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Bartholomé J, Frouin J, Brottier L, Cao TV, Boisnard A, Ahmadi N, Courtois B. Genomic selection for salinity tolerance in japonica rice. PLoS One 2023; 18:e0291833. [PMID: 37756295 PMCID: PMC10530037 DOI: 10.1371/journal.pone.0291833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Improving plant performance in salinity-prone conditions is a significant challenge in breeding programs. Genomic selection is currently integrated into many plant breeding programs as a tool for increasing selection intensity and precision for complex traits and for reducing breeding cycle length. A rice reference panel (RP) of 241 Oryza sativa L. japonica accessions genotyped with 20,255 SNPs grown in control and mild salinity stress conditions was evaluated at the vegetative stage for eight morphological traits and ion mass fractions (Na and K). Weak to strong genotype-by-condition interactions were found for the traits considered. Cross-validation showed that the predictive ability of genomic prediction methods ranged from 0.25 to 0.64 for multi-environment models with morphological traits and from 0.05 to 0.40 for indices of stress response and ion mass fractions. The performances of a breeding population (BP) comprising 393 japonica accessions were predicted with models trained on the RP. For validation of the predictive performances of the models, a subset of 41 accessions was selected from the BP and phenotyped under the same experimental conditions as the RP. The predictive abilities estimated on this subset ranged from 0.00 to 0.66 for the multi-environment models, depending on the traits, and were strongly correlated with the predictive abilities on cross-validation in the RP in salt condition (r = 0.69). We show here that genomic selection is efficient for predicting the salt stress tolerance of breeding lines. Genomic selection could improve the efficiency of rice breeding strategies for salinity-prone environments.
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Affiliation(s)
- Jérôme Bartholomé
- UMR AGAP Institut, CIRAD, Cali, Colombia
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- Alliance Bioversity-CIAT, Recta Palmira Cali, Colombia
| | - Julien Frouin
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Laurent Brottier
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Tuong-Vi Cao
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | | | - Nourollah Ahmadi
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Brigitte Courtois
- UMR AGAP Institut, Institut Agro, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
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Pasam RK, Kant S, Thoday-Kennedy E, Dimech A, Joshi S, Keeble-Gagnere G, Forrest K, Tibbits J, Hayden M. Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2367. [PMID: 37375992 DOI: 10.3390/plants12122367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.
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Affiliation(s)
- Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Adam Dimech
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
| | | | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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Pélissier R, Ducasse A, Ballini E, Frouin J, Violle C, Morel JB. A major genetic locus in neighbours controls changes of gene expression and susceptibility in intraspecific rice mixtures. THE NEW PHYTOLOGIST 2023; 238:835-844. [PMID: 36710512 DOI: 10.1111/nph.18778] [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: 07/27/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Reports indicate that intraspecific neighbours alter the physiology of focal plants, and with a few exceptions, their molecular responses to neighbours are unknown. Recently, changes in susceptibility to pathogen resulting from such interactions were demonstrated, a phenomenon called neighbour-modulated susceptibility (NMS). However, the genetics of NMS and the associated molecular responses are largely unexplored. Here, we analysed in rice the modification of biomass and susceptibility to the blast fungus pathogen in the Kitaake focal genotype in the presence of 280 different neighbours. Using genome-wide association studies, we identified the loci in the neighbour that determine the response in Kitaake. Using a targeted transcriptomic approach, we characterized the molecular responses in focal plants co-cultivated with various neighbours inducing a reduction in susceptibility. Our study demonstrates that NMS is controlled by one major locus in the rice genome of its neighbour. Furthermore, we show that this locus can be associated with characteristic patterns of gene expression in focal plant. Finally, we propose an hypothesis where Pi could play a role in explaining this case of NMS. Our study sheds light on how plants affect the physiology in their neighbourhood and opens perspectives for understanding plant-plant interactions.
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Affiliation(s)
- Rémi Pélissier
- PHIM, CEFE, Institut Agro, INRAE, CIRAD, Univ Montpellier, 34000, Montpellier, France
| | - Aurélie Ducasse
- PHIM, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34000, Montpellier, France
| | - Elsa Ballini
- PHIM, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34000, Montpellier, France
| | - Julien Frouin
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, 34000, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, EPHE, IRD, Univ Montpellier, 34000, Montpellier, France
| | - Jean-Benoit Morel
- PHIM, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34000, Montpellier, France
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Marè C, Zampieri E, Cavallaro V, Frouin J, Grenier C, Courtois B, Brottier L, Tacconi G, Finocchiaro F, Serrat X, Nogués S, Bundó M, San Segundo B, Negrini N, Pesenti M, Sacchi GA, Gavina G, Bovina R, Monaco S, Tondelli A, Cattivelli L, Valè G. Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice. RICE (NEW YORK, N.Y.) 2023; 16:2. [PMID: 36633713 PMCID: PMC9837369 DOI: 10.1186/s12284-023-00619-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Rice is one of the most salt sensitive crops at seedling, early vegetative and reproductive stages. Varieties with salinity tolerance at seedling stage promote an efficient growth at early stages in salt affected soils, leading to healthy vegetative growth that protects crop yield. Saltol major QTL confers capacity to young rice plants growing under salt condition by maintaining a low Na+/K+ molar ratio in the shoots. RESULTS Marker-assisted backcross (MABC) procedure was adopted to transfer Saltol locus conferring salt tolerance at seedling stage from donor indica IR64-Saltol to two temperate japonica varieties, Vialone Nano and Onice. Forward and background selections were accomplished using polymorphic KASP markers and a final evaluation of genetic background recovery of the selected lines was conducted using 15,580 SNP markers obtained from Genotyping by Sequencing. Three MABC generations followed by two selfing, allowed the identification of introgression lines achieving a recovery of the recurrent parent (RP) genome up to 100% (based on KASP markers) or 98.97% (based on GBS). Lines with highest RP genome recovery (RPGR) were evaluated for agronomical-phenological traits in field under non-salinized conditions. VN1, VN4, O1 lines were selected considering the agronomic evaluations and the RPGR% results as the most interesting for commercial exploitation. A physiological characterization was conducted by evaluating salt tolerance under hydroponic conditions. The selected lines showed lower standard evaluation system (SES) scores: 62% of VN4, and 57% of O1 plants reaching SES 3 or SES 5 respectively, while only 40% of Vialone Nano and 25% of Onice plants recorded scores from 3 to 5, respectively. VN1, VN4 and O1 showed a reduced electrolyte leakage values, and limited negative effects on relative water content and shoot/root fresh weight ratio. CONCLUSION The Saltol locus was successfully transferred to two elite varieties by MABC in a time frame of three years. The application of background selection until BC3F3 allowed the selection of lines with a RPGR up to 98.97%. Physiological evaluations for the selected lines indicate an improved salinity tolerance at seedling stage. The results supported the effectiveness of the Saltol locus in temperate japonica and of the MABC procedure for recovering of the RP favorable traits.
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Affiliation(s)
- Caterina Marè
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy.
| | - Elisa Zampieri
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Institute for Sustainable Plant Protection, National Research Council, Strada Delle Cacce 73, 10135, Turin, Italy
| | - Viviana Cavallaro
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Julien Frouin
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Cécile Grenier
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Laurent Brottier
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gianni Tacconi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Franca Finocchiaro
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Xavier Serrat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Nogués
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG)-CSIC-IRTA-UAB-UB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)-CSIC-IRTA-UAB-UB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Noemi Negrini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Michele Pesenti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Giacomo Gavina
- SIS Società Italiana Sementi, Via Mirandola, 5, 40068, San Lazzaro di Savena, Bologna, Italy
| | - Riccardo Bovina
- SIS Società Italiana Sementi, Via Mirandola, 5, 40068, San Lazzaro di Savena, Bologna, Italy
| | - Stefano Monaco
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Council for Agricultural Research and Economics, Research Centre for Engineering and Agro-Food Processing, Strada Delle Cacce 73, 10135, Turin, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Giampiero Valè
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy.
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Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
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Yu K, Ju F, Wang Z, Sun L, Huo Y, Zhu J, Pang J, Ali S, Chen W, Wang S, Zhou Z, Tang Q, Chen B. Potassium ameliorates cotton (Gossypium hirsutum L.) fiber length by regulating osmotic and K + /Na + homeostasis under salt stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13842. [PMID: 36543752 DOI: 10.1111/ppl.13842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Potassium (K) application can alleviate cotton salt stress, but the regulatory mechanisms affecting cotton fiber elongation and ion homeostasis are still unclear. A two-year field experiment was conducted to explore the effects of K on the osmolyte contents (soluble sugar, K+ content, and malate) and related enzyme activities during the fiber elongation of two cotton cultivars with contrasting salt sensitivity (CCRI-79; salt tolerant cultivar, and Simian 3; salt-sensitive cultivar). Three K application treatments (0, 150, and 300 kg K2 O ha-1 ) were applied at three soil salinity levels (low salinity, EC = 1.73 ± 0.05 dS m-1 ; medium salinity, EC = 6.32 ± 0.10 dS m-1 ; high salinity, EC = 10.84 ± 0.24 dS m-1 ). K application improved fiber length and alleviated salt stress by increasing the maximum velocity of fiber elongation (Vmax ). The increase rate of K on fiber length decreased with elevating salt stress, and the increase rate of K on Vmax of CCRI-79 was greater than that of Simian3. K application can increase the enzyme activities (phosphoenolpyruvate carboxylase, PEPC, E.C. 4.1.1.31; pyrophosphatase, PPase, E.C. 3.6.1.1; and plasma membrane H+ -ATPase, PM H+ -ATPase, E.C. 3.6.3.14) as well as the content of osmolytes associated with the enzymes mentioned above. K increased the osmolyte contents under salt stress, and the increase in the K+ content of the fibers was much higher than that of soluble sugar and malate. The results of this study indicated K fertilizer application rates regulate the metabolism of osmolytes in cotton fiber development under salt stress, K+ is more critical to fiber elongation.
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Affiliation(s)
- Kai Yu
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Feiyan Ju
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Zhuo Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Liyuan Sun
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Yuyang Huo
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Junjun Zhu
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Jiali Pang
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Saif Ali
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Weiping Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Shanshan Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
| | - Qiuxiang Tang
- College of Agronomy, Xinjiang Agricultural University, Xinjiang, People's Republic of China
| | - Binglin Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production cosponsored by Province and Ministry (CIC-MCP), Nanjing, People's Republic of China
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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Chen Z, Huang X, Fu R, Zhan A. Neighbours matter: Effects of genomic organization on gene expression plasticity in response to environmental stresses during biological invasions. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100992. [PMID: 35504120 DOI: 10.1016/j.cbd.2022.100992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Gene expression regulation has been widely recognized as an important molecular mechanism underlying phenotypic plasticity in environmental adaptation. However, it remains largely unexplored on the effects of genomic organization on gene expression plasticity under environmental stresses during biological invasions. Here, we use an invasive model ascidian, Ciona robusta, to investigate how genomic organization affects gene expression in response to salinity stresses during range expansions. Our study showed that neighboring genes were co-expressed and approximately 30% of stress responsive genes were physically clustered on chromosomes. Such coordinated expression was substantially affected by the physical distance and orientation of genes. Interestingly, the overall expression correlation of neighboring genes was significantly decreased under high salinity stresses, illustrating that the co-expression regulation could be disrupted by salinity challenges. Furthermore, the clustering of genes was associated with their function constraints and expression patterns - operon genes enriched in gene expression machinery had the highest transcriptional activity and expression stability. Notably, our analyses showed that the tail-to-tail genes, mainly involved in biological functions related to phosphorylation, homeostatic process, and ion transport, exhibited higher intrinsic expression variability and greater response to salinity challenges. Altogether, the results obtained here provide new insights into the effects of gene organization on gene expression plasticity under environmental challenges, hence improving our knowledge on mechanisms of rapid environmental adaptation during biological invasions.
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Affiliation(s)
- Zaohuang Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
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9
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Dai L, Li P, Li Q, Leng Y, Zeng D, Qian Q. Integrated Multi-Omics Perspective to Strengthen the Understanding of Salt Tolerance in Rice. Int J Mol Sci 2022; 23:ijms23095236. [PMID: 35563627 PMCID: PMC9105537 DOI: 10.3390/ijms23095236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.
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Affiliation(s)
- Liping Dai
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Peiyuan Li
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Qing Li
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
| | - Yujia Leng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Y.L.); (Q.Q.)
| | - Dali Zeng
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A & F University, Hangzhou 311300, China
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (L.D.); (P.L.); (Q.L.); (D.Z.)
- Correspondence: (Y.L.); (Q.Q.)
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10
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Park JC, Yoo Y, Lim H, Yun S, Win KTYS, Kim KM, Lee GS, Cho MH, Lee TH, Sano H, Lee SW. Intracellular Ca 2+ accumulation triggered by caffeine provokes resistance against a broad range of biotic stress in rice. PLANT, CELL & ENVIRONMENT 2022; 45:1049-1064. [PMID: 35098547 DOI: 10.1111/pce.14273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Chemical pesticides are still frequently overused to diminish such crop loss caused by biotic stress despite the threat to humans and the environment. Thus, it is urgent to find safer and more effective defense strategies. In this study, we report that caffeine, implanted through a transgenic approach, enhances resistance against variable biotic stresses in rice without fitness cost. Caffeine-producing rice (CPR) was generated by introducing three N-methyltransferase genes involved in the biosynthesis of caffeine in coffee plants. The CPR plants have no differences in morphology and growth compared to their wild-type counterparts, but they show strongly enhanced resistance to both bacterial leaf blight, rice blast, and attack of white-backed planthoppers. Caffeine acts as a repellent agent against rice pathogens. Moreover, caffeine triggers a series of Ca2+ signalling-like processes to synthesize salicylic acid (SA), a hormone associated with plant resistance. In CPR, phosphodiesterase was inhibited by caffeine, cAMP and cGMP increased, intracellular Ca2+ increased, phenylalanine lyase (PAL) was activated by OsCPK1, and SA synthesis was activated. This finding is a novel strategy to improve resistance against the biotic stresses of crops with a special type of defense inducer.
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Affiliation(s)
- Jong-Chan Park
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Youngchul Yoo
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Hyemin Lim
- Forest Bioresources Department, National Institute of Forest Science, Suwon-si, Gyeonggi-do, Korea
| | - Sopheap Yun
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, Republic of Korea
| | - Kay Tha Ye Soe Win
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu, Republic of Korea
| | - Gang-Seob Lee
- Genomics Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Man-Ho Cho
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Tae Hoon Lee
- Department of Applied Chemistry, Kyung Hee University, Yongin, Republic of Korea
| | - Hiroshi Sano
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Nara, Japan
| | - Sang-Won Lee
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Institute of Crop Biotechnology, Kyung Hee University, Yongin, Republic of Korea
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11
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Comparative Physiology of Indica and Japonica Rice under Salinity and Drought Stress: An Intrinsic Study on Osmotic Adjustment, Oxidative Stress, Antioxidant Defense and Methylglyoxal Detoxification. STRESSES 2022. [DOI: 10.3390/stresses2020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Salinity and drought stress are significant environmental threats, alone or in combination. The current study was conducted to investigate the morpho-physiology, osmotic adjustment, oxidative stress, antioxidant defense and methylglyoxal detoxification of three rice genotypes from the indica (cv. BRRI dhan29 and BRRI dhan48) and japonica (cv. Koshihikari) groups. Eighteen-day-old seedlings of these genotypes were exposed to either in alone salinity (150 mM NaCl) and drought (15% PEG 6000) or in the combination of salinity and drought (150 mM NaCl + 15% PEG 6000) stress in vitro for 72 h. Compared with the control, the water status, biomass and photosynthetic pigments were decreased, where a significant increase was seen in the mortality rate, hydrogen peroxide content, electrolyte leakage, lipoxygenase activity, level of malondialdehyde and methylglyoxal, indicating increased lipid peroxidation in rice genotypes in stress conditions. The non-enzymatic and enzymatic components of the ascorbate-glutathione (AsA-GSH) pool in rice genotypes were disrupted under all stress treatments, resulting imbalance in the redox equilibrium. In contrast, compared to other rice genotypes, BRRI dhan48 revealed a lower Na+/K+ ratio, greater proline (Pro) levels, higher activity of AsA, dehydroascorbate (DHA) and GSH, lower glutathione disulfide (GSSG) and a higher ratio of AsA/DHA and GSH/GSSG, whereas enzymatic components increased monodehydroascorbate reductase, dehydroascorbate reductase, glutathione peroxidase and glyoxalase enzymes. The results showed that a stronger tolerate ability for BRRI dhan48 against stress has been connected to a lower Na+/K+ ratio, an increase in Pro content and an improved performance of the glyoxalase system and antioxidant protection for scavenging of reactive oxygen species. These data can give insight into probable responses to single or combination salinity and drought stress in rice genotypes.
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12
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Kumar P, Choudhary M, Halder T, Prakash NR, Singh V, V. VT, Sheoran S, T. RK, Longmei N, Rakshit S, Siddique KHM. Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops. Heredity (Edinb) 2022; 128:497-518. [DOI: 10.1038/s41437-022-00516-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
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13
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Bundó M, Martín-Cardoso H, Pesenti M, Gómez-Ariza J, Castillo L, Frouin J, Serrat X, Nogués S, Courtois B, Grenier C, Sacchi GA, San Segundo B. Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines. FRONTIERS IN PLANT SCIENCE 2022; 12:797141. [PMID: 35126422 PMCID: PMC8813771 DOI: 10.3389/fpls.2021.797141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/13/2021] [Indexed: 05/24/2023]
Abstract
Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.
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Affiliation(s)
- Mireia Bundó
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | | | - Michele Pesenti
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, Italy
| | - Jorge Gómez-Ariza
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Laia Castillo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Julien Frouin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Xavier Serrat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Nogués
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Brigitte Courtois
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Cécile Grenier
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, Italy
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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14
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Zheng J, Zhang Z, Gong Z, Liang Y, Sang Z, Xu Y, Li X, Wang J. Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010097. [PMID: 35009100 PMCID: PMC8747425 DOI: 10.3390/plants11010097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/01/2021] [Accepted: 12/11/2021] [Indexed: 06/01/2023]
Abstract
Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.
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Affiliation(s)
- Juyun Zheng
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zeliang Zhang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Zhaolong Gong
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Yajun Liang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zhiwei Sang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology (China), Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang 455000, China;
| | - Xueyuan Li
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Junduo Wang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
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15
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Alam MNU, Jewel GMNA, Azim T, Seraj ZI. Novel QTLs for salinity tolerance revealed by genome-wide association studies of biomass, chlorophyll and tissue ion content in 176 rice landraces from Bangladesh. PLoS One 2021; 16:e0259456. [PMID: 34739483 PMCID: PMC8570475 DOI: 10.1371/journal.pone.0259456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022] Open
Abstract
Farmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth's people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 11 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Our explorations yielded 13 QTLs related to various traits in multiple trait classes. 10 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes potential novel functionality for a number of candidate genes. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.
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Affiliation(s)
- Md Nafis Ul Alam
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - G. M. Nurnabi Azad Jewel
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Tomalika Azim
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Zeba I. Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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16
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Chen C, Travis AJ, Hossain M, Islam MR, Price AH, Norton GJ. Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2315-2334. [PMID: 33942137 PMCID: PMC8263461 DOI: 10.1007/s00122-021-03828-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/30/2021] [Indexed: 05/17/2023]
Abstract
Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from the aus subpopulation. Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na+) and potassium (K+) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na+ and K+ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na+ and K+ concentration and Na+/K+ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na+ concentration and increased the K+ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na+, K+ concentration and Na+/K+ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na+ concentration and Na+/K+ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.
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Affiliation(s)
- Caijin Chen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Anthony J Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Mahmud Hossain
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Rafiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Adam H Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Gareth J Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
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17
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Le TD, Gathignol F, Vu HT, Nguyen KL, Tran LH, Vu HTT, Dinh TX, Lazennec F, Pham XH, Véry AA, Gantet P, Hoang GT. Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice. PLANTS 2021; 10:plants10061088. [PMID: 34071570 PMCID: PMC8228224 DOI: 10.3390/plants10061088] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.
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Affiliation(s)
- Thao Duc Le
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Floran Gathignol
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Huong Thi Vu
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Khanh Le Nguyen
- Faculty of Agricultural Technology, University of Engineering and Technology, Hanoi 00000, Vietnam;
| | - Linh Hien Tran
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Hien Thi Thu Vu
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi 00000, Vietnam;
| | - Tu Xuan Dinh
- Incubation and Support Center for Technology and Science Enterprises, Hanoi 00000, Vietnam;
| | - Françoise Lazennec
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Xuan Hoi Pham
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Anne-Aliénor Véry
- UMR BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France;
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
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18
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Frontini M, Boisnard A, Frouin J, Ouikene M, Morel JB, Ballini E. Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen. BMC PLANT BIOLOGY 2021; 21:99. [PMID: 33602120 PMCID: PMC7893971 DOI: 10.1186/s12870-021-02864-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/01/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. RESULTS A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL, other than NIS1, were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. CONCLUSIONS Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.
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Affiliation(s)
- Mathias Frontini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Julien Frouin
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Malika Ouikene
- Groupe de Valorisation des Produits Agricoles (GVAPRO), Alger, Algeria
| | - Jean Benoit Morel
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Elsa Ballini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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19
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Nayyeripasand L, Garoosi GA, Ahmadikhah A. Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage. RICE (NEW YORK, N.Y.) 2021; 14:9. [PMID: 33420909 PMCID: PMC7797017 DOI: 10.1186/s12284-020-00433-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/07/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. RESULTS Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79-42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. CONCLUSION Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.
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Affiliation(s)
- Leila Nayyeripasand
- Agricultural Biotechnology Department, Faculty of Agriculture, Imam Khomeini International University, Qazvin, Iran
| | - Ghasem Ali Garoosi
- Agricultural Biotechnology Department, Faculty of Agriculture, Imam Khomeini International University, Qazvin, Iran.
| | - Asadollah Ahmadikhah
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshi University, G.C. Velenjak, Tehran, Iran.
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20
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Al-Tamimi N, Oakey H, Tester M, Negrão S. Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods Mol Biol 2021; 2238:339-375. [PMID: 33471343 DOI: 10.1007/978-1-0716-1068-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.
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Affiliation(s)
- Nadia Al-Tamimi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Oakey
- School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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21
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Mirdar Mansuri R, Shobbar ZS, Babaeian Jelodar N, Ghaffari M, Mohammadi SM, Daryani P. Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach. BMC PLANT BIOLOGY 2020; 20:452. [PMID: 33004003 PMCID: PMC7528482 DOI: 10.1186/s12870-020-02679-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 09/24/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. RESULTS A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. CONCLUSIONS The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.
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Affiliation(s)
- Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
- Faculty of Crop Science, Department of Plant breeding and Biotechnology, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Nadali Babaeian Jelodar
- Faculty of Crop Science, Department of Plant breeding and Biotechnology, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Mohammadreza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Seyed Mahdi Mohammadi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
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22
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Saade S, Brien C, Pailles Y, Berger B, Shahid M, Russell J, Waugh R, Negrão S, Tester M. Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages. PLoS One 2020; 15:e0236037. [PMID: 32701981 PMCID: PMC7377408 DOI: 10.1371/journal.pone.0236037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/27/2020] [Indexed: 11/18/2022] Open
Abstract
Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an "interaction model", which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.
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Affiliation(s)
- Stephanie Saade
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Chris Brien
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
| | - Yveline Pailles
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Bettina Berger
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
| | - Mohammad Shahid
- International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Robbie Waugh
- School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, Urrbrae, South Australia, Australia
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
- Division of Plant Sciences, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Sónia Negrão
- School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Mark Tester
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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23
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Chen C, Norton GJ, Price AH. Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel. FRONTIERS IN PLANT SCIENCE 2020; 11:576479. [PMID: 33193518 PMCID: PMC7644878 DOI: 10.3389/fpls.2020.576479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/02/2020] [Indexed: 05/04/2023]
Abstract
Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.
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24
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Jaiswal S, Gautam RK, Singh RK, Krishnamurthy SL, Ali S, Sakthivel K, Iquebal MA, Rai A, Kumar D. Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective. RICE (NEW YORK, N.Y.) 2019; 12:89. [PMID: 31802312 PMCID: PMC6892996 DOI: 10.1186/s12284-019-0347-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 05/12/2023]
Abstract
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - R K Gautam
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India.
| | - R K Singh
- Division of Plant Breeding Genetics and Biotechnology, International Rice Research Institute, DAPO Box 7777, Los Banos, Metro Manila, Philippines
| | - S L Krishnamurthy
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - S Ali
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - K Sakthivel
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India.
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25
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Dilnur T, Peng Z, Pan Z, Palanga KK, Jia Y, Gong W, Du X. Association Analysis of Salt Tolerance in Asiatic cotton ( Gossypium arboretum) with SNP Markers. Int J Mol Sci 2019; 20:ijms20092168. [PMID: 31052464 PMCID: PMC6540053 DOI: 10.3390/ijms20092168] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.
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Affiliation(s)
- Tussipkan Dilnur
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Koffi Kibalou Palanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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26
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Forlani G, Bertazzini M, Cagnano G. Stress-driven increase in proline levels, and not proline levels themselves, correlates with the ability to withstand excess salt in a group of 17 Italian rice genotypes. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:336-342. [PMID: 30253007 DOI: 10.1111/plb.12916] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/19/2018] [Indexed: 05/23/2023]
Abstract
In most plant species, a rapid increase in free proline content occurs following exposure to hyperosmotic stress conditions. However, inconsistent results were reported concerning the role of such an increase on the plant response to water shortage or excess salt. Therefore, the possibility that proline accumulation may help the cell to withstand stress conditions, or that it simply represents a stress marker, is still a matter of debate. A possible relationship between proline accumulation and salt tolerance was investigated in a set of 17 Italian rice varieties. Rice seedlings were exposed to increasing salt concentrations during germination and early growth. The resulting levels of free proline were measured separately in shoots and roots and compared to those in untreated controls. Results were related to the corresponding ability of a given genotype to tolerate stress conditions. Neither absolute proline levels in untreated or in salt-stressed seedlings showed a straightforward relationship to the relative tolerance to salt, estimated as conductivity values able to reduce growth by 10 or 50%. Conversely, a highly significant correlation was found between the increase in proline levels in shoots and the ability to withstand stress. The results strengthen a recent hypothesis suggesting than an increase in proline metabolic rates, more than the resulting proline content, may help the cell to counteract the effects of abiotic stress conditions.
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Affiliation(s)
- G Forlani
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - M Bertazzini
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - G Cagnano
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
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27
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Mishra P, Jain A, Takabe T, Tanaka Y, Negi M, Singh N, Jain N, Mishra V, Maniraj R, Krishnamurthy SL, Sreevathsa R, Singh NK, Rai V. Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:217. [PMID: 30941150 PMCID: PMC6433796 DOI: 10.3389/fpls.2019.00217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/08/2019] [Indexed: 05/17/2023]
Abstract
UNLABELLED Among abiotic stresses, salt stress adversely affects growth and development in rice. Contrasting salt tolerant (CSR27), and salt sensitive (MI48) rice varieties provided information on an array of genes that may contribute for salt tolerance of rice. Earlier studies on transcriptome and proteome profiling led to the identification of salt stress-induced serine hydroxymethyltransferase-3 (SHMT3) gene. In the present study, the SHMT3 gene was isolated from salt-tolerant (CSR27) rice. OsSHMT3 exhibited salinity-stress induced accentuated and differential expression levels in different tissues of rice. OsSHMT3 was overexpressed in Escherichia coli and assayed for enzymatic activity and modeling protein structure. Further, Arabidopsis transgenic plants overexpressing OsSHMT3 exhibited tolerance toward salt stress. Comparative analyses of OsSHMT3 vis a vis wild type by ionomic, transcriptomic, and metabolic profiling, protein expression and analysis of various traits revealed a pivotal role of OsSHMT3 in conferring tolerance toward salt stress. The gene can further be used in developing gene-based markers for salt stress to be employed in marker assisted breeding programs. HIGHLIGHTS - The study provides information on mechanistic details of serine hydroxymethyl transferase gene for its salt tolerance in rice.
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Affiliation(s)
- Pragya Mishra
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- Banasthali Vidyapith, Jaipur, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Jaipur, India
| | - Teruhiro Takabe
- Plant Biotechnology Research Centre, Meijo University, Nagoya, Japan
| | - Yoshito Tanaka
- Plant Biotechnology Research Centre, Meijo University, Nagoya, Japan
| | - Manisha Negi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Neha Jain
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Vagish Mishra
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - R. Maniraj
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - Rohini Sreevathsa
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nagendra K. Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Vandna Rai
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- *Correspondence: Vandna Rai,
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