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Silva A, Montoya ME, Quintero C, Cuasquer J, Tohme J, Graterol E, Cruz M, Lorieux M. Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach. G3 (BETHESDA, MD.) 2023; 13:jkad223. [PMID: 37766452 PMCID: PMC10700108 DOI: 10.1093/g3journal/jkad223] [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: 06/12/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Rice hoja blanca (RHB) is one of the most serious diseases in rice-growing areas in tropical Americas. Its causal agent is RHB virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So far, only 1 major quantitative trait locus (QTL) of Oryza sativa ssp. japonica origin, qHBV4.1, that alters the incidence of the virus symptoms in 2 Colombian cultivars has been reported. This resistance has already started to be broken, stressing the urgent need for diversifying the resistance sources. In the present study, we performed a search for new QTLs of O. sativa indica origin associated with RHB resistance. We used 4 F2:3-segregating populations derived from indica-resistant varieties crossed with a highly susceptible japonica pivot parent. Besides the standard method for measuring disease incidence, we developed a new method based on computer-assisted image processing to determine the affected leaf area (ALA) as a measure of symptom severity. Based on the disease severity and incidence scores in the F3 families under greenhouse conditions and SNP genotyping of the F2 individuals, we identified 4 new indica QTLs for RHB resistance on rice chromosomes 4, 6, and 11, namely, qHBV4.2WAS208, qHBV6.1PTB25, qHBV11.1, and qHBV11.2, respectively. We also confirmed the wide-range action of qHBV4.1. Among the 5 QTLs, qHBV4.1 and qHBV11.1 had the largest effects on incidence and severity, respectively. These results provide a more complete understanding of the genetic bases of RHBV resistance in the cultivated rice gene pool and can be used to develop marker-aided breeding strategies to improve RHB resistance. The power of joint- and meta-analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the 2 major QTLs qHBV4.1 and qHBV11.1.
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Affiliation(s)
- Alexander Silva
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - María Elker Montoya
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Constanza Quintero
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Juan Cuasquer
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Joe Tohme
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Eduardo Graterol
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Maribel Cruz
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Mathias Lorieux
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
- DIADE, University of Montpellier, Cirad, IRD.IRD Occitanie, 911 Ave Agropolis, 34394 Montpellier Cedex 5, France
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2
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Reshetnyak G, Jacobs JM, Auguy F, Sciallano C, Claude L, Medina C, Perez-Quintero AL, Comte A, Thomas E, Bogdanove A, Koebnik R, Szurek B, Dievart A, Brugidou C, Lacombe S, Cunnac S. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection. Sci Rep 2021; 11:24141. [PMID: 34921170 PMCID: PMC8683429 DOI: 10.1038/s41598-021-03391-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023] Open
Abstract
Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.
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Affiliation(s)
- Ganna Reshetnyak
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jonathan M Jacobs
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43201, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43201, USA
| | - Florence Auguy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Coline Sciallano
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lisa Claude
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clemence Medina
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alvaro L Perez-Quintero
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Emilie Thomas
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Ralf Koebnik
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Dievart
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Severine Lacombe
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sebastien Cunnac
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Barrera NF, Melgarejo LM, Cruz-Gallego M, Cortés LJ, Guzmán F, Calvo JC. Conformationally Restricted Peptides from Rice Proteins Elicit Antibodies That Recognize the Corresponding Native Protein in ELISA Assays. Molecules 2018; 23:molecules23092262. [PMID: 30189617 PMCID: PMC6225240 DOI: 10.3390/molecules23092262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 01/13/2023] Open
Abstract
The rice hoja blanca virus (RHBV), transmitted by the planthopper insect Tagosodes orizicolus, is a disease that attacks rice and generates significant production losses in Colombia. Fedearroz 2000 and Colombia I commercial rice varieties, which have different resistance levels to the disease, were selected in this study. To identify proteins associated to the insect and virus signaling, a comparative proteomics study was performed. By comparing proteomic profiles, between virus-infected and control group plants in two-dimensional electrophoresis, proteins exhibiting significant changes in abundance were found. In another test, peptide dendrimers containing sequences conformationally restricted to α-helix from four of those rice proteins were synthesized. In the experiment, sera from mice inoculated with peptide dendrimers could recognize the corresponding native protein in ELISA assays. Reported comparative proteomic results provide new insights into the molecular mechanisms of plant response to the RHBV and comprehensive tools for the analysis of new crop varieties. Besides, results from conformational peptide dendrimer approach are promising and show that it is feasible to detect proteins as markers, and may have biological applications by decreasing the susceptibility to proteolytic degradation.
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Affiliation(s)
- Nubia F Barrera
- Doctorado en Biotecnología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 224, Bogotá 110111, Colombia.
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
| | - Luz M Melgarejo
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 421, Bogotá 110111, Colombia.
| | - Maribel Cruz-Gallego
- Centro Internacional de Agricultura Tropical, CIAT, Fondo Latinoamericano para Arroz de Riego, FLAR, Palmira, Valle 763537, Colombia.
| | - Lina Jimena Cortés
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Fanny Guzmán
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Julio C Calvo
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
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Ali J, Jewel ZA, Mahender A, Anandan A, Hernandez J, Li Z. Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice. Int J Mol Sci 2018; 19:E1762. [PMID: 29899204 PMCID: PMC6032200 DOI: 10.3390/ijms19061762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022] Open
Abstract
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.
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Affiliation(s)
- Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Zilhas Ahmed Jewel
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jose Hernandez
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
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Blanvillain‐Baufumé S, Reschke M, Solé M, Auguy F, Doucoure H, Szurek B, Meynard D, Portefaix M, Cunnac S, Guiderdoni E, Boch J, Koebnik R. Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:306-317. [PMID: 27539813 PMCID: PMC5316920 DOI: 10.1111/pbi.12613] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 05/04/2023]
Abstract
As a key virulence strategy to cause bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called transcription activator-like effectors (TALEs) that bind to effector-binding elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of the OsSWEET14 promoter through stable expression of TALE-nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.
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Affiliation(s)
- Servane Blanvillain‐Baufumé
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
- Present address: LabEx CeMEBUniversité de MontpellierMontpellierFrance
| | - Maik Reschke
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Montserrat Solé
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Sustainable Agro Solutions S.A.Almacelles (Lleida)Spain
| | - Florence Auguy
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Hinda Doucoure
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Boris Szurek
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Donaldo Meynard
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Murielle Portefaix
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Sébastien Cunnac
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
| | - Emmanuel Guiderdoni
- CIRADUMR AGAP (Amélioration génétique et Adaptation des Plantes)MontpellierFrance
| | - Jens Boch
- Institut für BiologieInstitutsbereich GenetikMartin‐Luther‐Universität Halle‐WittenbergHalle (Saale)Germany
- Present address: Institut für PflanzengenetikLeibniz Universität HannoverHannoverGermany
| | - Ralf Koebnik
- UMR Interactions Plantes Microorganismes Environnement (IPME)IRD‐CIRAD‐UniversitéMontpellierFrance
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Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:81. [PMID: 25705117 PMCID: PMC4328105 DOI: 10.1007/s11032-015-0276-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/29/2015] [Indexed: 05/04/2023]
Abstract
Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.
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Affiliation(s)
- Juan D. Arbelaez
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Laura T. Moreno
- School of Botany, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Namrata Singh
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 106 Taiwan
| | - Lyza G. Maron
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Yolima Ospina
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - César P. Martinez
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | | | - Mathias Lorieux
- DIADE Research Unit, Institut de Recherche Pour le Développement, 34394 Montpellier Cedex 5, France
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
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