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Khanna A, Anumalla M, Ramos J, Cruz MTS, Catolos M, Sajise AG, Gregorio G, Dixit S, Ali J, Islam MR, Singh VK, Rahman MA, Khatun H, Pisano DJ, Bhosale S, Hussain W. Genetic gains in IRRI's rice salinity breeding and elite panel development as a future breeding resource. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:37. [PMID: 38294550 PMCID: PMC10830834 DOI: 10.1007/s00122-024-04545-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE Estimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains. Genetic gain is a crucial parameter to check the breeding program's success and help optimize future breeding strategies for enhanced genetic gains. To estimate the genetic gains in IRRI's salinity breeding program and identify the best genotypes based on high breeding values for grain yield (kg/ha), we analyzed the historical data from the trials conducted in the IRRI, Philippines and Bangladesh. A two-stage mixed-model approach accounting for experimental design factors and a relationship matrix was fitted to obtain the breeding values for grain yield and estimate genetic trends. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha was observed in IRRI, Philippines. In Bangladesh, we observed a genetic gain of 0.31% per annum with a yield advantage of 14.02 kg/ha. In the released varieties, we observed a genetic gain of 0.12% per annum with a 2.2 kg/ha/year yield advantage in the IRRI, Philippines. For the Bangladesh dataset, a genetic gain of 0.14% per annum with a yield advantage of 5.9 kg/ha/year was observed in the released varieties. Based on breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of > 2400 kg/ha in the IRRI, Philippines, and > 3500 kg/ha in Bangladesh with a reliability of > 0.4 were selected to develop the elite breeding panel. Conclusively, a recurrent selection breeding strategy integrated with novel technologies like genomic selection and speed breeding is highly required to achieve higher genetic gains in IRRI's salinity breeding programs.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Andres Godwin Sajise
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Glenn Gregorio
- Southeast Asian Regional Center for Graduate Study and Research in Agriculture (SEARCA) and University of Philippines, 4031, Los Baños, Laguna, Philippines
| | - Shalabh Dixit
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Jauhar Ali
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Md Rafiqul Islam
- IRRI South Asia Regional Center (IRRI-SA Hub), Hyderabad, Telangana, 502324, India
| | - Vikas Kumar Singh
- IRRI South Asia Regional Center (IRRI-SA Hub), Hyderabad, Telangana, 502324, India
| | - Md Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, 1701, Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, 1701, Bangladesh
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.
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Liang H, Zhou GP, Gao SJ, Nie J, Xu CX, Wu J, Liu CZ, Lv YH, Huang YB, Geng MJ, Wang JH, He TG, Cao WD. Exploring site-specific N application rate to reduce N footprint and increase crop production for green manure-rice rotation system in southern China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119033. [PMID: 37757691 DOI: 10.1016/j.jenvman.2023.119033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/11/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Milk vetch (Astragalus sinicus L.) is leguminous green manure (GM) which produces organic nitrogen (N) for subsequent crops and is widely planted and utilized to simultaneously reduce the use of synthetic N fertilizer and its environmental costs in rice systems. Determination of an optimal N application rate specific to the GM-rice system is challenging because of the large temporal and spatial variations in soil, climate, and field management conditions. To solve this problem, we developed a framework to explore the site-specific N application rate for the low-N footprint rice production system in southern China based on multi-site field experiments, farmer field survey, and process-based model (WHCNS_Rice, soil water heat carbon nitrogen simulator for rice). The results showed that a process-based model can explain >83.3% (p < 0.01) of the variation in rice yield, aboveground biomass, crop N uptake, and soil mineral N. Based on the scenario analysis of the tested WHCNS_Rice model, the simple regression equation was developed to implement site-specific N application rates that considered variations in GM biomass, soil, and climatic conditions. Simulation evaluation on nine provinces in southern China showed that the site-specific N application rate reduced regional synthetic N fertilizer input by 29.6 ± 17.8% and 65.3 ± 23.0% for single and early rice, respectively; decreased their total N footprints (NFs) by 23.4% and 49.3%, respectively; and without reduction in rice yield, compared with traditional farming N practices. The reduction in total NF was attributed to the reduced emissions from ammonia volatilization by 35.2%, N leaching by 28.4%, and N runoff by 32.7%. In this study, we suggested a low NF rice production system that can be obtained by combining GM with site-specific N application rate in southern China.
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Affiliation(s)
- Hao Liang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Guo-Peng Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Song-Juan Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Jun Nie
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chang-Xu Xu
- Institute of Soil & Fertilizer and Resources & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ji Wu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Chun-Zeng Liu
- Institute of Plant Nutrition Agricultural Resources and Environmental Sciences, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yu-Hu Lv
- Xinyang Academy of Agricultural Sciences, Xinyang, China
| | - Yi-Bin Huang
- Institute of Soil and Fertilizer, Resources and Environment, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ming-Jian Geng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jian-Hong Wang
- Institute of Environment and Resource & Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tie-Guang He
- Agricultural Resources and Environmental Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, China
| | - Wei-Dong Cao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
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Bhuyan MI, Supit I, Mia S, Mulder M, Ludwig F. Effect of soil and water salinity on dry season boro rice production in the south-central coastal area of Bangladesh. Heliyon 2023; 9:e19180. [PMID: 37664704 PMCID: PMC10469569 DOI: 10.1016/j.heliyon.2023.e19180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/05/2023] Open
Abstract
Salinity varies with location and time of the year. It can significantly impact crop production. The level of negative impacts depends on the salt concentration and time of its occurrence, which, however, has not been studied for many crops, especially for rice grown in the coastal area of Bangladesh. Our study explored the impact of spatio-temporal fluctuations in soil and water salinity on boro rice production in the south-central coast of Bangladesh. Here, we simulated the soil salinity from November 2020 to May 2021 for fourteen locations classes using the SWAP-WOFOST model. The model was calibrated and validated with measured secondary data. Next, the yield of two salt-tolerant boro rice varieties (BRRI dhan47 and BRRI dhan67) was simulated using the customized soil, weather, and crop data. We also simulated the yield by adopting agronomic management practices (i.e., changing planting time and using fresh irrigation water). Our results showed that salinity levels varied with different soil textural classes, soil depth, location, and time of the year, and that had a significant influence on boro rice production, giving spatial variability. Specifically, boro rice had a higher yield in coarse texture soil than in fine texture soil. Simulated yields in areas proximate to the sea ranged from 668 to 1239 kg ha-1, yields that are significantly lower than those simulated in moderate (2098-4843 kg ha-1) and low salinity zones (4213-4843 kg ha-1). Moreover, the simulation of yield with sowing/planting rice earlier by fifteen days provided a higher yield than the current planting practice since it could avoid salinity at later stages of growth. For a similar reason, growing rice inside the polder provided a higher yield than outside the polder. The insights gained from our study carry significant implications for contemporary crop-level adaptation strategies and policy-making in coastal districts.
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Affiliation(s)
- Md Isfatuzzaman Bhuyan
- Water Systems and Global Change Group, Wageningen University and Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
- Department of Agronomy, Faculty of Agriculture, Patuakhali Science and Technology University, Patuakhali 8602, Bangladesh
| | - Iwan Supit
- Water Systems and Global Change Group, Wageningen University and Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Shamim Mia
- Department of Agronomy, Faculty of Agriculture, Patuakhali Science and Technology University, Patuakhali 8602, Bangladesh
| | - Martin Mulder
- Soil Physics and Land Management Group, Wageningen University and Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Fulco Ludwig
- Water Systems and Global Change Group, Wageningen University and Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
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Rathnasamy SA, Kambale R, Elangovan A, Mohanavel W, Shanmugavel P, Ramasamy G, Alagarsamy S, Marimuthu R, Rajagopalan VR, Manickam S, Ramanathan V, Muthurajan R, Vellingiri G. Altering Stomatal Density for Manipulating Transpiration and Photosynthetic Traits in Rice through CRISPR/Cas9 Mutagenesis. Curr Issues Mol Biol 2023; 45:3801-3814. [PMID: 37232714 DOI: 10.3390/cimb45050245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/12/2023] [Accepted: 02/28/2023] [Indexed: 05/27/2023] Open
Abstract
Stomata regulates conductance, transpiration and photosynthetic traits in plants. Increased stomatal density may contribute to enhanced water loss and thereby help improve the transpirational cooling process and mitigate the high temperature-induced yield losses. However, genetic manipulation of stomatal traits through conventional breeding still remains a challenge due to problems involved in phenotyping and the lack of suitable genetic materials. Recent advances in functional genomics in rice identified major effect genes determining stomatal traits, including its number and size. Widespread applications of CRISPR/Cas9 in creating targeted mutations paved the way for fine tuning the stomatal traits for enhancing climate resilience in crops. In the current study, attempts were made to create novel alleles of OsEPF1 (Epidermal Patterning Factor), a negative regulator of stomatal frequency/density in a popular rice variety, ASD 16, using the CRISPR/Cas9 approach. Evaluation of 17 T0 progenies identified varying mutations (seven multiallelic, seven biallelic and three monoallelic mutations). T0 mutant lines showed a 3.7-44.3% increase in the stomatal density, and all the mutations were successfully inherited into the T1 generation. Evaluation of T1 progenies through sequencing identified three homozygous mutants for one bp insertion. Overall, T1 plants showed 54-95% increased stomatal density. The homozygous T1 lines (# E1-1-4, # E1-1-9 and # E1-1-11) showed significant increase in the stomatal conductance (60-65%), photosynthetic rate (14-31%) and the transpiration rate (58-62%) compared to the nontransgenic ASD 16. Results demonstrated that the genetic alterations in OsEPF1 altered the stomatal density, stomatal conductance and photosynthetic efficiency in rice. Further experiments are needed to associate this technology with canopy cooling and high temperature tolerance.
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Affiliation(s)
- Sakthi Ambothi Rathnasamy
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Rohit Kambale
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Allimuthu Elangovan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Williams Mohanavel
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Priyanka Shanmugavel
- Agro-Climatology Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Gowtham Ramasamy
- Agro-Climatology Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Senthil Alagarsamy
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Rajavel Marimuthu
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Sudha Manickam
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | | | - Raveendran Muthurajan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Geethalakshmi Vellingiri
- Agro-Climatology Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
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Samsuddin Sah S, Abdul Maulud KN, A Karim O, Sharil S, Yaseen ZM. Extensive assessment of climate change impacts on coastal zone paddy growth using multispectral analysis and hydrodynamic modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161585. [PMID: 36681338 DOI: 10.1016/j.scitotenv.2023.161585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Global warming has led to sea levels raise (SLRs) and Malaysia is no exception to this problem. Especially for low-lying coastal areas including the Kuala Kedah area which is active in agricultural and fisheries activities. Farmers have had to bear up to 75 % of yield losses due to seawater breaches since 2016. Therefore, this study is designed to assess the impact of seawater encroachment on water quality through spatial technology approaches and hydrodynamic modeling related to the growth of paddy trees. The study was conducted during two different paddy cultivation seasons namely Season 1-2019 and Season 2-2019 which take place in the southwest and northeast monsoon in Kuala Kedah, Malaysia. The study involved three phases, which are the assessment of salinity and pH concentration levels, the assessment of the health of paddy crops through multispectral image analysis involving three plant indices (VI), namely Normalized Difference Vegetation Index (NDVI), Blue Normalized Difference Vegetation Index (BNDVI) and Normalized Difference Red Edge (NDRE), and finally, the assessment of the impact of SLR through the numerical method in MIKE 21 for hydrodynamic modeling considering two conditions that are without mitigation factor (K1) and with existing mitigating factor (K2). According to the findings, the salinity concentration trend is decreasing across the growth stage during Season 1-2019, whereas it is the contrary during Season 2-2019. It was discovered that during the study period for both tidal events, 73 % of the 44 sampling points in Season 1-2019, as opposed to just 3 % in Season 2-2019, were categorized as Class 4 and Class 5. Even though there were fluctuations throughout the observation, the pH reading is still within the allowed range of 6.5 to 9.0 for the estuary area. Following that, the ANOVA analysis proved that salinity concentration a statistically significant difference with tidal variations and pH levels. Moreover, the multispectral image analysis findings revealed that the VI value was correlated with both the yield and the health of the rice crop, with R-square values of 0.842 compared to 0.706 and 0.575 for NDVI and BNDVI values, respectively. It confirmed that NDRE granted a more accurate and reliable measurements. Additionally, the hydrodynamic simulation results demonstrated that, if the mitigation factors were considered in the modeling, overflow seawater to the mainland could be reduced by up to 20 %, reducing the impact of coastal flooding on the local area as well as the nearby rice cultivation area. Ultimately, these three elements-water quality, vegetation index, and hydrodynamic modeling-can assist in identifying the underlying cause of the problem and develop short and long-term solutions.
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Affiliation(s)
- Samera Samsuddin Sah
- Department of Civil Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Faculty of Chemical Engineering & Technology, Kompleks Pusat Pengajian Kejuruteraan Jejawi 3, Universiti Malaysia Perlis, 02600 Arau, Perlis, Malaysia; Centre of Excellence Water Research and Environmental Sustainability Growth (WAREG), Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, 02600 Jejawi, Perlis, Malaysia
| | - Khairul Nizam Abdul Maulud
- Department of Civil Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Earth Observation Centre, Institute of Climate Change, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| | - Othman A Karim
- Department of Civil Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Suraya Sharil
- Department of Civil Engineering, Faculty of Engineering & Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Zaher Mundher Yaseen
- Civil and Environmental Engineering Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
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Gao Q, Wang H, Yin X, Wang F, Hu S, Liu W, Chen L, Dai X, Liang M. Identification of Salt Tolerance Related Candidate Genes in 'Sea Rice 86' at the Seedling and Reproductive Stages Using QTL-Seq and BSA-Seq. Genes (Basel) 2023; 14:458. [PMID: 36833384 PMCID: PMC9956910 DOI: 10.3390/genes14020458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Salt stress seriously affects plant growth and development and reduces the yield of rice. Therefore, the development of salt-tolerant high-yielding rice cultivars through quantitative trait locus (QTL) identification and bulked segregant analysis (BSA) is the main focus of molecular breeding projects. In this study, sea rice (SR86) showed greater salt tolerance than conventional rice. Under salt stress, the cell membrane and chlorophyll were more stable and the antioxidant enzyme activity was higher in SR86 than in conventional rice. Thirty extremely salt-tolerant plants and thirty extremely salt-sensitive plants were selected from the F2 progenies of SR86 × Nipponbare (Nip) and SR86 × 9311 crosses during the whole vegetative and reproductive growth period and mixed bulks were generated. Eleven salt tolerance related candidate genes were located using QTL-seq together with BSA. Real time quantitative PCR (RT-qPCR) analysis showed that LOC_Os04g03320.1 and BGIOSGA019540 were expressed at higher levels in the SR86 plants than in Nip and 9311 plants, suggesting that these genes are critical for the salt tolerance of SR86. The QTLs identified using this method could be effectively utilized in future salt tolerance breeding programs, providing important theoretical significance and application value for rice salt tolerance breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Manzhong Liang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
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Ling X, Deng N, Xiong D, Yuan S, Peng S, Li T, Huang J. Effect of variation in the observations on the prediction uncertainty in crop model simulation: Use ORYZA (v3) as a case study. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Yin W, Lu T, Chen Z, Lu T, Ye H, Mao Y, Luo Y, Lu M, Zhu X, Yuan X, Rao Y, Wang Y. Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice. FRONTIERS IN PLANT SCIENCE 2023; 13:1041081. [PMID: 36726666 PMCID: PMC9886062 DOI: 10.3389/fpls.2022.1041081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subsp. indica cv. 'HZ') and a female variety of Nekken2 (Oryza sativa L. subsp. japonica cv. 'Nekken2') as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 (LOC_Os12g25200) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice.
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Affiliation(s)
- Wenjing Yin
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tianqi Lu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Zhengai Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tao Lu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hanfei Ye
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yijian Mao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Yiting Luo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Mei Lu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xudong Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Xi Yuan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
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Choudhary P, Muthamilarasan M. Modulating physiological and transcriptional regulatory mechanisms for enhanced climate resilience in cereal crops. JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153815. [PMID: 36150236 DOI: 10.1016/j.jplph.2022.153815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Climate change adversely affects the yield and productivity of cereal crops, which consequently impacts food security. Therefore, studying stress acclimation, particularly transcriptional patterns and morpho-physiological responses of cereal crops to different stresses, will provide insights into the molecular determinants underlying climate resilience. The availability of advanced tools and approaches has enabled the characterization of plants at morphological, physiological, biochemical, and molecular levels, which will lead to the identification of genomic regions regulating the stress responses at these levels. This will further facilitate using transgenic, breeding, or genome editing approaches to manipulate the identified regions (genes, alleles, or QTLs) to enhance stress resilience. Next-generation sequencing approaches have advanced the identification of causal genes and markers in the genomes through forward or reverse genetics. In this context, the review enumerates the progress of dissecting the molecular mechanisms underlying transcriptional and physiological responses of major cereals to climate-induced stresses. The review systematically discusses different tools and approaches available to study the response of plants to various stresses and identify the molecular determinants regulating stress-resilience. Further, the application of genomics-assisted breeding, transgene-, and targeted editing-based approaches for modulating the genetic determinants for enhanced climate resilience has been elaborated.
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Affiliation(s)
- Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India.
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Ajmera I, Henry A, Radanielson AM, Klein SP, Ianevski A, Bennett MJ, Band LR, Lynch JP. Integrated root phenotypes for improved rice performance under low nitrogen availability. PLANT, CELL & ENVIRONMENT 2022; 45:805-822. [PMID: 35141925 PMCID: PMC9303783 DOI: 10.1111/pce.14284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 05/06/2023]
Abstract
Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional-structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L-type and S-type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct-seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct-seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.
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Affiliation(s)
- Ishan Ajmera
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Amelia Henry
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
| | - Ando M. Radanielson
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
- Centre for Sustainable Agricultural Systems, Institute for Life Sciences and the Environment, Toowoomba CampusUniversity of Southern QueenslandToowoombaQueenslandAustralia
| | - Stephanie P. Klein
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Malcolm J. Bennett
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Leah R. Band
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Centre for Mathematical Medicine and Biology, School of Mathematical SciencesUniversity of NottinghamNottinghamUK
| | - Jonathan P. Lynch
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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11
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Cichota R, Vogeler I, Sharp J, Verburg K, Huth N, Holzworth D, Dalgliesh N, Snow V. A protocol to build soil descriptions for APSIM simulations. MethodsX 2022; 8:101566. [PMID: 35004200 PMCID: PMC8720820 DOI: 10.1016/j.mex.2021.101566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/30/2021] [Indexed: 11/04/2022] Open
Abstract
Introducing the models and user interface for characterising a soil in APSIM simulations. Listing and describing the parameters needed for building soil descriptions in APSIM. Providing recommendations for good practice when setting up soil parameters in APSIM.
Soil processes have a major impact on agroecosystems, controlling water and nutrient cycling, regulating plant growth and losses to the wider environment. Process-based agroecosystem simulation models generally encompass detailed descriptions of the soil, including a wide number of parameters that can be daunting to users with a limited soil science background. In this work we review and present an abridged description of the models used to simulate soil processes in the APSIM (Agricultural Production Systems sIMulator) framework. Such a resource is needed because this information is currently spread over multiple publications and some elements have become outdated. We list and briefly describe the parameters, and establish a protocol with guidelines, for building a soil description for APSIM. This protocol will promote consistency, enhancing the quality of the science done employing APSIM, and provide an easier pathway for new users. This compilation should also be of relevance to users of other models that require detailed soil information.This paper presents a brief description of the models for simulating soil processes in the APSIM model. The method stablishes guidelines to define the parameters for building a soil description for APSIM.
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Affiliation(s)
- Rogerio Cichota
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
| | - Iris Vogeler
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
| | - Joanna Sharp
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
| | | | - Neil Huth
- CSIRO Agriculture and Food, Toowoomba, Qld, Australia
| | | | | | - Val Snow
- AgResearch Limited, Lincoln, New Zealand
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12
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Comparison of Multi-Methods for Identifying Maize Phenology Using PhenoCams. REMOTE SENSING 2022. [DOI: 10.3390/rs14020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Accurately identifying the phenology of summer maize is crucial for both cultivar breeding and fertilizer controlling in precision agriculture. In this study, daily RGB images covering the entire growth of summer maize were collected using phenocams at sites in Shangqiu (2018, 2019 and 2020) and Nanpi (2020) in China. Four phenological dates, including six leaves, booting, heading and maturity of summer maize, were pre-defined and extracted from the phenocam-based images. The spectral indices, textural indices and integrated spectral and textural indices were calculated using the improved adaptive feature-weighting method. The double logistic function, harmonic analysis of time series, Savitzky–Golay and spline interpolation were applied to filter these indices and pre-defined phenology was identified and compared with the ground observations. The results show that the DLF achieved the highest accuracy, with the coefficient of determination (R2) and the root-mean-square error (RMSE) being 0.86 and 9.32 days, respectively. The new index performed better than the single usage of spectral and textural indices, of which the R2 and RMSE were 0.92 and 9.38 days, respectively. The phenological extraction using the new index and double logistic function based on the PhenoCam data was effective and convenient, obtaining high accuracy. Therefore, it is recommended the adoption of the new index by integrating the spectral and textural indices for extracting maize phenology using PhenoCam data.
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13
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Kumar G, Basu S, Singla-Pareek SL, Pareek A. Unraveling the contribution of OsSOS2 in conferring salinity and drought tolerance in a high-yielding rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13638. [PMID: 35092312 DOI: 10.1111/ppl.13638] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 05/24/2023]
Abstract
Abiotic stresses are emerging as a potential threat to sustainable agriculture worldwide. Soil salinity and drought will be the major limiting factors for rice productivity in years to come. The Salt Overly Sensitive (SOS) pathway plays a key role in salinity tolerance by maintaining the cellular ion homeostasis, with SOS2, a S/T kinase, being a vital component. The present study investigated the role of the OsSOS2, a SOS2 homolog from rice, in improving salinity and drought tolerance. Transgenic plants with either overexpression (OE) or knockdown (KD) of OsSOS2 were raised in one of the high-yielding cultivars of rice-IR64. Using a combined approach based on physiological, biochemical, anatomical, microscopic, molecular, and agronomic assessment, the evidence presented in this study advocates the role of OsSOS2 in improving salinity and drought tolerance in rice. The OE plants were found to have favorable ion and redox homeostasis when grown in the presence of salinity, while the KD plants showed the reverse pattern. Several key stress-responsive genes were found to work in an orchestrated manner to contribute to this phenotype. Notably, the OE plants showed tolerance to stress at both the seedling and the reproductive stages, addressing the two most sensitive stages of the plant. Keeping in mind the importance of developing crops plants with tolerance to multiple stresses, the present study established the potential of OsSOS2 for biotechnological applications to improve salinity and drought stress tolerance in diverse cultivars of rice.
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Affiliation(s)
- Gautam Kumar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sahana Basu
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
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14
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Paleari L, Movedi E, Zoli M, Burato A, Cecconi I, Errahouly J, Pecollo E, Sorvillo C, Confalonieri R. Sensitivity analysis using Morris: Just screening or an effective ranking method? Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2021.109648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice. BMC Genomics 2021; 22:612. [PMID: 34384368 PMCID: PMC8359061 DOI: 10.1186/s12864-021-07922-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently. RESULTS We sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar 'Nipponbare' (NB) and the salt-tolerant cultivar 'Sea Rice 86' (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5' ends to the 3' ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86. CONCLUSIONS This study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.
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16
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Ali MP, Rahman MS, Nowrin F, Haque SS, Qin X, Haque MA, Uddin MM, Landis DA, Howlader MTH. Salinity Influences Plant-Pest-Predator Tritrophic Interactions. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:1470-1479. [PMID: 34231849 DOI: 10.1093/jee/toab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Indexed: 06/13/2023]
Abstract
Climate change-induced salinity intrusion into agricultural soils is known to negatively impact crop production and food security. However, the effects of salinity increase on plant-herbivore-natural enemy systems and repercussions for pest suppression services are largely unknown. Here, we examine the effects of increased salinity on communities of rice (Oryza sativa), brown planthopper (BPH), Nilaparvata lugens, and green mirid bug (GMB), Cyrtorhinus lividipennis, under greenhouse conditions. We found that elevated salinity significantly suppressed the growth of two rice cultivars. Meanwhile, BPH population size also generally decreased due to poor host plant quality induced by elevated salinity. The highest BPH density occurred at 2.0 dS/m salinity and declined thereafter with increasing salinity, irrespective of rice cultivar. The highest population density of GMB also occurred under control conditions and decreased significantly with increasing salinity. Higher salinity directly affected the rice crop by reducing plant quality measured with reference to biomass production and plant height, whereas inducing population developmental asynchrony between BPH and GMB observed at 2 dS/m salinity and potentially uncoupling prey-predator dynamics. Our results suggest that increased salinity has harmful effects on plants, herbivores, natural enemies, as well as plant-pest-predator interactions. The effects measured here suggest that the bottom-up effects of predatory insects on rice pests will likely decline in rice produced in coastal areas where salinity intrusion is common. Our findings indicate that elevated salinity influences tritrophic interactions in rice production landscapes, and further research should address resilient rice insect pest management combining multipests and predators in a changing environment.
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Affiliation(s)
- M P Ali
- Entomology Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh
| | - M S Rahman
- Entomology Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh
| | - Farzana Nowrin
- Entomology Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh
| | - S S Haque
- Entomology Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh
| | - Xinghu Qin
- School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - M A Haque
- Department of Entomology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - M M Uddin
- Department of Entomology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Douglas A Landis
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - M T H Howlader
- Department of Entomology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
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17
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Solis CA, Yong MT, Venkataraman G, Milham P, Zhou M, Shabala L, Holford P, Shabala S, Chen ZH. Sodium sequestration confers salinity tolerance in an ancestral wild rice. PHYSIOLOGIA PLANTARUM 2021; 172:1594-1608. [PMID: 33619741 DOI: 10.1111/ppl.13352] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 05/27/2023]
Abstract
Wild rice Oryza rufipogon, a progenitor of cultivated rice Oryza sativa L., possesses superior salinity tolerance and is a potential donor for breeding salinity tolerance traits in rice. However, a mechanistic basis of salinity tolerance in this donor species has not been established. Here, we examined salinity tolerance from the early vegetative stage to maturity in O. rufipogon in comparison with a salt-susceptible (Koshihikari) and a salt-tolerant (Reiziq) variety of O. sativa. We assessed their phylogeny and agronomical traits, photosynthetic performance, ion contents, as well as gene expression in response to salinity stress. Salt-tolerant O. rufipogon exhibited efficient leaf photosynthesis and less damage to leaf tissues during the course of salinity treatment. In addition, O. rufipogon showed a significantly higher tissue Na+ accumulation that is achieved by vacuolar sequestration compared to the salt tolerant O. sativa indica subspecies. These findings are further supported by the upregulation of genes involved with ion transport and sequestration (e.g. high affinity K+ transporter 1;4 [HKT1;4], Na+ /H+ exchanger 1 [NHX1] and vacuolar H+ -ATPase c [VHA-c]) in salt-tolerant O. rufipogon as well as by the close phylogenetic relationship of key salt-responsive genes in O. rufipogon to these in salt-tolerant wild rice species such as O. coarctata. Thus, the high accumulation of Na+ in the leaves of O. rufipogon acts as a cheap osmoticum to minimize the high energy cost of osmolyte biosynthesis and excessive reactive oxygen species production. These mechanisms demonstrated that O. rufipogon has important traits that can be used for improving salinity tolerance in cultivated rice.
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Affiliation(s)
- Celymar Angela Solis
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Miing-Tiem Yong
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai, India
| | - Paul Milham
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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18
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Islam MA, Lobry de Bruyn L, Warwick NWM, Koech R. Salinity-affected threshold yield loss: A signal of adaptation tipping points for salinity management of dry season rice cultivation in the coastal areas of Bangladesh. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 288:112413. [PMID: 33845271 DOI: 10.1016/j.jenvman.2021.112413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/11/2021] [Accepted: 03/03/2021] [Indexed: 05/24/2023]
Abstract
The potential existence of threshold yield loss in dry season rice growing systems under coastal saline environment remains unexplored, a scenario that could have policy relevance in government planning of rice intensification in the coastal areas of Bangladesh. This study applied the adaptation tipping points (ATPs) approach to investigate threshold yield loss from multiple perspectives of farmers affected by salinity. Data were generated from 280 randomly-selected farmers (rice farmers, n = 109; shrimp farmers, n = 107; salt farmers, n = 64) from two coastal sub-districts using a semi-structured survey. Key informant interviews and focus group discussions were conducted to complement the survey results. Our study revealed that despite government actions to promote dry season rice cultivation, farmers have been growing less rice in this season, with salinity-affected yield loss being the prime reason. Most of the rice farmers have considered that they would discontinue rice cultivation in this season due to yield loss, while shrimp and salt farmers have already reduced rice cultivation for the same reason and shifted to shrimp and salt farming as they perceived these enterprises as highly profitable and require less labour than rice farming. Rice farmers would tolerate a greater rice yield loss (23%) under saline conditions compared with the shrimp (16%) and salt farmers (14%). The yield loss thresholds indicate the need for government actions to support and encourage integrated land management for rice, shrimp and salt farming, rather than research and extension efforts for dry season rice expansion alone. These actions could strengthen sustainable livelihood options to ensure food security, and contribute to the achievement of sustainable development goals, for instance no poverty (SDG-1), zero hunger (SDG-2), and good health and well-being (SDG-3).
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Affiliation(s)
- Md Aminul Islam
- School of Environmental and Rural Science, University of New England, Australia; Department of Agricultural Extension, Ministry of Agriculture, Bangladesh.
| | - Lisa Lobry de Bruyn
- School of Environmental and Rural Science, University of New England, Australia
| | - Nigel W M Warwick
- School of Environmental and Rural Science, University of New England, Australia
| | - Richard Koech
- School of Health, Medical and Applied Sciences, Central Queensland University, Australia
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Basu S, Kumar A, Benazir I, Kumar G. Reassessing the role of ion homeostasis for improving salinity tolerance in crop plants. PHYSIOLOGIA PLANTARUM 2021; 171:502-519. [PMID: 32320060 DOI: 10.1111/ppl.13112] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/03/2020] [Accepted: 04/16/2020] [Indexed: 05/23/2023]
Abstract
Soil salinity is a constraint for major agricultural crops leading to severe yield loss, which may increase with the changing climatic conditions. Disruption in the cellular ionic homeostasis is one of the primary responses induced by elevated sodium ions (Na+ ). Therefore, unraveling the mechanism of Na+ uptake and transport in plants along with the characterization of the candidate genes facilitating ion homeostasis is obligatory for enhancing salinity tolerance in crops. This review summarizes the current advances in understanding the ion homeostasis mechanism in crop plants, emphasizing the role of transporters involved in the regulation of cytosolic Na+ level along with the conservation of K+ /Na+ ratio. Furthermore, expression profiles of the candidate genes for ion homeostasis were also explored under various developmental stages and tissues of Oryza sativa based on the publicly available microarray data. The review also gives an up-to-date summary on the efforts to increase salinity tolerance in crops by manipulating selected stress-associated genes. Overall, this review gives a combined view on both the ionomic and molecular background of salt stress tolerance in plants.
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Affiliation(s)
- Sahana Basu
- Department of Biotechnology, Assam University, Silchar, 788011, India
| | - Alok Kumar
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
| | - Ibtesham Benazir
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
| | - Gautam Kumar
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
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20
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Parvin S, Van Geel M, Yeasmin T, Verbruggen E, Honnay O. Effects of single and multiple species inocula of arbuscular mycorrhizal fungi on the salinity tolerance of a Bangladeshi rice (Oryza sativa L.) cultivar. MYCORRHIZA 2020; 30:431-444. [PMID: 32367433 DOI: 10.1007/s00572-020-00957-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/15/2020] [Indexed: 05/02/2023]
Abstract
Soil salinization due to sea level rise and groundwater irrigation has become an important agronomic problem in many parts of the world. Symbiosis between crop species and arbuscular mycorrhizal fungi (AMF) may alleviate salt stress-induced detrimental effects on crop growth and yield, for example, through helping the host plant to selectively absorb potassium while avoiding uptake of excessive sodium. Here, we performed a greenhouse experiment to evaluate growth, grain yield, and salt tolerance of a Bangladeshi rice cultivar under three levels of salt stress (0, 75, and 120 mM) after inoculation with three different AMF species from three different genera (Funnelliformis mosseae (BEG12), Acaulospora laevis (BEG13), and Gigaspora margarita (BEG34)), singly and in combination. We found that under salt stress, AMF inoculation enhanced total chlorophyll concentration, shoot K+/Na+ ratio, and lowered shoot Na+/root Na+ ratio, accompanied by increased root biomass, spikelet fertility, and grain yield compared with the non-inoculated control plants. Specifically, we found that the combination of BEG13 and BEG34 increased rice yield by 125 and 143% as compared with the non-inoculated controls, at the 75 and 120mM salt levels, respectively. In general, the low AMF diversity treatments (one species or a combination of two AMF species) were found to be the most effective in mediating salt stress tolerance for the majority of the measured crop performance variables. Overall, our results indicate that specific AMF species can promote the salt tolerance and productivity of rice, likely by increasing photosynthetic efficiency and restricting Na+ uptake and transport from root to shoot in AMF-inoculated plants.
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Affiliation(s)
- Shanaz Parvin
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, 2435, 3001, Heverlee, Belgium.
| | - Maarten Van Geel
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, 2435, 3001, Heverlee, Belgium
| | - Tanzima Yeasmin
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Erik Verbruggen
- Department of Biology, Plants and Ecosystems, University of Antwerp, Wilrijk, 2610, Antwerp, Belgium
| | - Olivier Honnay
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, 2435, 3001, Heverlee, Belgium
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21
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Shahid M, Shah AA, Basit F, Noman M, Zubair M, Ahmed T, Naqqash T, Manzoor I, Maqsood A. Achromobacter sp. FB-14 harboring ACC deaminase activity augmented rice growth by upregulating the expression of stress-responsive CIPK genes under salinity stress. Braz J Microbiol 2020; 51:719-728. [PMID: 31820296 PMCID: PMC7203246 DOI: 10.1007/s42770-019-00199-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/22/2019] [Indexed: 11/26/2022] Open
Abstract
Soil salinity is one of the major plant growth and yield-limiting constraints in arid and semi-arid regions of the world. In addition to the oxidative damage, increasing salt stress is associated with elevated cellular ethylene levels due to the synthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) in large amounts. The objective of the current study was to elucidate the inoculation effect of an ACC deaminase (ACCD)-producing phytobeneficial strain Achromobacter sp. FB-14 on rice plants to alleviate the salinity effects by upregulation of the stress-responsive CIPK genes. The strain FB-14 was isolated by using nutrient agar medium at 855 mM NaCl concentration and it was taxonomically identified as Achromobacter sp. with more than 99% 16S rRNA gene sequence similarity with many Achromobacter species. The strain FB-14 demonstrated substantial in vitro potential for ACCD activity, synthesis of indole compounds, and phosphate solubilization up to 100 mM NaCl concentration in the culture medium. The gene corresponding to ACCD activity (acdS) was amplified and sequenced in order to confirm the inherent enzyme activity of the strain at a molecular level. The rifampicin-resistant derivative of strain FB-14 was recovered from the rice rhizosphere on antibiotic medium up to 21 days of sowing. Moreover, the strain FB-14 was inoculated on rice plants under salinity and it not only enhanced the growth of rice plants in terms of root and shoot length, and fresh and dry weight, but also upregulated the expression of stress-responsive CIPK genes (OsCIPK03, OsCIPK12, and OsCIPK15) according to the results of qRT-PCR analysis. To the best of our knowledge, this is the first report deciphering the role of plant-beneficial Achromobacter strain relieving the rice plants from salt stress by promoting the growth and enhancing the expression of stress-responsive CIPK genes.
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Affiliation(s)
- Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Asad Ali Shah
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan.
| | - Farwa Basit
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Muhammad Noman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Muhammad Zubair
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Temoor Ahmed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Awais Maqsood
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
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Adak S, Datta S, Bhattacharya S, Ghose TK, Lahiri Majumder A. Diversity analysis of selected rice landraces from West Bengal and their linked molecular markers for salinity tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:669-682. [PMID: 32255931 PMCID: PMC7113337 DOI: 10.1007/s12298-020-00772-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/15/2020] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
Study of genetic diversity in crop plants is essential for the selection of appropriate germplasm for crop improvement. As salinity posses a serious environmental challenge to rice production globally and especially in India, it is imperative that the study of large collections of germplasms be undertaken to search for salt tolerant stocks. In the present study, 64 indica germplasms were collected from different agro-climatic zones of West Bengal, India, from the Himalayan foothills in the northern part down to the southern saline belt of the state keeping in view the soil characteristics and other edaphic factors prevailing in the region. Salt tolerance parameters were used to screen the large set of germplasms in terms of root-shoot length, fresh-dry weight, chlorophyll content, Na+/K+ ratio and germination potential in presence of salt. Standard evaluation score or SES was calculated to find out tolerant to sensitive cultivar. Twenty-one SSR markers, some associated with the Saltol QTL and others being candidate gene based SSR (cgSSR) were used to study the polymorphism of collected germplasm. A wide diversity was detected among the collected germplasms at the phenotypic as well as molecular level. Of the 21 SSR markers, 15 markers were found to be polymorphic with 88 alleles. Based on phenotypic and biochemical results, 21 genotypes were identified as salinity tolerant, whereas 40 genotypes turned out to be salt susceptible. The present study shows that apart from the established salt tolerant lines, several other landraces like Bonkanta, Morisal, Ghiosh, Patni may be the source of salt tolerant donor in future breeding programs.
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Affiliation(s)
- Sanghamitra Adak
- Division of Plant Biology, Bose Institute, Kolkata, 700 054 India
| | - Sambit Datta
- Division of Plant Biology, Bose Institute, Kolkata, 700 054 India
| | - Somnath Bhattacharya
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Nadia, West Bengal 741252 India
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Buti M, Baldoni E, Formentin E, Milc J, Frugis G, Lo Schiavo F, Genga A, Francia E. A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice. Int J Mol Sci 2019; 20:E5662. [PMID: 31726733 PMCID: PMC6888222 DOI: 10.3390/ijms20225662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 12/16/2022] Open
Abstract
Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.
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Affiliation(s)
- Matteo Buti
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
- Present address: Department of Agriculture, Food, Environment and Forestry, University of Florence, 50144 Florence, Italy
| | - Elena Baldoni
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Elide Formentin
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Justyna Milc
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
| | - Giovanna Frugis
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Fiorella Lo Schiavo
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Annamaria Genga
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
| | - Enrico Francia
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
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24
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Wang WC, Lin TC, Kieber J, Tsai YC. Response Regulators 9 and 10 Negatively Regulate Salinity Tolerance in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:2549-2563. [PMID: 31359043 DOI: 10.1093/pcp/pcz149] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/19/2019] [Indexed: 05/23/2023]
Abstract
Cytokinins are involved in the regulation of many plant growth and development processes, and function in response to abiotic stress. Cytokinin signaling is similar to the prokaryotic two-component signaling systems and includes the transcriptional upregulation of type-A response regulators (RRs), which in turn act to inhibit cytokinin signal response via negative feedback. Cytokinin signaling consists of several gene families and only a handful full of genes is studied. In this study, we demonstrated the function of two highly identical type-A RR genes from rice, OsRR9 and OsRR10, which are induced by cytokinin and only OsRR10 repressed by salinity stress in rice. Loss-of-function mutations give rise to mutant genes, osrr9/osrr10, which have higher salinity tolerance than wild type rice seedlings. The transcriptomic analysis uncovered several ion transporter genes, which were upregulated in response to salt stress in the osrr9/osrr10 mutants relative to the wild type seedlings. These include high-affinity potassium transporters, such as OsHKT1;1, OsHKT1;3 and OsHKT2;1, which play an important role in sodium and potassium homeostasis. In addition, disruption of the genes OsRR9 and OsRR10 also affects the expression of multiple genes related to photosynthesis, transcription and phytohormone signaling. Taken together, these results suggest that the genes OsRR9 and OsRR10 function as negative regulators in response to salinity in rice.
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Affiliation(s)
- Wei-Chen Wang
- Department of Agronomy, National Taiwan University, Roosevelt Road, Taipei, Taiwan
| | - Te-Che Lin
- Department of Agronomy, National Taiwan University, Roosevelt Road, Taipei, Taiwan
| | - Joseph Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Yu-Chang Tsai
- Department of Agronomy, National Taiwan University, Roosevelt Road, Taipei, Taiwan
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Liu J, Liu Z, Zhu AX, Shen F, Lei Q, Duan Z. Global sensitivity analysis of the APSIM-Oryza rice growth model under different environmental conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:953-968. [PMID: 30257234 DOI: 10.1016/j.scitotenv.2018.09.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
This study conducted the global sensitivity analysis of the APSIM-Oryza rice growth model under eight climate conditions and two CO2 levels using the extended Fourier Amplitude Sensitivity Test method. Two output variables (i.e. total aboveground dry matter WAGT and dry weight of storage organs WSO) and twenty parameters were analyzed. The ±30% and ±50% perturbations of base values were used as the ranges of parameter variation, and local fertilization and irrigation managements were considered. Results showed that the influential parameters were the same under different environmental conditions, but their orders were often different. Climate conditions had obvious influence on the sensitivity index of several parameters (e.g. RGRLMX, WGRMX and SPGF). In particular, the sensitivity index of RGRLMX was larger under cold climate than under warm climate. Differences also exist for parameter sensitivity of early and late rice in the same site. The CO2 concentration did not have much influence on the results of sensitivity analysis. The range of parameter variation affected the stability of sensitivity analysis results, but the main conclusions were consistent between the results obtained from the ±30% perturbation and those obtained the ±50% perturbation in this study. Compared with existing studies, our study performed the sensitivity analysis of APSIM-Oryza under more environmental conditions, thereby providing more comprehensive insights into the model and its parameters.
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Affiliation(s)
- Junzhi Liu
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, China; Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Zhangcong Liu
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - A-Xing Zhu
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China; Department of Geography, University of Wisconsin-Madison, Madison, USA
| | - Fang Shen
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, China; State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Qiuliang Lei
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zheng Duan
- Chair of Hydrology and River Basin Management, Technical University of Munich, Munich, Germany.
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