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Wang C, Yu X, Wang J, Zhao Z, Wan J. Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice. J Genet Genomics 2024; 51:583-593. [PMID: 38325701 DOI: 10.1016/j.jgg.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.
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Affiliation(s)
- Chaolong Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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de Tombeur F, Pélissier R, Shihan A, Rahajaharilaza K, Fort F, Mahaut L, Lemoine T, Thorne SJ, Hartley SE, Luquet D, Fabre D, Lambers H, Morel JB, Ballini E, Violle C. Growth-defence trade-off in rice: fast-growing and acquisitive genotypes have lower expression of genes involved in immunity. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3094-3103. [PMID: 36840921 PMCID: PMC10199124 DOI: 10.1093/jxb/erad071] [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: 11/22/2022] [Accepted: 02/23/2023] [Indexed: 05/21/2023]
Abstract
Plant ecologists and molecular biologists have long considered the hypothesis of a trade-off between plant growth and defence separately. In particular, how genes thought to control the growth-defence trade-off at the molecular level relate to trait-based frameworks in functional ecology, such as the slow-fast plant economics spectrum, is unknown. We grew 49 phenotypically diverse rice genotypes in pots under optimal conditions and measured growth-related functional traits and the constitutive expression of 11 genes involved in plant defence. We also quantified the concentration of silicon (Si) in leaves to estimate silica-based defences. Rice genotypes were aligned along a slow-fast continuum, with slow-growing, late-flowering genotypes versus fast-growing, early-flowering genotypes. Leaf dry matter content and leaf Si concentrations were not aligned with this axis and negatively correlated with each other. Live-fast genotypes exhibited greater expression of OsNPR1, a regulator of the salicylic acid pathway that promotes plant defence while suppressing plant growth. These genotypes also exhibited greater expression of SPL7 and GH3.2, which are also involved in both stress resistance and growth. Our results do not support the hypothesis of a growth-defence trade-off when leaf Si and leaf dry matter content are considered, but they do when hormonal pathway genes are considered. We demonstrate the benefits of combining ecological and molecular approaches to elucidate the growth-defence trade-off, opening new avenues for plant breeding and crop science.
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Affiliation(s)
- Felix de Tombeur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, Australia
| | - Rémi Pélissier
- PHIM Plant Health Institute, Univ Montpellier, Institut Agro, INRAE, CIRAD, Montpellier, France
| | - Ammar Shihan
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Koloina Rahajaharilaza
- Faculty of Sciences, DS Life and Environmental Sciences, University of Antananarivo 101, Antananarivo, Madagascar
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
| | - Florian Fort
- CEFE, Univ Montpellier, Institut Agro, CNRS, EPHE, IRD, Univ Valéry, Montpellier, France
| | - Lucie Mahaut
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Taïna Lemoine
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Sarah J Thorne
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sue E Hartley
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Delphine Luquet
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Denis Fabre
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hans Lambers
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, Australia
| | - Jean-Benoît Morel
- PHIM Plant Health Institute, Univ Montpellier, Institut Agro, INRAE, CIRAD, Montpellier, France
| | - Elsa Ballini
- PHIM Plant Health Institute, Univ Montpellier, Institut Agro, INRAE, CIRAD, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Ma J, Morel JB, Riemann M, Nick P. Jasmonic acid contributes to rice resistance against Magnaporthe oryzae. BMC PLANT BIOLOGY 2022; 22:601. [PMID: 36539712 PMCID: PMC9764487 DOI: 10.1186/s12870-022-03948-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The annual yield losses caused by the Rice Blast Fungus, Magnaporthe oryzae, range to the equivalent for feeding 60 million people. To ward off infection by this fungus, rice has evolved a generic basal immunity (so called compatible interaction), which acts in concert with strain-specific defence (so-called incompatible interaction). The plant-defence hormone jasmonic acid (JA) promotes the resistance to M. oryzae, but the underlying mechanisms remain elusive. To get more insight into this open question, we employ the JA-deficient mutants, cpm2 and hebiba, and dissect the JA-dependent defence signalling in rice for both, compatible and incompatible interactions. RESULTS We observe that both JA-deficient mutants are more susceptible to M. oryzae as compared to their wild-type background, which holds true for both types of interactions as verified by cytological staining. Secondly, we observe that transcripts for JA biosynthesis (OsAOS2 and OsOPR7), JA signalling (OsJAZ8, OsJAZ9, OsJAZ11 and OsJAZ13), JA-dependent phytoalexin synthesis (OsNOMT), and JA-regulated defence-related genes, such as OsBBTI2 and OsPR1a, accumulate after fungal infection in a pattern that correlates with the amplitude of resistance. Thirdly, induction of defence transcripts is weaker during compatible interaction. CONCLUSION The study demonstrates the pivotal role of JA in basal immunity of rice in the resistance to M. oryzae in both, compatible and incompatible interactions.
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Affiliation(s)
- Junning Ma
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jean-Benoît Morel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Michael Riemann
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Barua D, Mishra A, Kirti PB, Barah P. Identifying Signal-Crosstalk Mechanism in Maize Plants during Combined Salinity and Boron Stress Using Integrative Systems Biology Approaches. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1027288. [PMID: 35505877 PMCID: PMC9057046 DOI: 10.1155/2022/1027288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/19/2022] [Indexed: 01/04/2023]
Abstract
Combined stress has been seen as a major threat to world agriculture production. Maize is one of the leading cereal crops of the world due to its wide spectrum of growth conditions and is moderately sensitive to salt stress. A saline soil environment is a major factor that hinders its growth and overall yield and causes an increase in the concentration of micronutrients like boron, leading to excess over the requirement of the plant. Boron toxicity combined with salinity has been reported to be a serious threat to the yield and quality of maize. The response signatures of the maize plants to the combined effect of salinity and boron stress have not been studied well. We carried out an integrative systems-level analysis of the publicly available transcriptomic data generated on tolerant maize (Lluteño maize from the Atacama Desert, Chile) landrace under combined salt and boron stress. We identified significant biological processes that are differentially regulated in combined salt and boron stress in the leaves and roots of maize, respectively. Protein-protein interaction network analysis identified important roles of aldehyde dehydrogenase (ALDH), galactinol synthase 2 (GOLS2) proteins of leaf and proteolipid membrane potential regulator (pmpm4), metallothionein lea protein group 3 (mlg3), and cold regulated 410 (COR410) proteins of root in salt tolerance and regulating boron toxicity in maize. Identification of transcription factors coupled with regulatory network analysis using machine learning approach identified a few heat shock factors (HSFs) and NAC (NAM (no apical meristem, Petunia), ATAF1-2 (Arabidopsis thaliana activating factor), and CUC2 (cup-shaped cotyledon, Arabidopsis)) family transcription factors (TFs) to play crucial roles in salt tolerance, maintaining reactive oxygen species (ROS) levels and minimizing oxidative damage to the cells. These findings will provide new ways to design targeted functional validation experiments for developing multistress-resistant maize crops.
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Affiliation(s)
- Drishtee Barua
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
| | - Asutosh Mishra
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
| | - P. B. Kirti
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad, 500030, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
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Eskew EA, Fraser D, Vonhof MJ, Pinsky ML, Maslo B. Host gene expression in wildlife disease: making sense of species-level responses. Mol Ecol 2021; 30:6517-6530. [PMID: 34516689 DOI: 10.1111/mec.16172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.
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Affiliation(s)
- Evan A Eskew
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.,Department of Biology, Pacific Lutheran University, Tacoma, Washington, USA
| | - Devaughn Fraser
- Wildlife Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, USA
| | - Maarten J Vonhof
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Malin L Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Brooke Maslo
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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Zuluaga AP, Bidzinski P, Chanclud E, Ducasse A, Cayrol B, Gomez Selvaraj M, Ishitani M, Jauneau A, Deslandes L, Kroj T, Michel C, Szurek B, Koebnik R, Morel JB. The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought. FRONTIERS IN PLANT SCIENCE 2020; 11:1265. [PMID: 33013945 PMCID: PMC7461821 DOI: 10.3389/fpls.2020.01265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive. RESULTS Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress. CONCLUSIONS Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.
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Affiliation(s)
- A. Paola Zuluaga
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | | | - Emilie Chanclud
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Aurelie Ducasse
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Bastien Cayrol
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | | | | | - Alain Jauneau
- Institut Fédératif de Recherche 3450, Université de Toulouse, CNRS, UPS, Plateforme Imagerie TRI-Genotoul, Castanet-Tolosan, France
| | | | - Thomas Kroj
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Corinne Michel
- BGPI, INRA, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Boris Szurek
- UMR Interactions Plantes-Microorganismes-Environnement (IPME), IRD-Cirad-Université Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Ralf Koebnik
- UMR Interactions Plantes-Microorganismes-Environnement (IPME), IRD-Cirad-Université Montpellier, Institut de Recherche pour le Développement, Montpellier, France
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Thomas E, Herrero S, Eng H, Gomaa N, Gillikin J, Noar R, Beseli A, Daub ME. Engineering Cercospora disease resistance via expression of Cercospora nicotianae cercosporin-resistance genes and silencing of cercosporin production in tobacco. PLoS One 2020; 15:e0230362. [PMID: 32176712 PMCID: PMC7075572 DOI: 10.1371/journal.pone.0230362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 11/18/2022] Open
Abstract
Fungi in the genus Cercospora cause crop losses world-wide on many crop species. The wide host range and success of these pathogens has been attributed to the production of a photoactivated toxin, cercosporin. We engineered tobacco for resistance to Cercospora nicotianae utilizing two strategies: 1) transformation with cercosporin autoresistance genes isolated from the fungus, and 2) transformation with constructs to silence the production of cercosporin during disease development. Three C. nicotianae cercosporin autoresistance genes were tested: ATR1 and CFP, encoding an ABC and an MFS transporter, respectively, and 71cR, which encodes a hypothetical protein. Resistance to the pathogen was identified in transgenic lines expressing ATR1 and 71cR, but not in lines transformed with CFP. Silencing of the CTB1 polyketide synthase and to a lesser extent the CTB8 pathway regulator in the cercosporin biosynthetic pathway also led to the recovery of resistant lines. All lines tested expressed the transgenes, and a direct correlation between the level of transgene expression and disease resistance was not identified in any line. Resistance was also not correlated with the degree of silencing in the CTB1 and CTB8 silenced lines. We conclude that expression of fungal cercosporin autoresistance genes as well as silencing of the cercosporin pathway are both effective strategies for engineering resistance to Cercospora diseases where cercosporin plays a critical role.
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Affiliation(s)
- Elizabeth Thomas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Sonia Herrero
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Hayde Eng
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Nafisa Gomaa
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
- Botany Department, Faculty of Science, Fayoum University, Al Fayoum, Egypt
| | - Jeff Gillikin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Roslyn Noar
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Aydin Beseli
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Margaret E. Daub
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
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Kim YA, Moon H, Park CJ. CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. oryzae. RICE (NEW YORK, N.Y.) 2019; 12:67. [PMID: 31446506 PMCID: PMC6708514 DOI: 10.1186/s12284-019-0325-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/13/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Genome editing tools are important for functional genomics research and biotechnology applications. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) system for gene knockout has emerged as the most effective genome-editing tool. It has previously been reported that, in rice plants, knockdown of the Os8N3 gene resulted in enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo), while displaying abnormal pollen development. RESULTS The CRISPR/Cas9 system was employed to knockout rice Os8N3, in order to confer enhanced resistance to Xoo. Analysis of the genotypes and edited Os8N3 in T0, T1, T2, and T3 transgenic rice plants showed that the mutations were transmitted to subsequent generations, and homozygous mutants displayed significantly enhanced resistance to Xoo. Stable transmission of CRISPR/Cas9-mediated Os8N3 gene editing without the transferred DNA (T-DNA) was confirmed by segregation in the T1 generation. With respect to many investigated agronomic traits including pollen development, there was no significant difference between homozygous mutants and non-transgenic control plants under greenhouse growth conditions. CONCLUSION Data from this study indicate that the CRISPR/Cas9-mediated Os8N3 edition can be successfully employed for non-transgenic crop improvements.
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Affiliation(s)
- Young-Ah Kim
- Department of Plant Biotechnology, Sejong University, Seoul, 05006 South Korea
| | - Hyeran Moon
- Department of Molecular Biology, Sejong University, Seoul, 05006 South Korea
| | - Chang-Jin Park
- Department of Plant Biotechnology, Sejong University, Seoul, 05006 South Korea
- Department of Molecular Biology, Sejong University, Seoul, 05006 South Korea
- Plant Engineering Research Institute, Sejong University, Seoul, 05006 South Korea
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. FRONTIERS IN PLANT SCIENCE 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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Kroj T, Chanclud E, Michel‐Romiti C, Grand X, Morel J. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. THE NEW PHYTOLOGIST 2016; 210:618-26. [PMID: 26848538 PMCID: PMC5067614 DOI: 10.1111/nph.13869] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 05/18/2023]
Abstract
Plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (NLR) proteins can contain additional domains besides canonical NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)) and leucine-rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance. Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger-BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over-expression and knock-out mutants. This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility. This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in-depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.
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Affiliation(s)
- Thomas Kroj
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Emilie Chanclud
- Université Montpellier2 Place Eugène Bataillon34095Montpellier Cedex 5France
| | - Corinne Michel‐Romiti
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Xavier Grand
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Jean‐Benoit Morel
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
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Niks RE, Qi X, Marcel TC. Quantitative resistance to biotrophic filamentous plant pathogens: concepts, misconceptions, and mechanisms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:445-70. [PMID: 26047563 DOI: 10.1146/annurev-phyto-080614-115928] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Quantitative resistance (QR) refers to a resistance that is phenotypically incomplete and is based on the joined effect of several genes, each contributing quantitatively to the level of plant defense. Often, QR remains durably effective, which is the primary driver behind the interest in it. The various terms that are used to refer to QR, such as field resistance, adult plant resistance, and basal resistance, reflect the many properties attributed to it. In this article, we discuss aspects connected to those attributions, in particular the hypothesis that much of the QR to biotrophic filamentous pathogens is basal resistance, i.e., poor suppression of PAMP-triggered defense by effectors. We discuss what role effectors play in suppressing defense or improving access to nutrients. Based on the functions of the few plant proteins identified as involved in QR, vesicle trafficking and protein/metabolite transportation are likely to be common physiological processes relevant to QR.
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Affiliation(s)
- Rients E Niks
- Laboratory of Plant Breeding, Wageningen University and Research Centre, 6700 AJ Wageningen, The Netherlands;
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Chao J, Jin J, Wang D, Han R, Zhu R, Zhu Y, Li S. Cytological and transcriptional dynamics analysis of host plant revealed stage-specific biological processes related to compatible rice-Ustilaginoidea virens interaction. PLoS One 2014; 9:e91391. [PMID: 24646527 PMCID: PMC3960121 DOI: 10.1371/journal.pone.0091391] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/09/2014] [Indexed: 01/22/2023] Open
Abstract
Rice false smut, a fungal disease caused by Ustilaginoidea virens is becoming a severe detriment to rice production worldwide. However, little is known about the molecular response of rice to attacks by the smut pathogen. In this article, we define the initial infection process as having three stages: initial colonization on the pistil (stage 1, S1), amplification on the anther (stage 2, S2) and sporulation in the anther chambers (stage 3, S3). Based on the transcriptome of rice hosts in response to U. virens in two separate years, we identified 126, 204, and 580 specific regulated genes in their respective stages S1, S2, and S3, respectively, by excluding common expression patterns in other openly biotic/abiotic databases using bioinformatics. As the disease progresses, several stage-specific biological processes (BP) terms were distinctively enriched: "Phosphorylation" in stage S1, "PCD" in S2, and "Cell wall biogenesis" in S3, implying a concise signal cascade indicative of the tactics that smut pathogens use to control host rice cells during infection. 113 regulated genes were coexpressed among the three stages. They shared highly conserved promoter cis-element in the promoters in response to the regulation of WRKY and Myb for up-regulation, and ABA and Ca2+ for down regulation, indicating their potentially critical roles in signal transduction during rice-U. virens interaction. We further analyzed seven highly regulated unique genes; four were specific to pollen development, implying that pollen-related genes play critical roles in the establishment of rice susceptibility to U. virens. To my knowledge, this is the first report about probing of molecular response of rice to smut pathogen infection, which will greatly expand our understanding of the molecular events surrounding infection by rice false smut.
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Affiliation(s)
- Jinquan Chao
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Jie Jin
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Dong Wang
- Department of Statistics, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Ran Han
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Renshan Zhu
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Yingguo Zhu
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory for Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
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