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Zheng X, Peng Y, Qiao J, Henry R, Qian Q. Wild rice: unlocking the future of rice breeding. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39150344 DOI: 10.1111/pbi.14443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild-type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars.
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Affiliation(s)
- Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Jiyue Qiao
- Yazhouwan National Laboratory, Sanya, China
| | - Robert Henry
- University of Queensland, Brisbane, Queensland, Australia
| | - Qian Qian
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing, China
- Yazhouwan National Laboratory, Sanya, China
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2
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Chen P, Wang J, Liu Q, Liu J, Mo Q, Sun B, Mao X, Jiang L, Zhang J, Lv S, Yu H, Chen W, Liu W, Li C. Transcriptome and Metabolome Analysis of Rice Cultivar CBB23 after Inoculation by Xanthomonas oryzae pv. oryzae Strains AH28 and PXO99 A. PLANTS (BASEL, SWITZERLAND) 2024; 13:1411. [PMID: 38794481 PMCID: PMC11124827 DOI: 10.3390/plants13101411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Bacterial leaf blight (BLB), among the most serious diseases in rice production, is caused by Xanthomonas oryzae pv. oryzae (Xoo). Xa23, the broadest resistance gene against BLB in rice, is widely used in rice breeding. In this study, the rice variety CBB23 carrying the Xa23 resistance gene was inoculated with AH28 and PXO99A to identify differentially expressed genes (DEGs) associated with the resistance. Transcriptome sequencing of the infected leaves showed 7997 DEGs between the two strains at different time points, most of which were up-regulated, including cloned rice anti-blight, peroxidase, pathology-related, protein kinase, glucosidase, and other coding genes, as well as genes related to lignin synthesis, salicylic acid, jasmonic acid, and secondary metabolites. Additionally, the DEGs included 40 cloned, five NBS-LRR, nine SWEET family, and seven phenylalanine aminolyase genes, and 431 transcription factors were differentially expressed, the majority of which belonged to the WRKY, NAC, AP2/ERF, bHLH, and MYB families. Metabolomics analysis showed that a large amount of alkaloid and terpenoid metabolite content decreased significantly after inoculation with AH28 compared with inoculation with PXO99A, while the content of amino acids and their derivatives significantly increased. This study is helpful in further discovering the pathogenic mechanism of AH28 and PXO99A in CBB23 rice and provides a theoretical basis for cloning and molecular mechanism research related to BLB resistance in rice.
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Affiliation(s)
- Pingli Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junjie Wang
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junjie Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qiaoping Mo
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Bingrui Sun
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xingxue Mao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Liqun Jiang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jing Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shuwei Lv
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hang Yu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Weixiong Chen
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China
| | - Wei Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chen Li
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, 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, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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3
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Su XX, Wan TT, Gao YD, Zhang SH, Chen X, Huang LQ, Wang W. Action mechanism of the potential biocontrol agent Brevibacillus laterosporus SN19-1 against Xanthomonas oryzae pv. oryzae causing rice bacterial leaf blight. Arch Microbiol 2023; 206:40. [PMID: 38142456 DOI: 10.1007/s00203-023-03754-y] [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: 09/09/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
The causal agent of rice bacterial leaf blight (BLB) is Xanthomonas oryzae pv. oryzae (Xoo), which causes serious damage to rice, leading to yield reduction or even crop failure. Brevibacillus laterosporus SN19-1 is a biocontrol strain obtained by long-term screening in our laboratory, which has a good antagonistic effect on a variety of plant pathogenic bacteria. In this study, we investigated the efficacy and bacterial inhibition of B. laterosporus SN19-1 against BLB to lay the theoretical foundation and research technology for the development of SN19-1 as a biopesticide of BLB. It was found that SN19-1 has the ability to fix nitrogen, detoxify organic phosphorus, and produce cellulase, protease, and siderophores, as well as IAA. In a greenhouse pot experiment, the control efficiency of SN19-1 against BLB was as high as 90.92%. Further investigation of the inhibitory mechanism of SN19-1 on Xoo found that the biofilm formation ability of Xoo was inhibited and the pathogenicity was weakened after the action of SN19-1 sterile supernatant on Xoo. The activities of enzymes related to respiration and the energy metabolism of Xoo were significantly inhibited, while the level of intracellular reactive oxygen species was greatly increased. Scanning electron microscopy observations showed folds on the surface of Xoo. A significant increase in cell membrane permeability and outer membrane permeability and a decrease in cell membrane fluidity resulted in the extravasation of intracellular substances and cell death. The results of this study highlight the role of B. laterosporus SN19-1 against the pathogen of BLB and help elucidate the underlying molecular mechanisms.
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Affiliation(s)
- Xin-Xin Su
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Tian-Tian Wan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong-Dong Gao
- Agriculture Technology Extension Service Center of Shanghai, Shanghai, 201103, China
| | - Song-Han Zhang
- Agriculture Technology Extension Service Center of Shanghai, Shanghai, 201103, China
| | - Xiu Chen
- Agriculture Technology Extension Service Center of Shanghai, Shanghai, 201103, China
| | - Lan-Qi Huang
- Agriculture Technology Extension Service Center of Shanghai, Shanghai, 201103, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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4
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Singh G, Singh N, Ellur RK, Balamurugan A, Prakash G, Rathour R, Mondal KK, Bhowmick PK, Gopala Krishnan S, Nagarajan M, Seth R, Vinod KK, Singh V, Bollinedi H, Singh AK. Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding. Int J Mol Sci 2023; 24:16081. [PMID: 38003271 PMCID: PMC10671030 DOI: 10.3390/ijms242216081] [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: 07/24/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 11/26/2023] Open
Abstract
Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers.
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Affiliation(s)
- Gagandeep Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Niraj Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - G. Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - Rajeev Rathour
- Department of Agriculture Biotechnology, CSKHPKV, Palampur 176062, Himachal Pradesh, India
| | - Kalyan Kumar Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (G.P.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - S. Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India
| | - Rakesh Seth
- Regional Station, ICAR-Indian Agricultural Research Institute, Karnal 132001, Haryana, India;
| | - K. K. Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Varsha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India (N.S.); (P.K.B.); (S.G.K.); (K.K.V.)
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5
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Sinha P, Kumar T. D, Sk H, Solanki M, Gokulan CG, Das A, Miriyala A, Gonuguntala R, Elumalai P, M. B. V. N K, S. K. M, Kumboju C, Arra Y, G. S. L, Chirravuri NN, Patel HK, Ghazi IA, Kim SR, Jena KK, Hanumanth SR, Oliva R, Mangrauthia SK, Sundaram RM. Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice ( Oryza officinalis) that confers bacterial blight resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1173063. [PMID: 37692438 PMCID: PMC10485833 DOI: 10.3389/fpls.2023.1173063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023]
Abstract
Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t.
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Affiliation(s)
- Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Dilip Kumar T.
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Manish Solanki
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. G. Gokulan
- Crop Improvement, Council of Scientific & Industrial Research (CSIR)-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ayyappa Das
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Anila Miriyala
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - Punniakoti Elumalai
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kousik M. B. V. N
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Masthani S. K.
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Chaitra Kumboju
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Yugander Arra
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Institute of Molecular Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Laha G. S.
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - N. Neerja Chirravuri
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Hitendra Kumar Patel
- Crop Improvement, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sung-Ryul Kim
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Kshirod K. Jena
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha, India
| | | | - Ricardo Oliva
- Safe and Sustainable Value Chain, World Vegetable Center, Tainan, Taiwan
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6
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Taura S, Ichitani K. Chromosomal Location of xa19, a Broad-Spectrum Rice Bacterial Blight Resistant Gene from XM5, a Mutant Line from IR24. PLANTS (BASEL, SWITZERLAND) 2023; 12:602. [PMID: 36771686 PMCID: PMC9919685 DOI: 10.3390/plants12030602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Bacterial blight is an important rice disease caused by bacteria named Xanthomonas oryzae pv. oryzae (Xoo). XM5 is an Xoo resistant mutant line with the genetic background of IR24, an Indica Xoo susceptible cultivar, induced by a chemical mutagen N-methyl-N-nitrosourea (MNU). XM5 carries a recessive Xoo resistant gene, xa19. Trisomic analysis was conducted using the cross between XM5 and the trisomic series under the genetic background of IR24, showing that xa19 was located on chromosome 7. The approximate chromosomal location was found using 37 surely resistant plants in the F2 population from XM5 × Kinmaze, which was susceptible to most Japanese Xoo races. The IAS44 line carries a Japonica cultivar Asominori chromosomal segment covering the xa19 locus under the IR24 genetic background. Linkage analysis using the F2 population from the cross between XM5 and IAS44 revealed that xa19 was located within the 0.8 cM region between RM8262 and RM6728. xa19 is not allelic to the known Xoo resistant genes. However, its location suggests that it might be allelic to a lesion-mimic mutant gene spl5, some alleles of which are resistant to several Xoo races. Together with xa20 and xa42, three Xoo resistant genes were induced from IR24 by MNU. The significance of chemical mutagen as a source of Xoo resistance was discussed.
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Affiliation(s)
- Satoru Taura
- Institute of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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7
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Bai X, Fang H, He Y, Zhang J, Tao M, Wu Q, Yang G, Wei Y, Tang Y, Tang L, Lou B, Deng S, Yang Y, Feng X. Dynamic UAV Phenotyping for Rice Disease Resistance Analysis Based on Multisource Data. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0019. [PMID: 37040287 PMCID: PMC10076055 DOI: 10.34133/plantphenomics.0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/09/2022] [Indexed: 05/27/2023]
Abstract
Bacterial blight poses a threat to rice production and food security, which can be controlled through large-scale breeding efforts toward resistant cultivars. Unmanned aerial vehicle (UAV) remote sensing provides an alternative means for the infield phenotype evaluation of crop disease resistance to relatively time-consuming and laborious traditional methods. However, the quality of data acquired by UAV can be affected by several factors such as weather, crop growth period, and geographical location, which can limit their utility for the detection of crop disease and resistant phenotypes. Therefore, a more effective use of UAV data for crop disease phenotype analysis is required. In this paper, we used time series UAV remote sensing data together with accumulated temperature data to train the rice bacterial blight severity evaluation model. The best results obtained with the predictive model showed an R p 2 of 0.86 with an RMSEp of 0.65. Moreover, model updating strategy was used to explore the scalability of the established model in different geographical locations. Twenty percent of transferred data for model training was useful for the evaluation of disease severity over different sites. In addition, the method for phenotypic analysis of rice disease we built here was combined with quantitative trait loci (QTL) analysis to identify resistance QTL in genetic populations at different growth stages. Three new QTLs were identified, and QTLs identified at different growth stages were inconsistent. QTL analysis combined with UAV high-throughput phenotyping provides new ideas for accelerating disease resistance breeding.
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Affiliation(s)
- Xiulin Bai
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Hui Fang
- Huzhou Institute of Zhejiang University, Huzhou 313000, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Mingzhu Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Qingguan Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Guofeng Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yuzhen Wei
- School of Information Engineering, Huzhou University, Huzhou 313000, China
| | - Yu Tang
- Academy of Interdisciplinary Studies, Guangdong Polytechnic Normal University, Guangzhou 510665, China
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011-3270, USA
| | - Binggan Lou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou 31002, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
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8
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Javed MA, Ali SW, Ashfaq M, Tabassam J, Ali M, IhsanUllah M, Nayab SF, Kaya Y, Khalili E, Ali Q, Yau TE. Molecular profiling of bacterial blight resistance in Malaysian rice cultivars. BRAZ J BIOL 2022; 82:e256189. [PMID: 36541981 DOI: 10.1590/1519-6984.256189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022] Open
Abstract
Bacteria blight is one of the most serious bacterial diseases of rice worldwide. The identification of genetic potential against bacterial blight in the existing rice resources is a prerequisite to develop multigenic resistance to combat the threat of climate change. This investigation was conducted to evaluate alleles variation in 38 Malaysian cultivars using thirteen Simple Sequences Repeats markers and one Sequence Tagged Sites (STS) marker which were reported to be linked with the resistance to bacterial blight. Based on molecular data, a dendrogram was constructed which classified the rice cultivars into seven major clusters at 0.0, 0.28 and 0.3 of similarity coefficient. Cluster 5 was the largest group comprised of ten rice cultivars where multiple genes were identified. However, xa13 could not be detected in the current rice germplasm, whereas xa2 was detected in 25 cultivars. Molecular analysis revealed that Malaysian rice cultivars possess multigenic resistance.
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Affiliation(s)
- M A Javed
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan.,Universiti Teknologi Malaysia - UTM Skudai, Faculty of Science, Department of Biosciences, Johor Bahru, Malaysia
| | - S W Ali
- University of the Punjab, Department of Food Science and Technology, Faculty of Agricultural Sciences, Lahore, Pakistan
| | - M Ashfaq
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - J Tabassam
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - M Ali
- University of the Punjab, Faculty of Agricultural Sciences, Department of Entomology, Lahore, Pakistan
| | - M IhsanUllah
- Cotton Research Institute Multan, Multan, Pakistan
| | - S F Nayab
- Sorghum Research Sub Station, Dera Ghazi Khan, Pakistan
| | - Y Kaya
- Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - E Khalili
- Tarbiat Modarres University, Faculty of Science, Department of Plant Science, Tehran, Iran
| | - Q Ali
- University of the Punjab, Faculty of Agricultural Sciences, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - T E Yau
- Universiti Teknologi Malaysia - UTM Skudai, Faculty of Science, Department of Biosciences, Johor Bahru, Malaysia
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9
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Lu Y, Zhong Q, Xiao S, Wang B, Ke X, Zhang Y, Yin F, Zhang D, Jiang C, Liu L, Li J, Yu T, Wang L, Cheng Z, Chen L. A new NLR disease resistance gene Xa47 confers durable and broad-spectrum resistance to bacterial blight in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1037901. [PMID: 36507384 PMCID: PMC9730417 DOI: 10.3389/fpls.2022.1037901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 06/01/2023]
Abstract
Bacterial blight (BB) induced by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating bacterial disease in rice. The use of disease resistance (R) genes is the most efficient method to control BB. Members of the nucleotide-binding domain and leucine-rich repeat containing protein (NLR) family have significant roles in plant defense. In this study, Xa47, a new bacterial blight R gene encoding a typical NLR, was isolated from G252 rice material, and XA47 was localized in the nucleus and cytoplasm. Among 180 rice materials tested, Xa47 was discovered in certain BB-resistant materials. Compared with the wild-type G252, the knockout mutants of Xa47 was more susceptible to Xoo. By contrast, overexpression of Xa47 in the susceptible rice material JG30 increased BB resistance. The findings indicate that Xa47 positively regulates the Xoo stress response. Consequently, Xa47 may have application potential in the genetic improvement of plant disease resistance. The molecular mechanism of Xa47 regulation merits additional examination.
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Affiliation(s)
- Yuanda Lu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Qiaofang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Suqin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Bo Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Xue Ke
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Yun Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Fuyou Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Dunyu Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Cong Jiang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Li Liu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Jinlu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Tengqiong Yu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Lingxian Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Zaiquan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, China
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10
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Chen S, Feng A, Wang C, Zhao J, Feng J, Chen B, Yang J, Wang W, Zhang M, Chen K, Chen W, Su J, Liu B, Zhu X. Identification and fine-mapping of Xo2, a novel rice bacterial leaf streak resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3195-3209. [PMID: 35871691 DOI: 10.1007/s00122-022-04179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
A novel rice resistance gene, Xo2, influencing pathogenesis of the bacterial leaf streak disease, has been identified, and candidate genes for Xo2 in the fine mapping region have been shown to be involved in bacterial leaf streak resistance. Rice (Oryza sativa) bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola (Xoc), is one of the most serious rice bacterial diseases. The deployment of host resistance genes is an effective approach for controlling this disease. The cultivar BHADOIA 303 (X455) from Bangladesh is resistant to most of Chinese Xoc races. To identify and map the resistance gene(s) involved in Xoc resistance, we examined the association between phenotypic and genotypic variations in two F2 populations derived from crosses between X455/Jingang 30 and X455/Wushansimiao. The segregation ratios of the F2 progeny were consistent with the action of a single dominant resistance gene, which was designated as Xo2. Based on rice SNP chip (GSR40K) assays of X455, Jingang 30, and resistant and susceptible pools thereof, we mapped Xo2 to the region from 10 Mb to 12.5 Mb on chromosome 2. The target gene was further finely mapped between the markers RM12941 and D6-1 within an approximately 110-kb region. The de novo sequencing and gene annotation of X455 and Jingang 30 revealed nineteen predicted genes within the target region. RNA-seq and expression analysis showed that four candidate genes, including Osa002T0115800, encoding an NLR resistance protein, were distinctly upregulated. Differential sequence and synteny analysis between X455 and Jingang 30 suggested that Osa002T0115800 is likely the functional Xo2 gene. This study lays a foundation for marker-assisted selection resistance breeding against rice bacterial leaf streak and the further cloning of Xo2.
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Affiliation(s)
- Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aiqing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Congying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Junliang Zhao
- Rice Research Institute and Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jinqi Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bing Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jianyuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenjuan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Meiying Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Kailing Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Weiqin Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bin Liu
- Rice Research Institute and Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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11
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Identification of Putative SNP Markers Associated with Resistance to Egyptian Loose Smut Race(s) in Spring Barley. Genes (Basel) 2022; 13:genes13061075. [PMID: 35741837 PMCID: PMC9223236 DOI: 10.3390/genes13061075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/03/2023] Open
Abstract
Loose smut (LS) disease is a serious problem that affects barley yield. Breeding of resistant cultivars and identifying new genes controlling LS has received very little attention. Therefore, it is important to understand the genetic basis of LS control in order to genetically improve LS resistance. To address this challenge, a set of 57 highly diverse barley genotypes were inoculated with Egyptian loose smut race(s) and the infected seeds/plants were evaluated in two growing seasons. Loose smut resistance (%) was scored on each genotype. High genetic variation was found among all tested genotypes indicating considerable differences in LS resistance that can be used for breeding. The broad-sense heritability (H2) of LS (0.95) was found. Moreover, genotyping-by-sequencing (GBS) was performed on all genotypes and generated in 16,966 SNP markers which were used for genetic association analysis using single-marker analysis. The analysis identified 27 significant SNPs distributed across all seven chromosomes that were associated with LS resistance. One SNP (S6_17854595) was located within the HORVU6Hr1G010050 gene model that encodes a protein kinase domain-containing protein (similar to the Un8 LS resistance gene, which contains two kinase domains). A TaqMan marker (0751D06 F6/R6) for the Un8 gene was tested in the diverse collection. The results indicated that none of the Egyptian genotypes had the Un8 gene. The result of this study provided new information on the genetic control of LS resistance. Moreover, good resistance genotypes were identified and can be used for breeding cultivars with improved resistance to Egyptian LS.
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12
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Sanya DRA, Syed-Ab-Rahman SF, Jia A, Onésime D, Kim KM, Ahohuendo BC, Rohr JR. A review of approaches to control bacterial leaf blight in rice. World J Microbiol Biotechnol 2022; 38:113. [PMID: 35578069 DOI: 10.1007/s11274-022-03298-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 01/16/2023]
Abstract
The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
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Affiliation(s)
| | | | - Aiqun Jia
- School of Environmental & Biological Engineering, Nanjing University of Science and Technology, Xiaolingwei No. 200, Xuanwu District, 210014, Nanjing, Jiangsu, China
| | - Djamila Onésime
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kyung-Min Kim
- School of Applied BioSciences, College of Agriculture & Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-Gu, 41566, Daegu, Korea
| | - Bonaventure Cohovi Ahohuendo
- Faculty of Agricultural Sciences, University of Abomey-Calavi, 526 Recette Principale, Cotonou 01, 01 BP, Abomey-Calavi, Benin
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Eck Institute of Global Health, Environmental Change Initiative, 178 Galvin Life Science Center, 46556, Notre Dame, IN, USA
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13
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Yugander A, Ershad M, Muthuraman PP, Prakasam V, Ladhalakshmi D, Sheshu Madhav M, Srinivas Prasad M, Sundaram RM, Laha GS. Understanding the variability of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae in Andhra Pradesh, India. J Basic Microbiol 2021; 62:185-196. [PMID: 34913505 DOI: 10.1002/jobm.202100406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/03/2021] [Accepted: 11/27/2021] [Indexed: 11/07/2022]
Abstract
Bacterial blight (BB) of rice is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). The evolution of new pathogenic races of bacterial blight pathogen is always a potential threat for rice production. The deployment of pathotype-specific resistant genes in the host plants is a feasible strategy to develop BB-resistant varieties. Therefore, continuous disease monitoring, identification of Xoo pathotypes, and their distribution are crucial to managing BB. In this study, 71 Xoo isolates were collected from the Godavari delta in Andhra Pradesh (India) and their virulence profiles on rice BB differentials were characterized. Data revealed that different International Rice Bacterial Blight (IRBB) lines with single BB resistance genes were susceptible to 73.2%-97.2% of the isolates, except IRBB13 (possessing BB resistance gene, xa13) which showed a moderately susceptible or susceptible reaction to 47.9% of the isolates. Three gene combination rice differentials like IRBB56 (Xa4 + xa5 + xa13), IRBB57 (Xa4 + xa5 + Xa21), IRBB58 (Xa4 + xa13 + Xa21), and IRBB59 (xa5 + xa13 + Xa21) showed very broad-spectrum resistance to majority of the Xoo isolates from the region. None of the tested Xoo isolates were virulent on IRBB58 (Xa4 + xa13 + Xa21), IRBB60 (Xa4 + xa5 + xa13 + Xa21), and IRBB66 (Xa4 + xa5 + Xa7 + xa13 + Xa21). Based on the virulence reaction, 71 Xoo isolates were grouped into 10 major pathotypes. Highly virulent pathotypes viz., IXoPt # 14, 17, 19, and 22 can break the resistance of major BB-resistant genes and were commonly distributed throughout the surveyed regions. Genotypic data of 71 Xoo isolates using J3 primer divided them into three major clusters. Cluster I consisted of 24 Xoo isolates that belonged to pathotype IXoPt-19. Cluster II consisted of 41 Xoo isolates belonging to seven different pathotypes, and Cluster III was composed of six isolates from three different pathotypes. The findings of this study will be helpful to develop rice varieties with pathotype-specific broad-spectrum resistance against BB.
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Affiliation(s)
- Arra Yugander
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India.,Institute for Molecular Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Md Ershad
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Pitchiah P Muthuraman
- Department of Transfer of Technology and Training, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Vellaisamy Prakasam
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Duraisamy Ladhalakshmi
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Maganti Sheshu Madhav
- Department of Plant Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | | | - Raman M Sundaram
- Department of Plant Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Gouri S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
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14
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Xing J, Zhang D, Yin F, Zhong Q, Wang B, Xiao S, Ke X, Wang L, Zhang Y, Zhao C, Lu Y, Chen L, Cheng Z, Chen L. Identification and Fine-Mapping of a New Bacterial Blight Resistance Gene, Xa47(t), in G252, an Introgression Line of Yuanjiang Common Wild Rice ( Oryza rufipogon). PLANT DISEASE 2021; 105:4106-4112. [PMID: 34261357 DOI: 10.1094/pdis-05-21-0939-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F2 population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F2 progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.
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Affiliation(s)
- Jiaxin Xing
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Dunyu Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Fuyou Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Qiaofang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Bo Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Suqin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Xue Ke
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lingxian Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Yun Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Caimei Zhao
- College of Life Science, Yunnan University, Kunming, Yunnan 650091, P.R. China
| | - Yuanda Lu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Zaiquan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, Yunnan 650205, P.R. China
| | - Lijuan Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming, Yunnan 650201, P.R. China
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15
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Zhang F, Hu Z, Wu Z, Lu J, Shi Y, Xu J, Wang X, Wang J, Zhang F, Wang M, Shi X, Cui Y, Vera Cruz C, Zhuo D, Hu D, Li M, Wang W, Zhao X, Zheng T, Fu B, Ali J, Zhou Y, Li Z. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics. THE PLANT CELL 2021; 33:2538-2561. [PMID: 34467412 PMCID: PMC8408478 DOI: 10.1093/plcell/koab146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 05/15/2021] [Indexed: 05/23/2023]
Abstract
A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Zhiqiang Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jialing Lu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Mingming Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiaorong Shi
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Yanru Cui
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Dalong Zhuo
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Dandan Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Yongli Zhou
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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16
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Chen X, Liu P, Mei L, He X, Chen L, Liu H, Shen S, Ji Z, Zheng X, Zhang Y, Gao Z, Zeng D, Qian Q, Ma B. Xa7, a new executor R gene that confers durable and broad-spectrum resistance to bacterial blight disease in rice. PLANT COMMUNICATIONS 2021; 2:100143. [PMID: 34027390 PMCID: PMC8132130 DOI: 10.1016/j.xplc.2021.100143] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 05/03/2023]
Abstract
Bacterial blight (BB) is a globally devastating rice disease caused by Xanthomonas oryzae pv. oryzae (Xoo). The use of disease resistance (R) genes in rice breeding is an effective and economical strategy for the control of this disease. Nevertheless, a majority of R genes lack durable resistance for long-term use under global warming conditions. Here, we report the isolation of a novel executor R gene, Xa7, that confers extremely durable, broad-spectrum, and heat-tolerant resistance to Xoo. The expression of Xa7 was induced by incompatible Xoo strains that secreted the transcription activator-like effector (TALE) AvrXa7 or PthXo3, which recognized effector binding elements (EBEs) in the Xa7 promoter. Furthermore, Xa7 induction was faster and stronger under high temperatures. Overexpression of Xa7 or co-transformation of Xa7 with avrXa7 triggered a hypersensitive response in plants. Constitutive expression of Xa7 activated a defense response in the absence of Xoo but inhibited the growth of transgenic rice plants. In addition, analysis of over 3000 rice varieties showed that the Xa7 locus was found primarily in the indica and aus subgroups. A variation consisting of an 11-bp insertion and a base substitution (G to T) was found in EBEAvrXa7 in the tested varieties, resulting in a loss of Xa7 BB resistance. Through a decade of effort, we have identified an important BB resistance gene and characterized its distinctive interaction with Xoo strains; these findings will greatly facilitate research on the molecular mechanism of Xa7-mediated resistance and promote the use of this valuable gene in breeding.
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Affiliation(s)
- Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Pengcheng Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Le Mei
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoling He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Long Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Hui Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Shurong Shen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhandong Ji
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xixi Zheng
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuchen Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhenyu Gao
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Dali Zeng
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Qian Qian
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Corresponding author
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17
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Jiang N, Fu J, Zeng Q, Liang Y, Shi Y, Li Z, Xiao Y, He Z, Wu Y, Long Y, Wang K, Yang Y, Liu X, Peng J. Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice. PLANTA 2021; 253:94. [PMID: 33830376 DOI: 10.1007/s00425-021-03612-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Using genome-wide SNP association mapping, a total of 77 and 7 loci were identified for rice bacterial blight and bacterial leaf streak resistance, respectively, which may facilitate rice resistance improvement. Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.
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Affiliation(s)
- Nan Jiang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China
- Huazhi Bio-Tech Company Ltd., Changsha, China
- Key Laboratory of Southern Rice Innovation and Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Company Ltd., Changsha, China
| | - Jun Fu
- Key Laboratory of Southern Rice Innovation and Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Company Ltd., Changsha, China
| | - Qin Zeng
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Yi Liang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Yanlong Shi
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Zhouwei Li
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Youlun Xiao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhizhou He
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Yuntian Wu
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Yu Long
- Huazhi Bio-Tech Company Ltd., Changsha, China
| | - Kai Wang
- Key Laboratory of Southern Rice Innovation and Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Company Ltd., Changsha, China
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation and Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Company Ltd., Changsha, China
| | - Xionglun Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China.
| | - Junhua Peng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China.
- Huazhi Bio-Tech Company Ltd., Changsha, China.
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18
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Xu X, Xu Z, Ma W, Haq F, Li Y, Shah SMA, Zhu B, Zhu C, Zou L, Chen G. TALE-triggered and iTALE-suppressed Xa1-mediated resistance to bacterial blight is independent of rice transcription factor subunits OsTFIIAγ1 or OsTFIIAγ5. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3249-3262. [PMID: 33544818 DOI: 10.1093/jxb/erab054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Xa1-mediated resistance to rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is triggered by transcription activator-like effectors (TALEs) and suppressed by interfering TALEs (iTALEs). TALEs interact with the rice transcription factor OsTFIIAγ1 or OsTFIIAγ5 (Xa5) to activate expression of target resistance and/or susceptibility genes. However, it is not clear whether OsTFIIAγ is involved in TALE-triggered and iTALE-suppressed Xa1-mediated resistance. In this study, genome-edited mutations in OsTFIIAγ5 or OsTFIIAγ1 of Xa1-containing rice 'IRBB1' and Xa1-transgenic plants of xa5-containing rice 'IRBB5' did not impair the activation or suppression of Xa1-mediated resistance. Correspondingly, the expression pattern of Xa1 in mutated OsTFIIAγ5 and OsTFIIAγ1 rice lines and 'IRBB1' rice was similar. In contrast, the expression of OsSWEET11 was repressed in rice lines mutated in OsTFIIAγ5 and OsTFIIAγ1. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation assays showed that both TALE PthXo1 and iTALE Tal3a interacted with OsTFIIAγ1 and OsTFIIAγ5 in plant nuclei. These results indicated that TALE-triggered and iTALE-suppressed Xa1-mediated resistance to bacterial blight is independent of OsTFIIAγ1 or OsTFIIAγ5 in rice, and suggest that an unknown factor is potentially involved in the interaction of Xa1, TALEs and iTALEs.
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Affiliation(s)
- Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Li
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Changxiang Zhu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Lifang Zou
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai, China
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19
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Msami JA, Kawaguchi Y, Ichitani K, Taura S. Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24. BREEDING SCIENCE 2021; 71:144-154. [PMID: 34377062 PMCID: PMC8329881 DOI: 10.1270/jsbbs.20104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 06/13/2023]
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F2 population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F2 population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F2 population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.
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Affiliation(s)
- Jessey Anderson Msami
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yoshiki Kawaguchi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Satoru Taura
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Division of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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20
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Identification of Bacterial Blight Resistance Loci in Rice ( Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study. PLANTS 2021; 10:plants10030518. [PMID: 33802191 PMCID: PMC8001028 DOI: 10.3390/plants10030518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1–6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.
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21
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Dai A, Zhang R, Li C, Yu L, Wang Y, Wu J. Synthesis and Biological Activity of N-Cyano Sulfonimide Derivatives Bearing Trifluoromethyl Pyridinamide. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202102017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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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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23
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain. Front Microbiol 2020; 11:579504. [PMID: 33193207 PMCID: PMC7610140 DOI: 10.3389/fmicb.2020.579504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) constrains production in major rice growing countries of Asia. Xoo injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” (S) genes that are important for disease. The bacterial blight resistance gene xa5, which reduces TALE activity generally, has been widely deployed. However, strains defeating xa5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major S gene SWEET11 strongly enough to be effective even when diminished by xa5. The findings suggest international migration of the xa5-compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Prasanta K Dash
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gouri S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jagjeet S Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K Singh
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
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