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Phosuwan S, Nounjan N, Theerakulpisut P, Siangliw M, Charoensawan V. Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways. Front Plant Sci 2024; 15:1264909. [PMID: 38463565 PMCID: PMC10920293 DOI: 10.3389/fpls.2024.1264909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.
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Affiliation(s)
- Sunadda Phosuwan
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Noppawan Nounjan
- Biodiversity and Environmental Management Division, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Piyada Theerakulpisut
- Salt-tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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2
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Pannak S, Wanchana S, Aesomnuk W, Pitaloka MK, Jamboonsri W, Siangliw M, Meyers BC, Toojinda T, Arikit S. Functional Bph14 from Rathu Heenati promotes resistance to BPH at the early seedling stage of rice (Oryza sativa L.) as revealed by QTL-seq. Theor Appl Genet 2023; 136:25. [PMID: 36781491 DOI: 10.1007/s00122-023-04318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
A QTL associated with BPH resistance at the early seedling stage was identified on chromosome 3. Functional Bph14 in Rathu Heenati was associated with BPH resistance at the early seedling stage. Brown planthopper (BPH; Nilaparvata lugens Stål) is considered the most important rice pest in many Asian countries. Several BPH resistance genes have previously been identified. However, there are few reports of genes specific for BPH resistance at the early seedling stage, a crucial stage for direct-seeding cultivation. In this study, we performed a QTL-seq analysis using two bulks (20 F2 lines in each bulk) of the F2 population (n = 300) derived from a cross of Rathu Heenati (RH) × HCS-1 to identify QTL/genes associated with BPH resistance at the early seedling stage. An important QTL was identified on chromosome 3 and Bph14 was identified as a potential candidate gene based on the differences in gene expression and sequence variation when compared with the two parents. All plants in the resistant bulks possessed the functional Bph14 from RH and all plants in the susceptible bulk and HCS-1 contained a large deletion (2703 bp) in Bph14. The functional Bph14 gene of RH appears to be important for BPH resistance at the early seedling stage of rice and could be used in conjunction with other BPH resistance genes in rice breeding programs that confer resistance to BPH at the early and later growth stages.
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Affiliation(s)
- Sarinthip Pannak
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence On Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, 10900, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Wanchana Aesomnuk
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Mutiara K Pitaloka
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Watchareewan Jamboonsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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Lertngim N, Ruangsiri M, Klinsawang S, Raksatikan P, Thunnom B, Siangliw M, Toojinda T, Siangliw JL. Photosynthetic Plasticity and Stomata Adjustment in Chromosome Segment Substitution Lines of Rice Cultivar KDML105 under Drought Stress. Plants (Basel) 2022; 12:94. [PMID: 36616222 PMCID: PMC9823560 DOI: 10.3390/plants12010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
The impact of increasing drought periods on crop yields as a result of global climate change is a major concern in modern agriculture. Thus, a greater understanding of crop physiological responses under drought stress can guide breeders to develop new cultivars with enhanced drought tolerance. In this study, selected chromosome segment substitution lines of KDML105 (KDML105-CSSL) were grown in the Plant Phenomics Center of Kasetsart University in Thailand under well-watered and drought-stressed conditions. Physiological traits were measured by observing gas exchange dynamics and using a high-throughput phenotyping platform. Furthermore, because of its impact on plant internal gas and water regulation, stomatal morphological trait variation was recorded. The results show that KDML105-CSS lines exhibited plasticity responses to enhance water-use efficiency which increased by 3.62%. Moreover, photosynthesis, stomatal conductance and transpiration decreased by approximately 40% and plant height was reduced by 17.69%. Stomatal density tended to decrease and was negatively correlated with stomatal size, and stomata on different sides of the leaves responded differently under drought stress. Under drought stress, top-performing KDML105-CSS lines with high net photosynthesis had shorter plant height and improved IWUE, as influenced by an increase in stomatal density on the upper leaf side and a decrease on the lower leaf side.
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Affiliation(s)
- Narawitch Lertngim
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Mathurada Ruangsiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Suparad Klinsawang
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Pimpa Raksatikan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Burin Thunnom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonaliza Lanceras Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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Nguyen VQ, Sreewongchai T, Siangliw M, Roytrakul S, Yokthongwattana C. Comparative proteomic analysis of chromosome segment substitution lines of Thai jasmine rice KDML105 under short-term salinity stress. Planta 2022; 256:12. [PMID: 35710953 DOI: 10.1007/s00425-022-03929-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/26/2022] [Indexed: 05/21/2023]
Abstract
Heat shock proteins, ROS detoxifying enzymes, and ion homeostasis proteins, together with proteins in carbohydrate metabolism, cell structure, brassinosteroids, and carotenoid biosynthesis pathway were up-regulated in CSSLs under salinity stress. Rice is one of the most consumed staple foods worldwide. Salinity stress is a serious global problem affecting rice productivity. Many attempts have been made to select or produce salinity-tolerant rice varieties. Genetics and biochemical approaches were used to study the salinity-responsive pathway in rice to develop salinity tolerant strains. This study investigated the proteomic profiles of chromosome segment substitution lines (CSSLs) developed from KDML105 (Khao Dawk Mali 105, a Thai jasmine rice cultivar) under salinity stress. The CSSLs showed a clear resistant phenotype in response to 150 mM NaCl treatment compared to the salinity-sensitive line, IR29. Liquid chromatography-tandem mass spectrometry using the Ultimate 3000 Nano/Capillary LC System coupled to a Hybrid Quadrupole Q-Tof Impact II™ equipped with a nano-captive spray ion source was applied for proteomic analysis. Based on our criteria, 178 proteins were identified as differentially expressed proteins under salinity stress. Protein functions in DNA replication and transcription, and stress and defense accounted for the highest proportions in response to salinity stress, followed by protein transport and trafficking, carbohydrate metabolic process, signal transduction, and cell structure. The protein interaction network among the 75 up-regulated proteins showed connections between proteins involved in cell wall synthesis, transcription, translation, and in defense responses.
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Affiliation(s)
- Vinh Quang Nguyen
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkok, 10900, Thailand
| | - Tanee Sreewongchai
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Meechai Siangliw
- Rice Science Center (RSC), Rice Gene Discovery Unit (RGDU), Kasetsart University, Kamphaengsaen, Nakhon Pathom, 73140, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd, Pathumthani, 12120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd, Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok, 10900, Thailand.
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Darwell CT, Wanchana S, Ruanjaichon V, Siangliw M, Thunnom B, Aesomnuk W, Toojinda T. riceExplorer: Uncovering the Hidden Potential of a National Genomic Resource Against a Global Database. Front Plant Sci 2022; 13:781153. [PMID: 35574109 PMCID: PMC9100803 DOI: 10.3389/fpls.2022.781153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Agricultural crop breeding programs, particularly at the national level, typically consist of a core panel of elite breeding cultivars alongside a number of local landrace varieties (or other endemic cultivars) that provide additional sources of phenotypic and genomic variation or contribute as experimental materials (e.g., in GWAS studies). Three issues commonly arise. First, focusing primarily on core development accessions may mean that the potential contributions of landraces or other secondary accessions may be overlooked. Second, elite cultivars may accumulate deleterious alleles away from nontarget loci due to the strong effects of artificial selection. Finally, a tendency to focus solely on SNP-based methods may cause incomplete or erroneous identification of functional variants. In practice, integration of local breeding programs with findings from global database projects may be challenging. First, local GWAS experiments may only indicate useful functional variants according to the diversity of the experimental panel, while other potentially useful loci-identifiable at a global level-may remain undiscovered. Second, large-scale experiments such as GWAS may prove prohibitively costly or logistically challenging for some agencies. Here, we present a fully automated bioinformatics pipeline (riceExplorer) that can easily integrate local breeding program sequence data with international database resources, without relying on any phenotypic experimental procedure. It identifies associated functional haplotypes that may prove more robust in determining the genotypic determinants of desirable crop phenotypes. In brief, riceExplorer evaluates a global crop database (IRRI 3000 Rice Genomes) to identify haplotypes that are associated with extreme phenotypic variation at the global level and recorded in the database. It then examines which potentially useful variants are present in the local crop panel, before distinguishing between those that are already incorporated into the elite breeding accessions and those only found among secondary varieties (e.g., landraces). Results highlight the effectiveness of our pipeline, identifying potentially useful functional haplotypes across the genome that are absent from elite cultivars and found among landraces and other secondary varieties in our breeding program. riceExplorer can automatically conduct a full genome analysis and produces annotated graphical output of chromosomal maps, potential global diversity sources, and summary tables.
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Chutimanukul P, Saputro TB, Mahaprom P, Plaimas K, Comai L, Buaboocha T, Siangliw M, Toojinda T, Chadchawan S. Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice. Front Plant Sci 2021; 12:704549. [PMID: 34512689 PMCID: PMC8427287 DOI: 10.3389/fpls.2021.704549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/06/2021] [Indexed: 06/04/2023]
Abstract
Salinity stress tolerance is a complex polygenic trait involving multi-molecular pathways. This study aims to demonstrate an effective transcriptomic approach for identifying genes regulating salt tolerance in rice. The chromosome segment substitution lines (CSSLs) of "Khao Dawk Mali 105 (KDML105)" rice containing various regions of DH212 between markers RM1003 and RM3362 displayed differential salt tolerance at the booting stage. CSSL16 and its nearly isogenic parent, KDML105, were used for transcriptome analysis. Differentially expressed genes in the leaves of seedlings, flag leaves, and second leaves of CSSL16 and KDML105 under normal and salt stress conditions were subjected to analyses based on gene co-expression network (GCN), on two-state co-expression with clustering coefficient (CC), and on weighted gene co-expression network (WGCN). GCN identified 57 genes, while 30 and 59 genes were identified using CC and WGCN, respectively. With the three methods, some of the identified genes overlapped, bringing the maximum number of predicted salt tolerance genes to 92. Among the 92 genes, nine genes, OsNodulin, OsBTBZ1, OsPSB28, OsERD, OsSub34, peroxidase precursor genes, and three expressed protein genes, displayed SNPs between CSSL16 and KDML105. The nine genes were differentially expressed in CSSL16 and KDML105 under normal and salt stress conditions. OsBTBZ1 and OsERD were identified by the three methods. These results suggest that the transcriptomic approach described here effectively identified the genes regulating salt tolerance in rice and support the identification of appropriate QTL for salt tolerance improvement.
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Affiliation(s)
- Panita Chutimanukul
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Triono Bagus Saputro
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Puriphot Mahaprom
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing Research Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California Davis Genome Center, UC Davis, Davis, CA, United States
| | - Teerapong Buaboocha
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Theerawitaya C, Samphumphuang T, Tisarum R, Siangliw M, Cha-Um S, Takabe T, Toojinda T. Expression level of Na + homeostasis-related genes and salt-tolerant abilities in backcross introgression lines of rice crop under salt stress at reproductive stage. Protoplasma 2020; 257:1595-1606. [PMID: 32671620 DOI: 10.1007/s00709-020-01533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Salt stress in the rice field is one of the most common abiotic stresses, reducing crop productivity, especially at reproductive stage, which is very sensitive to salt stress. The aim of this investigation was to study mRNA-related Na+ uptake/translocation and Na+ enrichment in the cellular level, leading to physiological changes, growth characteristics, and yield attributes in FL530 [salt-tolerant genotype; carrying SKC1 (in relation to high-affinity potassium transporters controlling Na+ and K+ translocation) and qSt1b (linking to salt injury score) QTLs] and KDML105 (salt-sensitive cultivar; lacking both QTLs) parental lines and 221-48 (carrying SKC1 and qSt1b QTLs) derived from BILs (backcross introgression lines) at 50% flowering of rice, under 150-mM NaCl until harvesting process. The upregulation of OsHKT1;5 (mediating Na+ exclusion into xylem parenchyma cells) and OsNHX1 (Na+/H+ exchanger to secrete Na+ into vacuole) and downregulation of OsHKT2;1 and OsHKT2;2 (mediating Na+ restriction in the roots, leaf sheath and older leaves) in cvs. FL530 and 221-48 (+ SKC1; + qSt1b) under salt stress were observed. It restricted Na+ level in flag leaf, thereby preventing salt toxicity, as indicated by maintenance of photon yield of PSII (ΦPSII), net photosynthetic rate (Pn), transpiration rate (E) and overall growth performances. In contrast, Na+ enrichment in flag leaf of cv. KDML105 (-SKC1;-qSt1b) caused the reduction in ΦPSII by 30.5% over the control, leading to the reduction in Pn by 62.3%, in seed sterility by 88.2%, and yield loss by 85.1%. Moreover, the negative relationships between Na+ enrichment in flag leaf, physiological changes, and yield traits in rice crop grown under salt stress were demonstrated. Based on this investigation, rice genotype 221-48 was found to possess salt-tolerant traits at reproductive stage and thus could prove to be a potential candidate for future breeding programs.
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Affiliation(s)
- Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Thapanee Samphumphuang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Meechai Siangliw
- Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC, NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Teruhiro Takabe
- Research Institute, Meijo University, 1-501 Shiogamagushi, Tenpaku-ku, Nagoya, 468-8502, Japan
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
- Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC, NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
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Chutimanukul P, Kositsup B, Plaimas K, Buaboocha T, Siangliw M, Toojinda T, Comai L, Chadchawan S. Data in support of photosynthetic responses in a chromosome segment substitution line of 'Khao Dawk Mali 105' rice at seedling stage. Data Brief 2018; 21:307-312. [PMID: 30364694 PMCID: PMC6197707 DOI: 10.1016/j.dib.2018.09.128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/24/2018] [Accepted: 09/30/2018] [Indexed: 11/26/2022] Open
Abstract
The rice chromosome segment substitution lines (CSSLs) of ‘Khao Dawk Mali 105’ (‘KDML105’) genetic background were developed by backcrossing with ‘KDML105’ rice and transferring the region from chromosome 1 of DH212 which was expected to contain the full putative salt tolerance genetic region. Line of CSSL11, CSSL12, and CSSL16 contained the full putative salt tolerance genetic region were evaluated with the parental lines, ‘KDML105’ and DH212 at seedling stage of rice. The physiological responses in rice plants were grown under normal condition and 75 mM of NaCl, and then comparative photosynthetic parameters, chlorophyll fluorescence parameters, PhiPS2, ETR, NPQ, as well as growth analysis. In this article, the data of physiological response evaluation in rice at seedling stage after salt stress treatment can be found. This can be useful as the information of the photosynthesis response to salt stress to other rice cultivars and related species.
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Affiliation(s)
- Panita Chutimanukul
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
| | - Boonthida Kositsup
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
| | - Kitiporn Plaimas
- AVIC Research Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
| | - Teerapong Buaboocha
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand.,Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
| | - Meechai Siangliw
- Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom 73140, Thailand
| | - Theerayut Toojinda
- Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom 73140, Thailand
| | - Luca Comai
- Department of Plant Biology, UC Davis Genome Center, UC Davis, Davis, CA 95616, USA
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand.,Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10300, Thailand
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Vanavichit A, Kamolsukyeunyong W, Siangliw M, Siangliw JL, Traprab S, Ruengphayak S, Chaichoompu E, Saensuk C, Phuvanartnarubal E, Toojinda T, Tragoonrung S. Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System. Rice (N Y) 2018; 11:20. [PMID: 29633040 PMCID: PMC5891439 DOI: 10.1186/s12284-018-0212-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/20/2018] [Indexed: 05/09/2023]
Abstract
The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection, it was officially named as Khao Dawk Mali 105, (KDML105). Because of its superb fragrance and cooking quality, KDML105 has been a model variety for studying genes controlling grain quality and aroma. The aromatic gene was cloned in KDML105, as an amino aldehyde dehydrogenase (AMADH) or better known as BADH2 located on chromosome 8. Later on, all other aromatic rice genes were discovered as allelic to the AMADH. As a selection of local landrace variety found in rainfed areas, the Thai Jasmine rice showed adaptive advantages over improved irrigated rice in less fertile lowland rainfed conditions. Because KDML105 was susceptible to most diseases and insect pests, marker-assisted backcross selection (MABC) was used for the genetic improvement since 2000. After nearly 17 years of MABC for integrating new traits into KDML105, a new generation of KDML105, designated HM84, was developed which maintains the cooking quality and fragrance, and has gained advantages during flash flooding, disease, and insect outbreak.
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Affiliation(s)
- Apichart Vanavichit
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
- Agronomy Department, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Wintai Kamolsukyeunyong
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Meechai Siangliw
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Jonaliza L. Siangliw
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Suniyom Traprab
- Bureau of Rice Research and Development (Rice Department), 50 Paholyothin Rd, Chatuchak, Bangkok, 10900 Thailand
| | - Siriphat Ruengphayak
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Ekawat Chaichoompu
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | - Chatree Saensuk
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
| | | | - Theerayut Toojinda
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140 Thailand
- Plant Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, 113 Thailand Science Park, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, 113 Thailand Science Park, Khlong Luang, Pathum Thani, 12120 Thailand
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Siebers N, Siangliw M, Tongcumpou C. Cadmium uptake and subcellular distribution in rice plants as affected by phosphorus: Soil and hydroponic experiments. J Soil Sci Plant Nutr 2013:0-0. [PMID: 0 DOI: 10.4067/s0718-95162013005000066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Toojinda T, Siangliw M, Tragoonrung S, Vanavichit A. Molecular genetics of submergence tolerance in rice: QTL analysis of key traits. Ann Bot 2003; 91 Spec No:243-53. [PMID: 12509344 PMCID: PMC4244984 DOI: 10.1093/aob/mcf072] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Flash flooding of young rice plants is a common problem for rice farmers in south and south-east Asia. It severely reduces grain yield and increases the unpredictability of cropping. The inheritance and expression of traits associated with submergence stress tolerance at the seedling stage are physiologically and genetically complex. We exploited naturally occurring differences between certain rice lines in their tolerance to submergence and used quantitative trait loci (QTL) mapping to improve understanding of the genetic and physiological basis of submergence tolerance. Three rice populations, each derived from a single cross between two cultivars differing in their response to submergence, were used to identify QTL associated with plant survival and various linked traits. These included total shoot elongation under water, the extent of stimulation of shoot elongation caused by submergence, a visual submergence tolerance score, and leaf senescence under different field conditions, locations and years. Several major QTL determining plant survival, plant height, stimulation of shoot elongation, visual tolerance score and leaf senescence each mapped to the same locus on chromosome 9. These QTL were detected consistently in experiments across all years and in the genetic backgrounds of all three mapping populations. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 5, 7, 10 and 11. These QTL were specific to particular traits, environments, or genetic backgrounds. All identified QTL contributed to increased submergence tolerance through their effects on decreased underwater shoot elongation or increased maintenance of chlorophyll levels, or on both. These findings establish the foundations of a marker-assisted scheme for introducing submergence tolerance into agriculturally desirable cultivars of rice.
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Affiliation(s)
- T Toojinda
- BIOTEC, Rice Gene Discovery Unit, DNA Technology Laboratory, Dept. of Agronomy, National Center for Genetic Engineering, Kasetsart Univ., Kampangsaen Campus, Nakorn Pathom, Thailand.
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Kamolsukyunyong W, Ruanjaichon V, Siangliw M, Kawasaki S, Sasaki T, Vanavichit A, Tragoonrung S. Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking. DNA Res 2001; 8:163-71. [PMID: 11572482 DOI: 10.1093/dnares/8.4.163] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.
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Affiliation(s)
- W Kamolsukyunyong
- National Center for Genetic Engineering and Biotechnology, Kasetsart University, Nakorn Pathom, Thailand.
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