins from the landraces namely Casebatta, Tadukan, Varun dhan, Govind, Acharmita, HPR-2083, Budda, Jatto, MTU-4870, Dobeja-1, CN-1789, Indira sona, Kulanji pille and Motebangarkaddi cultivars show stronger binding with the AvrPi54 protein, thus these alleles can be effectively used for the rice blast resistance breeding program in future.
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Affiliation(s)
- Chiranjib Sarkar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Banita Kumari Saklani
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Pankaj Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | | | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
- * E-mail:
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28
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Madhusudhan P, Sinha P, Rajput LS, Bhattacharya M, Sharma T, Bhuvaneshwari V, Gaikwad K, Krishnan SG, Singh AK. Effect of temperature on Pi54-mediated leaf blast resistance in rice. World J Microbiol Biotechnol 2019; 35:148. [PMID: 31549233 DOI: 10.1007/s11274-019-2724-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022]
Abstract
Assessment of temperature effect on plant resistance against diseases has become essential under climate change scenario as temperature rise is anticipated to modify host resistance. To determine temperature influence on resistance gene, a pair of near-isogenic rice lines differing for the Pi54 resistance gene was assessed against leaf blast. Blast resistance was determined as the extent of infection efficiency (IE) and sporulation (SP) at suboptimal (22 °C and 32 °C) and optimal temperature (27 °C) of pathogen aggressiveness. Relative resistance for IE and SP was higher at suboptimal temperature as compared to that of optimal temperature. Maximum level of resistance was at 22 °C where higher levels of expression of Pi54 and defence-regulatory transcription factor WRKY45 were also noted. At 32 °C, although some level of resistance noted, but level of Pi54 and WRKY45 expression was too low, suggesting that resistance recorded at higher temperature was due to reduced pathogen aggressiveness. At the optimal temperature for pathogen aggressiveness, comparatively lower levels of Pi54 and WRKY45 expression suggest possible temperature-induced interruption of the defence processes. The variation in resistance patterns modulated by temperature is appeared to be due to pathogen's sensitivity to temperature that leads to varying levels of Pi54 gene activation. Quick and violent activity of the pathogen at optimal temperature came into sight for the interruption of defence process activated by Pi54 gene. Evaluation of blast resistance genes under variable temperature conditions together with weather data could be applied in screening rice genotypes for selection of resistance having resilience to temperature rise.
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Affiliation(s)
- P Madhusudhan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Agricultural Research Station, Acharya N G Ranga Agricultural University, Nellore, Andhra Pradesh, 524003, India
| | - P Sinha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - L S Rajput
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Protection, ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, 452001, India
| | - M Bhattacharya
- Department of Agronomy, IOWA State University, Ames, IA, 5001-1051, USA
| | - Taru Sharma
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - V Bhuvaneshwari
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University, Maruteru, Andhra Pradesh, 534122, India
| | - Kishore Gaikwad
- National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Kalia S, Rathour R. Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice. 3 Biotech 2019; 9:209. [PMID: 31093479 PMCID: PMC6509304 DOI: 10.1007/s13205-019-1738-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/29/2019] [Indexed: 12/15/2022] Open
Abstract
Blast disease caused by fungal pathogen Pyricularia oryzae is a major threat to rice productivity worldwide. The rice-blast pathogen can infect both leaves and panicle neck nodes. Nearly, 118 genes for resistance to leaf blast have been identified and 25 of these have been molecularly characterized. A great majority of these genes encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins and are organized into clusters as allelic or tightly linked genes. Compared to ever expanding list of leaf-blast-resistance genes, a few major genes mediating protection to neck blast have been identified. A great majority of the genetic studies conducted with the genotypes differing in the degree of susceptibility/resistance to neck blast have suggested quantitative inheritance for the trait. Several reports on co-localization of gene/QTLs for leaf- and neck-blast resistance in rice genome have suggested the existence of common genes for resistance to both phases of the disease albeit inconsistencies in the genomic positions leaf- and neck-blast-resistance genes in some instances have presented the contrasting scenario. There is a strong evidence to suggest that developmentally regulated expression of many blast-resistance genes is a key determinant deciding their effectiveness against leaf or neck blast. Testing of currently characterized leaf-blast-resistance genes for their reaction to neck blast is required to expand the existing repertoire resistance genes against neck blast. Current developments in the understanding of molecular basis of host-pathogen interactions in rice-blast pathosystem offer novel possibilities for achieving durable resistance to blast through exploitation of natural or genetically engineered loss-of-function alleles of host susceptibility genes.
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Affiliation(s)
- S. Kalia
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh 176062 India
| | - R. Rathour
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh 176062 India
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Li J, Wang Q, Li C, Bi Y, Fu X, Wang R. Novel haplotypes and networks of AVR-Pik alleles in Magnaporthe oryzae. BMC PLANT BIOLOGY 2019; 19:204. [PMID: 31096914 PMCID: PMC6524238 DOI: 10.1186/s12870-019-1817-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/02/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice and trigger race-specific resistance. The variation in AVR is one of the major drivers of new races. Detecting the variation in the AVR gene in isolates from a population of Magnaporthe oryzae collected from rice production fields will aid in evaluating the effectiveness of R genes in rice production areas. The Pik gene contains 5 R alleles (Pik, Pikh, Pikp, Pikm and Piks) corresponding to the AVR alleles (AVR-Pik/kh/kp/km/ks) of M. oryzae. The Pik gene specifically recognizes and prevents infections by isolates of M. oryzae that contain AVR-Pik. The molecular variation in AVR-Pik alleles of M. oryzae and Pik alleles of rice remains unclear. RESULTS We studied the possible evolutionary pathways of AVR-Pik alleles by analyzing their DNA sequence variation and assaying their avirulence to the cognate Pik alleles of resistance genes under field conditions in China. The results of PCR products from genomic DNA showed that 278 of the 366 isolates of M. oryzae collected from Yunnan Province, China, carried AVR-Pik alleles. Among the isolates from six regions of Yunnan, 66.7-90.3% carried AVR-Pik alleles. Moreover, 10 AVR-Pik haplotypes encoding five novel AVR-Pik variants were identified among 201 isolates. The AVR-Pik alleles evolved to virulent from avirulent forms via stepwise base substitution. These findings demonstrate that AVR-Pik alleles are under positive selection and that mutations are responsible for defeating race-specific resistant Pik alleles in nature. CONCLUSIONS We demonstrated the polymorphism and distribution of AVR-Pik alleles in Yunnan Province, China. By pathogenicity assays used to detect the function of the different haplotypes of AVR-Pik, for the first time, we showed the avoidance and stepwise evolution of AVR-Pik alleles in rice production areas of Yunnan. The functional AVR-Pik possesses diversified sequence structures and is under positive selection in nature.
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Affiliation(s)
- Jinbin Li
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qun Wang
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Chengyun Li
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Yunnan Agricultural University, Kunming, China
| | - Yunqing Bi
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xue Fu
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Raoquan Wang
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Fang N, Wei X, Shen L, Yu Y, Li M, Yin C, He W, Guan C, Chen H, Zhang H, Bao Y. Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding. RICE (NEW YORK, N.Y.) 2019; 12:18. [PMID: 30911847 PMCID: PMC6434012 DOI: 10.1186/s12284-019-0275-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/26/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Rice blast caused by Magnaporthe oryzae is the most devastating disease in rice production. Compared with seedling blast, panicle blast is considered to be more destructive, which can occur without being preceded by severe seedling blast. However, panicle blast resistance research is rarely reported. RESULTS Bodao, a japonica landrace from Taihu Lake region, showed a high level of panicle blast resistance. In this study, a mapping population of 212 recombination inbreeding lines (RILs) was developed from a cross of Bodao and the susceptible cultivar Suyunuo, and the RILs were evaluated for panicle blast resistance in three trials. Two quantitative trait loci (QTLs) qPb11-1 and qPb6-1 for panicle-blast resistance were identified, including a major QTL qPb11-1 (Pb-bd1) on chromosome 11 of Bodao explaining from 55.31% to 71.68% of the phenotype variance, and a minor QTL qPb6-1 on chromosome 6 of Suyunuo explaining from 3.54% to 6.98% of the phenotype variance. With the various segregation populations, Pb-bd1 was fine mapped in a 40.6 Kb region flanked by markers BS83 and BS98, and six candidate genes were identified within this region, including one gene encoding NAC domain-containing protein, one gene encoding unknown expression proteins, two genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) type disease resistance proteins, and two genes encoding von Willebrand factor type A (VWA) domain containing proteins. For application in rice breeding, three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by using molecular assisted method (MAS) from the commercial variety Nanjing46 (NJ46). CONCLUSION Two QTLs, qPb11-1(Pb-bd1) and qPb6-1 conferring panicle blast resistance, were identified from japonica landrace Bodao and Suyunuo.qPb11-1(Pb-bd1) was fine mapped in a 40.6 Kb region flanked by marker BS83 and BS98. Three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by MAS method from the commercial variety NJ46. It indicated that Pb-bd1 would be useful gene source in panicle blast resistance breeding.
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Affiliation(s)
- Nengyan Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Crop Science, Fujian Academy of Agricultural Science, Fuzhou, 350013, China
| | - Xiaorui Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lingtong Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengya Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Congfei Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanwan He
- Xuzhou Academy of Agricultural Science, Xuzhou, 221131, China
| | - Changhong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Seed Industry, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Wu Y, Xiao N, Chen Y, Yu L, Pan C, Li Y, Zhang X, Huang N, Ji H, Dai Z, Chen X, Li A. Comprehensive evaluation of resistance effects of pyramiding lines with different broad-spectrum resistance genes against Magnaporthe oryzae in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2019; 12:11. [PMID: 30825053 PMCID: PMC6397272 DOI: 10.1186/s12284-019-0264-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/17/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Broad-spectrum resistance gene pyramiding helps the development of varieties with broad-spectrum and durable resistance to M. oryzae. However, detailed information about how these different sources of broad-spectrum resistance genes act together or what are the best combinations to achieve broad-spectrum and durable resistance is limited. RESULTS Here a set of fifteen different polygene pyramiding lines (PPLs) were constructed using marker-assisted selection (MAS). Using artificial inoculation assays at seedling and heading stage, combined with natural induction identification under multiple field environments, we evaluated systematically the resistance effects of different alleles of Piz locus (Pigm, Pi40, Pi9, Pi2 and Piz) combined with Pi1, Pi33 and Pi54, respectively, and the interaction effects between different R genes. The results showed that the seedling blast and panicle blast resistance levels of PPLs were significantly higher than that of monogenic lines. The main reason was that most of the gene combinations produced transgressive heterosis, and the transgressive heterosis for panicle blast resistance produced by most of PPLs was higher than that of seedling blast resistance. Different gene pyramiding with broad-spectrum R gene produced different interaction effects, among them, the overlapping effect (OE) between R genes could significantly improve the seedling blast resistance level of PPLs, while the panicle blast resistance of PPLs were remarkably correlated with OE and complementary effect (CE). In addition, we found that gene combinations, Pigm/Pi1, Pigm/Pi54 and Pigm/Pi33 displayed broad-spectrum resistance in artificial inoculation at seedling and heading stage, and displayed stable broad-spectrum resistance under different disease nursery. Besides, agronomic traits evaluation also showed PPLs with these three gene combinations were at par to the recurrent parent. Therefore, it would provide elite gene combination model and germplasms for rice blast resistance breeding program. CONCLUSIONS The development of PPLs and interaction effect analysis in this study provides valuable theoretical foundation and innovative resources for breeding broad-spectrum and durable resistant varieties.
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Affiliation(s)
- Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Yu Chen
- Colleges of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Ling Yu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, China
| | - Yuhong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Niansheng Huang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Hongjuan Ji
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Zhengyuan Dai
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, China
| | - Xijun Chen
- Colleges of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, China.
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
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Sureshkumar V, Dutta B, Kumar V, Prakash G, Mishra DC, Chaturvedi KK, Rai A, Sevanthi AM, Solanke AU. RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5310415. [PMID: 30753479 PMCID: PMC6369264 DOI: 10.1093/database/baz015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 12/13/2022]
Abstract
Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development. Retrieval of candidate genes using different search options like genotypes, tissue, developmental stage of the host, strain, hours/days post-inoculation, physical position and SSR marker information is facilitated in the database. Search options like 'common genes among varieties' and 'strains' have been enabled to identify robust candidate genes. A 2D representation of the data can be used to compare expression profiles across genes, genotypes and strains. To demonstrate the utility of this database, we queried for blast-responsive WRKY genes (fold change ≥5) using their gene IDs. The structural variations in the 12 WRKY genes so identified and their promoter regions were explored in two rice genotypes contrasting for their reaction to blast infection. Expression analysis of these genes in panicle tissue infected with a virulent and an avirulent strain of Magnaporthe oryzae could identify WRKY7, WRKY58, WRKY62, WRKY64 and WRKY76 as potential candidate genes for resistance to panicle blast, as they showed higher expression only in the resistant genotype against the virulent strain. Thus, we demonstrated that RiceMetaSysB can play an important role in providing robust candidate genes for rice blast and BB.
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Affiliation(s)
- V Sureshkumar
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Bipratip Dutta
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vishesh Kumar
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.,Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - G Prakash
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Amolkumar U Solanke
- Indian Council of Agricultural Research (ICAR)-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
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Liu X, Li J, Noman A, Lou Y. Silencing OsMAPK20-5 has different effects on rice pests in the field. PLANT SIGNALING & BEHAVIOR 2019; 14:e1640562. [PMID: 31284822 PMCID: PMC6768226 DOI: 10.1080/15592324.2019.1640562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) play important roles in plant development and adaptive responses to biotic and abiotic stresses. Recently, a rice MAPK gene, OsMAPK20-5, has been reported to protect rice plants against autotoxicity by suppressing herbivore-induced ethylene and nitric oxide signaling. In this context, we observed that silencing OsMAPK20-5 increased the percentage of leaf roll caused by leaf folder Cnaphalocrocis medinalis and the severity of rice blast caused by Magnaporthe grisea but decreased the severity of sheath blight caused by Rhizoctonia solani. These findings show that silencing OsMAPK20-5 has different effects on rice pests in the field, and these differences have important implications for the evolution and exploitation of resistance strategies in plants.
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Affiliation(s)
- Xiaoli Liu
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Jiancai Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ali Noman
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Yonggen Lou
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
- CONTACT Yonggen Lou State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
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Arora K, Rai AK, Devanna BN, Kumari B, Sharma TR. Functional validation of the Pi54 gene by knocking down its expression in a blast-resistant rice line using RNA interference and its effects on other traits. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1241-1250. [PMID: 32291014 DOI: 10.1071/fp18083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/13/2018] [Indexed: 06/11/2023]
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the major diseases affecting the rice (Oryza sativa L.) crop. A major blast resistance gene, Pi54, has already been cloned and deployed in different rice varieties. To understand the role of Pi54 in providing rice blast resistance, we used the RNA interferences (RNAi) approach to knock down the expression of this gene. We showed a high frequency of Agrobacterium tumefaciens-mediated transformation of rice line Taipei 309 containing a single gene (Pi54) for blast resistance. Pi54 RNAi leads to a decreased level of Pi54 transcripts, leading to the susceptibility of otherwise M. oryzae-resistant rice lines. However, among the RNAi knockdown plants, the severity of blast disease varied between the lines. Histochemical analysis of the leaves of knockdown plants inoculated with M. oryzae spores also showed typical cell death and blast lesions. Additionally, Pi54 RNAi also showed an effect on the Hda3 gene, a florigen gene playing a role in rice flowering. By using the RNAi technique, for the first time, we showed that the directed degradation of Pi54 transcripts results in a significant reduction in the rice blast resistance response, suggesting that RNAi is a powerful tool for functional validation of genes.
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Affiliation(s)
- Kirti Arora
- Indian Council of Agricultural Research (ICAR) National Research Centre on Plant Biotechnology, New Delhi-110012, India
| | - Amit Kumar Rai
- Indian Council of Agricultural Research (ICAR) National Research Centre on Plant Biotechnology, New Delhi-110012, India
| | - Basavantraya N Devanna
- Indian Council of Agricultural Research (ICAR) National Research Centre on Plant Biotechnology, New Delhi-110012, India
| | - Banita Kumari
- Indian Council of Agricultural Research (ICAR) National Research Centre on Plant Biotechnology, New Delhi-110012, India
| | - Tilak Raj Sharma
- Indian Council of Agricultural Research (ICAR) National Research Centre on Plant Biotechnology, New Delhi-110012, India
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Marker-aided selection and validation of various
$${ Pi}$$
Pi
gene combinations for rice blast resistance in elite rice variety ADT 43. J Genet 2018. [DOI: 10.1007/s12041-018-0988-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Divya D, Madhavi KR, Dass MA, Maku RV, Mallikarjuna G, Sundaram RM, Laha GS, Padmakumari AP, Patel HK, Prasad MS, Sonti RV, Bentur JS. Expression Profile of Defense Genes in Rice Lines Pyramided with Resistance Genes Against Bacterial Blight, Fungal Blast and Insect Gall Midge. RICE (NEW YORK, N.Y.) 2018; 11:40. [PMID: 30006850 PMCID: PMC6045563 DOI: 10.1186/s12284-018-0231-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/02/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Rice, a major food crop of the world, endures many major biotic stresses like bacterial blight (BB), fungal blast (BL) and the insect Asian rice gall midge (GM) that cause significant yield losses. Progress in tagging, mapping and cloning of several resistance (R) genes against aforesaid stresses has led to marker assisted multigene introgression into elite cultivars for multiple and durable resistance. However, no detailed study has been made on possible interactions among these genes when expressed simultaneously under combined stresses. RESULTS Our studies monitored expression profiles of 14 defense related genes in 11 rice breeding lines derived from an elite cultivar with different combination of R genes against BB, BL and GM under single and multiple challenge. Four of the genes found implicated earlier under combined GM and BB stress were confirmed to be induced (≥ 2 fold) in stem tissue following GM infestation; while one of these, cytochrome P450 family protein, was also induced in leaf in plants challenged by either BB or BL but not together. Three of the genes highlighted earlier in plants challenged by both BB and BL were also found induced in stem under GM challenge. Pi54 the target R gene against BL was also found induced when challenged by GM. Though expression of some genes was noted to be inhibited under combined pest challenge, such effects did not result in compromise in resistance against any of the target pests. CONCLUSION While R genes generally tended to respond to specific pest challenge, several of the downstream defense genes responded to multiple pest challenge either single, sequential or simultaneous, without any distinct antagonism in expression of resistance to the target pests in two of the pyramided lines RPNF05 and RPNF08.
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Affiliation(s)
| | | | | | - Roshan Venkata Maku
- CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
| | | | | | - Gouri Sankar Laha
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030 India
| | | | - Hitendra Kumar Patel
- CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
| | | | - Ramesh Venkata Sonti
- CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007 India
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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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Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 2018; 50:285-296. [DOI: 10.1038/s41588-018-0040-0] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
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Stacking of blast resistance orthologue genes in susceptible indica rice line improves resistance against Magnaporthe oryzae. 3 Biotech 2018; 8:37. [PMID: 29291150 DOI: 10.1007/s13205-017-1062-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023] Open
Abstract
The emergence of new strains of Magnaporthe oryzae (M. oryzae) is associated with recurrent failure of resistance response mediated by single resistance (R) gene in rice. Therefore, stacking or combining of multiple R genes could improve the durability of resistance against multiple strains of M. oryzae. To achieve this, in the present study, intragenic stacking of rice blast resistance orthologue genes Pi54 and Pi54rh was performed through co-transformation approach. Both these genes were expressed under the control of independent promoters and blast susceptible indica rice line IET17021 was used for transformation. The highly virulent M. oryzae strain Mo-ei-ger1 that could knock down most of the major single blast R genes including Pi54 and exhibiting 89% virulence spectrum was used for phenotypic analysis. The stacked transgenic IET17021 lines (Pi54 + Pi54rh) have shown complete resistance to Mo-ei-ger1 strain in comparison to non-transgenic lines. These two R gene stacked indica transgenic lines could serves as a novel germplasm for rice blast resistance breeding programmes.
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Kumari M, Rai AK, Devanna BN, Singh PK, Kapoor R, Rajashekara H, Prakash G, Sharma V, Sharma TR. Co-transformation mediated stacking of blast resistance genes Pi54 and Pi54rh in rice provides broad spectrum resistance against Magnaporthe oryzae. PLANT CELL REPORTS 2017; 36:1747-1755. [PMID: 28905253 DOI: 10.1007/s00299-017-2189-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/27/2017] [Indexed: 05/25/2023]
Abstract
This is the first report of stacking two major blast resistance genes in blast susceptible rice variety using co-transformation method to widen the resistance spectrum against different isolates of Magnaporthe oryzae. Single resistance (R-) gene mediated approach for the management of rice blast disease has met with frequent breakdown in resistance response. Besides providing the durable resistance, gene pyramiding or stacking also imparts broad spectrum resistance against plant pathogens, including rice blast. In the present study, we stacked two R-genes; Pi54 and Pi54rh having broad spectrum resistance against multiple isolates of Magnaporthe oryzae (M. oryzae). Both Pi54 and Pi54rh expressed under independent promoters were transferred into the blast susceptible japonica rice Taipei 309 (TP309) using particle gun bombardment method. Functional complementation analysis of stacked transgenic rice lines showed higher level of resistance to a set of highly virulent M. oryzae isolates collected from different rice growing regions. qRT-PCR analysis has shown M. oryzae induced expression of both the R-genes in stacked transgenic lines. The present study also demonstrated the effectiveness of the strategy for rapid single step gene stacking using co-transformation approach to engineer durable resistance against rice blast disease and also this is the first report in which two blast R-genes are stacked together using co-transformation approach. The two-gene-stacked transgenic line developed in this study can be used further to understand the molecular aspects of defense-related pathways vis-a-vis single R-gene containing transgenic lines.
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Affiliation(s)
- Mandeep Kumari
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Amit Kumar Rai
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - B N Devanna
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Pankaj Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ritu Kapoor
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - H Rajashekara
- Crop Protection Section, Vivekananda Institute of Hill Agriculture, Almora, 263 601, Uttarakhand, India
| | - G Prakash
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.
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Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS One 2017; 12:e0176236. [PMID: 28445532 PMCID: PMC5405977 DOI: 10.1371/journal.pone.0176236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/08/2017] [Indexed: 11/25/2022] Open
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the most destructive disease causing huge losses to rice yield in different parts of the world. Therefore, an attempt has been made to find out the resistance by screening and studying the genetic diversity of eighty released rice varieties by National Rice Research Institute, Cuttack (NRVs) using molecular markers linked to twelve major blast resistance (R) genes viz Pib, Piz, Piz-t, Pik, Pik-p, Pikm Pik-h, Pita/Pita-2, Pi2, Pi9, Pi1 and Pi5. Out of which, nineteen varieties (23.75%) showed resistance, twenty one were moderately resistant (26.25%) while remaining forty varieties (50%) showed susceptible in uniform blast nursery. Rice varieties possessing blast resistance genes varied from four to twelve and the frequencies of the resistance genes ranged from 0 to 100%. The cluster analysis grouped the eighty NRVs into two major clusters at 63% level of genetic similarity coefficient. The PIC value for seventeen markers varied from 0 to 0.37 at an average of 0.20. Out of seventeen markers, only five markers, 195R-1, Pi9-i, Pita3, YL155/YL87 and 40N23r corresponded to three broad spectrum R genes viz. Pi9, Pita/Pita2 and Pi5 were found to be significantly associated with the blast disease with explaining phenotypic variance from 3.5% to 7.7%. The population structure analysis and PCoA divided the entire 80 NRVs into two sub-groups. The outcome of this study would help to formulate strategies for improving rice blast resistance through genetic studies, plant-pathogen interaction, identification of novel R genes, development of new resistant varieties through marker-assisted breeding for improving rice blast resistance in India and worldwide.
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Imam J, Mandal NP, Variar M, Shukla P. Allele Mining and Selective Patterns of Pi9 Gene in a Set of Rice Landraces from India. FRONTIERS IN PLANT SCIENCE 2016; 7:1846. [PMID: 28018384 PMCID: PMC5156731 DOI: 10.3389/fpls.2016.01846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/22/2016] [Indexed: 05/31/2023]
Abstract
Allelic variants of the broad-spectrum blast resistance gene, Pi9 (nucleotide binding site-leucine-rich repeat region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions, and insertion and deletions (InDels) were identified in the 2.9 kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima's D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the leucine-rich repeat domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region, and under low pathotype pressure.
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Affiliation(s)
- Jahangir Imam
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Nimai P. Mandal
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
| | - Mukund Variar
- Biotechnology Laboratory, Central Rainfed Upland Rice Research StationHazaribagh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Azizi P, Rafii MY, Abdullah SNA, Hanafi MM, Maziah M, Sahebi M, Ashkani S, Taheri S, Jahromi MF. Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:773. [PMID: 27379107 PMCID: PMC4911359 DOI: 10.3389/fpls.2016.00773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/17/2016] [Indexed: 05/04/2023]
Abstract
Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.
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Affiliation(s)
- Parisa Azizi
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd Y. Rafii
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Siti N. A. Abdullah
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohamed M. Hanafi
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - M. Maziah
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mahbod Sahebi
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Sadegh Ashkani
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Department of Agronomy and Plant Breeding, Shahr-e-Rey Branch, Islamic Azad UniversityTehran, Iran
| | - Sima Taheri
- Depatment of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohammad F. Jahromi
- Laboratory of animal production, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
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46
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Chen S, Wang WJ, Su J, Wang CY, Feng AQ, Yang JY, Zeng LX, Zhu XY. Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1159528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Wen-juan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Cong-ying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Ai-qing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Jian-yuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Lie-xian Zeng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Xiao-yuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
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Shi J, Li D, Li Y, Li X, Guo X, Luo Y, Lu Y, Zhang Q, Xu Y, Fan J, Huang F, Wang W. Identification of rice blast resistance genes in the elite hybrid rice restorer line Yahui2115. Genome 2016; 58:91-7. [PMID: 26158382 DOI: 10.1139/gen-2015-0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most serious rice diseases worldwide. We previously developed an elite hybrid rice restorer line with high resistance to rice blast, Yahui2115 (YH2115). To identify the blast resistance genes in YH2115, we first performed expression profiling on previously reported blast resistance genes and disease assay on monogenic lines, and we found that Pi2, Pi9, and Pikm were the most likely resistance candidates in YH2115. Furthermore, RNA interference and linkage analysis demonstrated that silencing of Pi2 reduced the blast resistance of YH2115 and a Pi2 linkage marker was closely associated with blast resistance in an F2 population generated from YH2115. These data suggest that the broad-spectrum blast resistance gene Pi2 contributes greatly to the blast resistance of YH2115. Thus, YH2115 could be used as a new germplasm to facilitate rice blast resistance breeding in hybrid rice breeding programs.
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Affiliation(s)
- Jun Shi
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,b Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan 621023, China.,c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Deqiang Li
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Li
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Li
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyi Guo
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China.,e Rice and Sorghum Institute, Sichuan Academy of Agricultural Sciences / Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Deyang 618000, China
| | - Yiwan Luo
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuangen Lu
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Qin Zhang
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Yongju Xu
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Fan
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Fu Huang
- a Department of Plant Pathology, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Wang
- c Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.,d Provincial Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
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Li W, Liu Y, Wang J, He M, Zhou X, Yang C, Yuan C, Wang J, Chern M, Yin J, Chen W, Ma B, Wang Y, Qin P, Li S, Ronald P, Chen X. The durably resistant rice cultivar Digu activates defence gene expression before the full maturation of Magnaporthe oryzae appressorium. MOLECULAR PLANT PATHOLOGY 2016; 17:354-68. [PMID: 26095454 PMCID: PMC6638526 DOI: 10.1111/mpp.12286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice-M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.
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Affiliation(s)
- Weitao Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ya Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jing Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Min He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaogang Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chao Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Can Yuan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jichun Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Junjie Yin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Weilan Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bingtian Ma
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuping Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin at Sichuan, Chengdu, Sichuan, 611130, China
| | - Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shigui Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin at Sichuan, Chengdu, Sichuan, 611130, China
| | - Pamela Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Xuewei Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Key Laboratory of Major Crop Diseases, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin at Sichuan, Chengdu, Sichuan, 611130, China
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Hasan MM, Rafii MY, Ismail MR, Mahmood M, Alam MA, Abdul Rahim H, Malek MA, Latif MA. Introgression of blast resistance genes into the elite rice variety MR263 through marker-assisted backcrossing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:1297-1305. [PMID: 25892666 DOI: 10.1002/jsfa.7222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 04/06/2015] [Accepted: 04/14/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Blast caused by the fungus Magnaporthe oryzae is a significant disease threat to rice across the world and is especially prevalent in Malaysia. An elite, early-maturing, high-yielding Malaysian rice variety, MR263, is susceptible to blast and was used as the recurrent parent in this study. To improve MR263 disease resistance, the Pongsu Seribu 1 rice variety was used as donor of the blast resistance Pi-7(t), Pi-d(t)1 and Pir2-3(t) genes and qLN2 quantitative trait locus (QTL). The objective was to introgress these blast resistance genes into the background of MR263 using marker-assisted backcrossing with both foreground and background selection. RESULTS Improved MR263-BR-3-2, MR263-BR-4-3, MR263-BR-13-1 and MR263-BR-26-4 lines carrying the Pi-7(t), Pi-d(t)1 and Pir2-3(t) genes and qLN2 QTL were developed using the simple sequence repeat (SSR) markers RM5961 and RM263 (linked to the blast resistance genes and QTL) for foreground selection and a collection of 65 polymorphic SSR markers for background selection in backcrossed and selfed generations. A background analysis revealed that the highest rate of recurrent parent genome recovery was 96.1% in MR263-BR-4-3 and 94.3% in MR263-BR-3-2. CONCLUSION The addition of blast resistance genes can be used to improve several Malaysian rice varieties to combat this major disease.
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Affiliation(s)
- Muhammad M Hasan
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Razi Ismail
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Maziah Mahmood
- Deparment of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Md Amirul Alam
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Harun Abdul Rahim
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohammad A Malek
- Bangladesh Institute of Nuclear agriculture (BINA), BAU Campus, 2202, Mymensingh, Bangladesh
| | - Mohammad Abdul Latif
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Bangladesh Rice Research Institute (BRRI), 1701, Gazipur, Bangladesh
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Abhilash Kumar V, Balachiranjeevi CH, Bhaskar Naik S, Rambabu R, Rekha G, Harika G, Hajira SK, Pranathi K, Anila M, Kousik M, Vijay Kumar S, Yugander A, Aruna J, Dilip Kumar T, Vijaya Sudhakara Rao K, Hari Prasad AS, Madhav MS, Laha GS, Balachandran SM, Prasad MS, Viraktamath BC, Ravindra Babu V, Sundaram RM. Development of Gene-Pyramid Lines of the Elite Restorer Line, RPHR-1005 Possessing Durable Bacterial Blight and Blast Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1195. [PMID: 27555861 PMCID: PMC4977911 DOI: 10.3389/fpls.2016.01195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/26/2016] [Indexed: 05/04/2023]
Abstract
RPHR-1005, the stable restorer line of the popular medium slender (MS) grain type rice hybrid, DRRH-3 was improved in this study for resistance against bacterial blight (BB) and blast diseases through marker-assisted backcross breeding (MABB). In this study, four major resistance genes (i.e., Xa21 and Xa33 for BB resistance and Pi2 and Pi54 for blast resistance) have been transferred to RPHR-1005 using RPBio Patho-1 (possessing Xa21 + Pi2), RPBio Patho-2 (possessing Xa21 + Pi54) and FBR1-15EM (possessing Xa33) as the donors. Foreground selection was carried out using PCR-based molecular markers specific for the target resistance genes and the major fertility restorer genes, Rf3 and Rf4, while background selection was carried out using a set of parental polymorphic rice SSR markers and backcrossing was continued uptoBC2 generation. At BC2F2, plants possessing the gene combination- Xa21 + Pi2, Xa21 + Pi54 and Xa33 in homozygous condition and with >92% recovery of the recurrent parent genome (RPG) were identified and intercrossed to combine all the four resistance genes. Twenty-two homozygous, pyramid lines of RPHR-1005 comprising of three single-gene containing lines, six 2-gene containing lines, eight 3-gene containing lines, and five 4-gene containing lines were identified among the double intercross lines at F3 generation (DICF3). They were then evaluated for their resistance against BB and blast, fertility restoration ability and for key agro-morphological traits. While single gene containing lines were resistant to either BB or blast, the 2-gene, 3-gene, and 4-gene pyramid lines showed good level of resistance against both and/or either of the two diseases. Most of the 2-gene, 3-gene, and 4-gene containing pyramid lines showed yield levels and other key agro-morphological and grain quality traits comparable to the original recurrent parent and showed complete fertility restoration ability, with a few showing higher yield as compared to RPHR-1005. Further, the experimental hybrids derived by crossing the gene-pyramid lines of RPHR-1005 with APMS6A (the female parent of DRRH-3), showed heterosis levels equivalent to or higher than DRRH-3. The results of present study exemplify the utility of MABB for targeted improvement of multiple traits in hybrid rice.
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