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Naveenkumar R, Anandan A, Prabhukarthikeyan SR, Mahender A, Sangeetha G, Vaish SS, Singh PK, Hussain W, Ali J. Dissecting genomic regions and underlying sheath blight resistance traits in rice ( Oryza sativa L.) using a genome-wide association study. PLANT DIRECT 2023; 7:e540. [PMID: 38028647 PMCID: PMC10667636 DOI: 10.1002/pld3.540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023]
Abstract
The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.
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Affiliation(s)
- R Naveenkumar
- Crop Improvement DivisionICAR‐National Rice Research Institute (NRRI)CuttackOdishaIndia
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
- Division of Plant Pathology, School of Agricultural SciencesKarunya Institute of Technology and SciencesCoimbatoreTamil NaduIndia
| | - Annamalai Anandan
- Crop Improvement DivisionICAR‐National Rice Research Institute (NRRI)CuttackOdishaIndia
- ICAR‐Indian Institute of Seed ScienceBangaloreKarnatakaIndia
| | | | - Anumalla Mahender
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
| | - Ganesan Sangeetha
- Division of Crop ProtectionICAR‐Indian Institute of Horticultural ResearchBangaloreKarnatakaIndia
| | - Shyam Saran Vaish
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
| | - Pawan Kumar Singh
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
| | - Waseem Hussain
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
| | - Jauhar Ali
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
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Chen YN, Wu DH, Chen MC, Hsieh MT, Jwo WS, Lin GC, Chen RK, Chou HP, Chen PC. Dynamics of spatial and temporal population structure of Pyricularia oryzae in Taiwan. PEST MANAGEMENT SCIENCE 2023; 79:4254-4263. [PMID: 37341444 DOI: 10.1002/ps.7621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/28/2023] [Accepted: 06/21/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND To gain a better understanding of how Pyricularia oryzae population shifts is important for selecting suitable resistance genes for rice breeding programs. However, the relationships between P. oryzae pathogenic dynamics, geographic distribution, rice varieties, and timeline are not well studied. RESULTS Resistance genes Piz-5, Pi9(t), Pi12(t), Pi20(t), Pita-2, and Pi11 showed stable resistance to the Taiwan rice blast fungus over 8 years of observations. Furthermore, 1749 rice blast isolates were collected from 2014 to 2021 and categorized into five pathotype clusters based on their correlation analysis between the geographic sources and virulence of Lijiangxintuanheigu monogenic lines. A detailed map of their distributions in Taiwan is presented. Isolates collected from the western region of Taiwan had greater pathotype diversity than those from the east region. Isolates collected from the subtropical region had greater diversity than those from the tropical region. Rice cultivars carrying Pik alleles were highly susceptible to pathotype L4. Cultivars with Piz-t were highly susceptible to pathotype L5, and those with Pish were highly susceptible to pathotype L1. The geographical distribution of each pathotype was distinct, and the population size of each pathotype fluctuated significantly each year. CONCLUSION The regional mega cultivars significantly impact the evolution of Pyricularia oryzae in Taiwan within the span of 8 years. However, the annual fluctuation of pathotype populations likely correlate to the rising annual temperatures that selected pathotype clusters by their optimal growth temperature. The results will provide useful information for effective disease management, and enable the R-genes to prolong their function in the fields. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yi-Nian Chen
- Plant Pathology Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taiwan
- Department of Plant Pathology, National Chung Hsing University, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taiwan
| | - Mei-Chun Chen
- Plant Pathology Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taiwan
| | - Meng-Ting Hsieh
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taiwan
| | - Woei-Shyuan Jwo
- Technical Service Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taiwan
| | - Guo-Cih Lin
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Taiwan
| | - Rong-Kuen Chen
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Taiwan
| | - Hau-Ping Chou
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Taiwan
| | - Pei-Chen Chen
- Department of Plant Pathology, National Chung Hsing University, Taiwan
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Xie Y, Wang Y, Yu X, Lin Y, Zhu Y, Chen J, Xie H, Zhang Q, Wang L, Wei Y, Xiao Y, Cai Q, Zheng Y, Wang M, Xie H, Zhang J. SH3P2, an SH3 domain-containing protein that interacts with both Pib and AvrPib, suppresses effector-triggered, Pib-mediated immunity in rice. MOLECULAR PLANT 2022; 15:1931-1946. [PMID: 36321201 DOI: 10.1016/j.molp.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/03/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Plants usually keep resistance (R) proteins in a static state under normal conditions to avoid autoimmunity and save energy for growth, but R proteins can be rapidly activated upon perceiving pathogen invasion. Pib, the first cloned blast disease R gene in rice, encoding a nucleotide-binding leucine-rich repeat (NLR) protein, mediates resistance to the blast fungal (Magnaporthe oryzae) isolates carrying the avirulence gene AvrPib. However, the molecular mechanisms about how Pib recognizes AvrPib and how it is inactivated and activated remain largely unclear. In this study, through map-based cloning and CRISPR-Cas9 gene editing, we proved that Pib contributes to the blast disease resistance of rice cultivar Yunyin (YY). Furthermore, an SH3 domain-containing protein, SH3P2, was found to associate with Pib mainly at clathrin-coated vesicles in rice cells, via direct binding with the coiled-coil (CC) domain of Pib. Interestingly, overexpression of SH3P2 in YY compromised Pib-mediated resistance to M. oryzae isolates carrying AvrPib and Pib-AvrPib recognition-induced cell death. SH3P2 competitively inhibits the self-association of the Pib CC domain in vitro, suggesting that binding of SH3P2 with Pib undermines its homodimerization. Moreover, SH3P2 can also interact with AvrPib and displays higher affinity to AvrPib than to Pib, which leads to dissociation of SH3P2 from Pib in the presence of AvrPib. Taken together, our results suggest that SH3P2 functions as a "protector" to keep Pib in a static state by direct interaction during normal growth but could be triggered off by the invasion of AvrPib-carrying M. oryzae isolates. Our study reveals a new mechanism about how an NLR protein is inactivated under normal conditions but is activated upon pathogen infection.
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Affiliation(s)
- Yunjie Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yupeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Xiangzhen Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yuelong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yongsheng Zhu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Jinwen Chen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Qingqing Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lanning Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yanjia Xiao
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yanmei Zheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Mo Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaan Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China.
| | - Jianfu Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China.
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Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. PLANT COMMUNICATIONS 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors. Proc Natl Acad Sci U S A 2021; 118:2110751118. [PMID: 34702740 PMCID: PMC8612214 DOI: 10.1073/pnas.2110751118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/21/2022] Open
Abstract
In this study, we generated a mutant of the rice nucleotide-binding and leucine-rich repeat (NLR) immunity receptor RGA5 by engineering its heavy metal–associated domain that recognizes the noncorresponding Magnaporthe oryzae Avrs- and ToxB-like effector AvrPib and confers resistance in transgenic rice to the blast fungus isolates with AvrPib, which is known to trigger blast resistance in rice cultivars carrying the R gene Pib, albeit by unknown mechanisms. Thus, this work demonstrates that integrated domain-containing plant NLR receptors can be engineered to confer resistance to pathogens carrying avirulence effectors that trigger plant immunity by unknown mechanisms, thereby providing a practical approach for developing multilines and cultivars with broad race spectrum resistance. Plant nucleotide-binding and leucine-rich repeat (NLR) receptors recognize avirulence effectors directly through their integrated domains (IDs) or indirectly via the effector-targeted proteins. Previous studies have succeeded in generating designer NLR receptors with new recognition profiles by engineering IDs or targeted proteins based on prior knowledge of their interactions with the effectors. However, it is yet a challenge to design a new plant receptor capable of recognizing effectors that function by unknown mechanisms. Several rice NLR immune receptors, including RGA5, possess an integrated heavy metal–associated (HMA) domain that recognizes corresponding Magnaporthe oryzae Avrs and ToxB-like (MAX) effectors in the rice blast fungus. Here, we report a designer rice NLR receptor RGA5HMA2 carrying an engineered, integrated HMA domain (RGA5-HMA2) that can recognize the noncorresponding MAX effector AvrPib and confers the RGA4-dependent resistance to the M. oryzae isolates expressing AvrPib, which originally triggers the Pib-mediated blast resistance via unknown mechanisms. The RGA5-HMA2 domain is contrived based on the high structural similarity of AvrPib with two MAX effectors, AVR-Pia and AVR1-CO39, recognized by cognate RGA5-HMA, the binding interface between AVR1-CO39 and RGA5-HMA, and the distinct surface charge of AvrPib and RAG5-HMA. This work demonstrates that rice NLR receptors with the HMA domain can be engineered to confer resistance to the M. oryzae isolates noncorresponding but structurally similar MAX effectors, which manifest cognate NLR receptor–mediated resistance with unknown mechanisms. Our study also provides a practical approach for developing rice multilines and broad race spectrum–resistant cultivars by introducing a series of engineered NLR receptors.
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Liu Z, Zhu Y, Shi H, Qiu J, Ding X, Kou Y. Recent Progress in Rice Broad-Spectrum Disease Resistance. Int J Mol Sci 2021; 22:11658. [PMID: 34769087 PMCID: PMC8584176 DOI: 10.3390/ijms222111658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.
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Affiliation(s)
- Zhiquan Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Yujun Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Huanbin Shi
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China;
| | - Yanjun Kou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (Z.L.); (Y.Z.); (H.S.); (J.Q.)
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Peng M, Lin X, Xiang X, Ren H, Fan X, Chen K. Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54. RICE (NEW YORK, N.Y.) 2021; 14:78. [PMID: 34494175 PMCID: PMC8423957 DOI: 10.1186/s12284-021-00512-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Emergence of new pathogen strains of Magnaporthe oryzae is a major reason for recurrent failure of the resistance mediated by a single resistance gene (Pi) in rice. Stacking various Pi genes in the genome through marker-assisted selection is thus an effective strategy in rice breeding for achieving durable resistance against the pathogen. However, the effect of pyramiding of multiple Pi genes using transgenesis still remains largely unknown. RESULTS Three Pi genes Pib, Pi25 and Pi54 were transferred together into two rice varieties, the indica variety Kasalath and the japonica variety Zhenghan 10. Transgenic plants of both Kasalath and Zhenghan 10 expressing the Pi transgenes showed imparted pathogen resistance. All the transgenic lines of both cultivars also exhibited shorter growth periods with flowering 2-4 days early, and shorter plant heights with smaller panicle. Thus, pyramiding of the Pi genes resulted in reduced grain yields in both rice cultivars. However, tiller numbers and grain weight were generally similar between the pyramided lines and corresponding parents. A global analysis of gene expression by RNA-Seq suggested that both enhancement and, to a lesser extent, inhibition of gene transcription occurred in the pyramided plants. A total of 264 and 544 differentially expressed genes (DEGs) were identified in Kasalath and Zhenghan 10, respectively. Analysis of the DEGs suggested that presence of the Pi transgenes did not alter gene expression only related to disease resistance, but also impacted many gene transcriptions in the pathways for plant growth and development, in which several were common for both Kasalath and Zhenghan 10. CONCLUSION Pyramiding of the Pi genes Pib, Pi25 and Pi54 via transgenesis is a potentially promising approach for improving rice resistance to the pathogen Magnaporthe oryzae. However, pleiotropic effects of the Pi genes could potentially result in yield loss. These findings support the idea that immunity is often associated with yield penalties. Rational combination of the Pi genes based on the genetic background may be important to balance yield and disease resistance.
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Affiliation(s)
- Meifang Peng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China
| | - Xiaomin Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China
| | - Xiaoli Xiang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China
| | - Huibo Ren
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China
| | - Xiaoli Fan
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China
| | - Kegui Chen
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, 106 Shizishan Road, Chengdu, 610061, Sichuan, China.
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Schwarz TR, Li C, Yencho GC, Pecota KV, Heim CR, Davis EL. Screening Sweetpotato Genotypes for Resistance to a North Carolina Isolate of Meloidogyne enterolobii. PLANT DISEASE 2021; 105:1101-1107. [PMID: 32880532 DOI: 10.1094/pdis-02-20-0389-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Potential resistance to the guava root-knot nematode, Meloidogyne enterolobii, in 91 selected sweetpotato (Ipomoea batatas [L.] Lam.) genotypes was evaluated in six greenhouse experiments. Ten thousand eggs of M. enterolobii were inoculated on each sweetpotato genotype grown in a 3:1 sand to soil mixture. Sixty days after inoculation, the percentage of total roots with nematode-induced galls was determined, and nematode eggs were extracted from roots. Significant differences (P < 0.001) between sweetpotato genotypes were found in all six tests for gall rating, total eggs, and eggs per gram of root. Resistant sweetpotato genotypes were calculated as final eggs per root system divided by the initial inoculum, where Pf/Pi < 1 (reproduction factor; final egg count divided by initial inoculum of 10,000 eggs), and statistical mean separations were confirmed by Fisher's least significant difference t test. Our results indicated that 19 out of 91 tested sweetpotato genotypes were resistant to M. enterolobii. Some of the susceptible genotypes included 'Covington,' 'Beauregard,' 'NCDM04-001', and 'Hernandez.' Some of the resistant sweetpotato genotypes included 'Tanzania,' 'Murasaki-29,' 'Bwanjule,' 'Dimbuka-Bukulula,' 'Jewel,' and 'Centennial.' Most of the 19 resistant sweetpotato genotypes supported almost no M. enterolobii reproduction, with <20 eggs/g root of M. enterolobii. A number of segregants from a 'Tanzania' × 'Beauregard' cross demonstrated strong resistance to M. enterolobii observed in the 'Tanzania' parent. In collaboration with North Carolina State University sweetpotato breeding program, several genotypes evaluated in these tests are being used to incorporate the observed resistance to M. enterolobii into commercial sweetpotato cultivars.
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Affiliation(s)
- Tanner R Schwarz
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Chunying Li
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695
| | - Kenneth V Pecota
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695
| | - Chris R Heim
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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A Meta-Analysis of Quantitative Trait Loci Associated with Multiple Disease Resistance in Rice ( Oryza sativa L.). PLANTS 2020; 9:plants9111491. [PMID: 33167299 PMCID: PMC7694349 DOI: 10.3390/plants9111491] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Rice blast, sheath blight and bacterial leaf blight are major rice diseases found worldwide. The development of resistant cultivars is generally perceived as the most effective way to combat these diseases. Plant disease resistance is a polygenic trait where a combinatorial effect of major and minor genes affects this trait. To locate the source of this trait, various quantitative trait loci (QTL) mapping studies have been performed in the past two decades. However, investigating the congruency between the reported QTL is a daunting task due to the heterogeneity amongst the QTLs studied. Hence, the aim of our study is to integrate the reported QTLs for resistance against rice blast, sheath blight and bacterial leaf blight and objectively analyze and consolidate the location of QTL clusters in the chromosomes, reducing the QTL intervals and thus identifying candidate genes within the selected meta-QTL. A total of twenty-seven studies for resistance QTLs to rice blast (8), sheath blight (15) and bacterial leaf blight (4) was compiled for QTL projection and analyses. Cumulatively, 333 QTLs associated with rice blast (114), sheath blight (151) and bacterial leaf blight (68) resistance were compiled, where 303 QTLs could be projected onto a consensus map saturated with 7633 loci. Meta-QTL analysis on 294 QTLs yielded 48 meta-QTLs, where QTLs with membership probability lower than 60% were excluded, reducing the number of QTLs within the meta-QTL to 274. Further, three meta-QTL regions (MQTL2.5, MQTL8.1 and MQTL9.1) were selected for functional analysis on the basis that MQTL2.5 harbors the highest number of QTLs; meanwhile, MQTL8.1 and MQTL9.1 have QTLs associated with all three diseases mentioned above. The functional analysis allows for determination of enriched gene ontology and resistance gene analogs (RGAs) and other defense-related genes. To summarize, MQTL2.5, MQTL8.1 and MQTL9.1 have a considerable number of R-genes that account for 10.21%, 4.08% and 6.42% of the total genes found in these meta-QTLs, respectively. Defense genes constitute around 3.70%, 8.16% and 6.42% of the total number of genes in MQTL2.5, MQTL8.1 and MQTL9.1, respectively. This frequency is higher than the total frequency of defense genes in the rice genome, which is 0.0096% (167 defense genes/17,272 total genes). The integration of the QTLs facilitates the identification of QTL hotspots for rice blast, sheath blight and bacterial blight resistance with reduced intervals, which helps to reduce linkage drag in breeding. The candidate genes within the promising regions could be utilized for improvement through genetical engineering.
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Molecular profiling of blast resistance genes and evaluation of leaf and neck blast disease reaction in rice. J Genet 2020. [DOI: 10.1007/s12041-020-01212-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yadav MK, Aravindan S, Ngangkham U, Raghu S, Prabhukarthikeyan SR, Keerthana U, Marndi BC, Adak T, Munda S, Deshmukh R, Pramesh D, Samantaray S, Rath PC. Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers. PLoS One 2019; 14:e0211061. [PMID: 30673751 PMCID: PMC6343911 DOI: 10.1371/journal.pone.0211061] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/07/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well–known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twenty-eight gene specific markers were investigated in landraces originated from nine diverse rice ecologies of India. Based on phenotypic evaluation, landraces were classified into three distinct groups: highly resistant (21), moderately resistant (70) and susceptible (70). The landraces harbour a range of five to nineteen genes representing blast resistance allele with the frequency varied from 4.96% to 100%. The cluster analysis grouped entire 161 landraces into two major groups. Population structure along with other parameters was also analyzed to understand the evolution of blast resistance gene in rice. The population structure analysis and principal coordinate analysis classified the landraces into two sub–populations. Analysis of molecular variance showed maximum (93%) diversity within the population and least (7%) between populations. Five markers viz; K3957, Pikh, Pi2–i, RM212and RM302 were strongly associated with blast disease with the phenotypic variance of 1.4% to 7.6%. These resistant landraces will serve as a valuable genetic resource for future genomic studies, host–pathogen interaction, identification of novel R genes and rice improvement strategies.
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Affiliation(s)
| | - S. Aravindan
- ICAR-National Rice Research Institute, Odisha, India
| | | | - S. Raghu
- ICAR-National Rice Research Institute, Odisha, India
| | | | - U. Keerthana
- ICAR-National Rice Research Institute, Odisha, India
| | - B. C. Marndi
- ICAR-National Rice Research Institute, Odisha, India
| | - Totan Adak
- ICAR-National Rice Research Institute, Odisha, India
| | - Susmita Munda
- ICAR-National Rice Research Institute, Odisha, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab, India
| | - D. Pramesh
- Rice Pathology Laboratory, AICRIP, Gangavathi, University of Agricultural Sciences, Raichur, India
| | | | - P. C. Rath
- ICAR-National Rice Research Institute, Odisha, India
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