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Panigrahi S, Kumar U, Swami S, Singh Y, Balyan P, Singh KP, Dhankher OP, Varshney RK, Roorkiwal M, Amiri KM, Mir RR. Meta QTL analysis for dissecting abiotic stress tolerance in chickpea. BMC Genomics 2024; 25:439. [PMID: 38698307 PMCID: PMC11067088 DOI: 10.1186/s12864-024-10336-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Chickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea. RESULTS A meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc. CONCLUSION: The results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.
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Affiliation(s)
- Sourav Panigrahi
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India.
- Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India.
| | - Sonu Swami
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
- Department of Botany & Plant Physiology, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University, Meerut, 245206, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, GB Pant University of Agriculture & Technology, Pantnagar, 263145, India
- Vice-Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, USA
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Khaled Ma Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, J&K, India.
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Cao G, Huang H, Yang Y, Xie B, Tang L. Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses. PeerJ 2024; 12:e17255. [PMID: 38708347 PMCID: PMC11067907 DOI: 10.7717/peerj.17255] [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: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds.
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Affiliation(s)
- Gaohui Cao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hao Huang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuejiao Yang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Xie
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan City, Hubei Province, China
| | - Lulu Tang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Wang DR, Jamshidi S, Han R, Edwards JD, McClung AM, McCouch SR. Positive effects of public breeding on US rice yields under future climate scenarios. Proc Natl Acad Sci U S A 2024; 121:e2309969121. [PMID: 38498708 PMCID: PMC10990131 DOI: 10.1073/pnas.2309969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024] Open
Abstract
In this study, we model and predict rice yields by integrating molecular marker variation, varietal productivity, and climate, focusing on the Southern U.S. rice-growing region. This region spans the states of Arkansas, Louisiana, Texas, Mississippi, and Missouri and accounts for 85% of total U.S. rice production. By digitizing and combining four decades of county-level variety acreage data (1970 to 2015) with varietal information from genotyping-by-sequencing data, we estimate annual historical county-level allele frequencies. These allele frequencies are used together with county-level weather and yield data to develop ten machine learning models for yield prediction. A two-layer meta-learner ensemble model that combines all ten methods is externally evaluated against observations from historical Uniform Regional Rice Nursery trials (1980 to 2018) conducted in the same states. Finally, the ensemble model is used with forecasted weather from the Coupled Model Intercomparison Project across the 110 rice-growing counties to predict production in the coming decades for Composite Variety Groups assembled based on year of release, breeding program, and several breeding trends. Results indicate positive effects over time of public breeding on rice resilience to future climates, and potential reasons are discussed.
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Affiliation(s)
- Diane R. Wang
- Department of Agronomy, Purdue University, West Lafayette, IN47901
| | - Sajad Jamshidi
- Department of Agronomy, Purdue University, West Lafayette, IN47901
| | - Rongkui Han
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR72160
| | - Anna M. McClung
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR72160
| | - Susan R. McCouch
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY14853
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5
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Agathokleous E, Frei M, Knopf OM, Muller O, Xu Y, Nguyen TH, Gaiser T, Liu X, Liu B, Saitanis CJ, Shang B, Alam MS, Feng Y, Ewert F, Feng Z. Adapting crop production to climate change and air pollution at different scales. NATURE FOOD 2023; 4:854-865. [PMID: 37845546 DOI: 10.1038/s43016-023-00858-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Air pollution and climate change are tightly interconnected and jointly affect field crop production and agroecosystem health. Although our understanding of the individual and combined impacts of air pollution and climate change factors is improving, the adaptation of crop production to concurrent air pollution and climate change remains challenging to resolve. Here we evaluate recent advances in the adaptation of crop production to climate change and air pollution at the plant, field and ecosystem scales. The main approaches at the plant level include the integration of genetic variation, molecular breeding and phenotyping. Field-level techniques include optimizing cultivation practices, promoting mixed cropping and diversification, and applying technologies such as antiozonants, nanotechnology and robot-assisted farming. Plant- and field-level techniques would be further facilitated by enhancing soil resilience, incorporating precision agriculture and modifying the hydrology and microclimate of agricultural landscapes at the ecosystem level. Strategies and opportunities for crop production under climate change and air pollution are discussed.
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Affiliation(s)
- Evgenios Agathokleous
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, People's Republic of China
| | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, Giessen, Germany
| | - Oliver M Knopf
- Institute of Bio- and Geoscience 2: plant sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Onno Muller
- Institute of Bio- and Geoscience 2: plant sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Yansen Xu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, People's Republic of China
| | | | | | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Liu
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Costas J Saitanis
- Lab of Ecology and Environmental Science, Agricultural University of Athens, Athens, Greece
| | - Bo Shang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science & Technology, Nanjing, People's Republic of China
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, People's Republic of China
| | - Muhammad Shahedul Alam
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, Giessen, Germany
| | - Yanru Feng
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, Giessen, Germany
| | | | - Zhaozhong Feng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science & Technology, Nanjing, People's Republic of China.
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, People's Republic of China.
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6
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Pan YH, Chen L, Zhu XY, Li JC, Rashid MAR, Chen C, Qing DJ, Zhou WY, Yang XH, Gao LJ, Zhao Y, Deng GF. Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice. BMC PLANT BIOLOGY 2023; 23:256. [PMID: 37189032 DOI: 10.1186/s12870-023-04260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Heat stress threatens rice yield and quality at flowering stage. In this study, average relative seed setting rate under heat stress (RHSR) and genotypes of 284 varieties were used for a genome-wide association study. RESULTS We identified eight and six QTLs distributed on chromosomes 1, 3, 4, 5, 7 and 12 in the full population and indica, respectively. qHTT4.2 was detected in both the full population and indica as an overlapping QTL. RHSR was positively correlated with the accumulation of heat-tolerant superior alleles (SA), and indica accession contained at least two heat-tolerant SA with average RHSR greater than 43%, meeting the needs of stable production and heat-tolerant QTLs were offer yield basic for chalkiness degree, amylose content, gel consistency and gelatinization temperature. Chalkiness degree, amylose content, and gelatinization temperature under heat stress increased with accumulation of heat-tolerant SA. Gel consistency under heat stress decreased with polymerization of heat-tolerant SA. The study revealed qHTT4.2 as a stable heat-tolerant QTL that can be used for breeding that was detected in the full population and indica. And the grain quality of qHTT4.2-haplotype1 (Hap1) with chalk5, wx, and alk was better than that of qHTT4.2-Hap1 with CHALK5, WX, and ALK. Twelve putative candidate genes were identified for qHTT4.2 that enhance RHSR based on gene expression data and these genes were validated in two groups. Candidate genes LOC_Os04g52830 and LOC_Os04g52870 were induced by high temperature. CONCLUSIONS Our findings identify strong heat-tolerant cultivars and heat-tolerant QTLs with great potential value to improve rice tolerance to heat stress, and suggest a strategy for the breeding of yield-balance-quality heat-tolerant crop varieties.
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Affiliation(s)
- Ying-Hua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Xiao-Yang Zhu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jing-Cheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Chao Chen
- State Key Laboratory of Crop Germplasm Innovation and Molecular Breeding/Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, China
| | - Dong-Jin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Wei-Yong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Xing-Hai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Li-Jun Gao
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China.
| | - Guo-Fu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
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Singh BK, Venkadesan S, Ramkumar MK, Shanmugavadivel PS, Dutta B, Prakash C, Pal M, Solanke AU, Rai A, Singh NK, Mohapatra T, Sevanthi AM. Meta-Analysis of Microarray Data and Their Utility in Dissecting the Mapped QTLs for Heat Acclimation in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:1697. [PMID: 37111920 PMCID: PMC10142300 DOI: 10.3390/plants12081697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/19/2023]
Abstract
In the current global warming scenario, it is imperative to develop crops with improved heat tolerance or acclimation, for which knowledge of major heat stress-tolerant genes or genomic regions is a prerequisite. Though several quantitative trait loci (QTLs) for heat tolerance have been mapped in rice, candidate genes from these QTLs have not been reported yet. The meta-analysis of microarray datasets for heat stress in rice can give us a better genomic resource for the dissection of QTLs and the identification of major candidate genes for heat stress tolerance. In the present study, a database, RiceMetaSys-H, comprising 4227 heat stress-responsive genes (HRGs), was created using seven publicly available microarray datasets. This included in-house-generated microarray datasets of Nagina 22 (N22) and IR64 subjected to 8 days of heat stress. The database has provisions for searching the HRGs through genotypes, growth stages, tissues, and physical intervals in the genome, as well as Locus IDs, which provide complete information on the HRGs with their annotations and fold changes, along with the experimental material used for the analysis. The up-regulation of genes involved in hormone biosynthesis and signalling, sugar metabolism, carbon fixation, and the ROS pathway were found to be the key mechanisms of enhanced heat tolerance. Integrating variant and expression analysis, the database was used for the dissection of the major effect of QTLs on chromosomes 4, 5, and 9 from the IR64/N22 mapping population. Out of the 18, 54, and 62 genes in these three QTLs, 5, 15, and 12 genes harboured non-synonymous substitutions. Fifty-seven interacting genes of the selected QTLs were identified by a network analysis of the HRGs in the QTL regions. Variant analysis revealed that the proportion of unique amino acid substitutions (between N22/IR64) in the QTL-specific genes was much higher than the common substitutions, i.e., 2.58:0.88 (2.93-fold), compared to the network genes at a 0.88:0.67 (1.313-fold) ratio. An expression analysis of these 89 genes showed 43 DEGs between IR64/N22. By integrating the expression profiles, allelic variations, and the database, four robust candidates (LOC_Os05g43870, LOC_Os09g27830, LOC_Os09g27650, andLOC_Os09g28000) for enhanced heat stress tolerance were identified. The database thus developed in rice can be used in breeding to combat high-temperature stress.
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Affiliation(s)
- Bablee Kumari Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | | | - M. K. Ramkumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - P. S. Shanmugavadivel
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur 208024, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Chandra Prakash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India
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Liu H, Zeng B, Zhao J, Yan S, Wan J, Cao Z. Genetic Research Progress: Heat Tolerance in Rice. Int J Mol Sci 2023; 24:ijms24087140. [PMID: 37108303 PMCID: PMC10138502 DOI: 10.3390/ijms24087140] [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: 03/08/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/29/2023] Open
Abstract
Heat stress (HS) caused by high-temperature weather seriously threatens international food security. Indeed, as an important food crop in the world, the yield and quality of rice are frequently affected by HS. Therefore, clarifying the molecular mechanism of heat tolerance and cultivating heat-tolerant rice varieties is urgent. Here, we summarized the identified quantitative trait loci (Quantitative Trait Loci, QTL) and cloned rice heat tolerance genes in recent years. We described the plasma membrane (PM) response mechanisms, protein homeostasis, reactive oxygen species (ROS) accumulation, and photosynthesis under HS in rice. We also explained some regulatory mechanisms related to heat tolerance genes. Taken together, we put forward ways to improve heat tolerance in rice, thereby providing new ideas and insights for future research.
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Affiliation(s)
- Huaqing Liu
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Bohong Zeng
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Jialiang Zhao
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Song Yan
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Jianlin Wan
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Zhibin Cao
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
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Identification of QTLs for Heat Tolerance at the Flowering Stage Using Chromosome Segment Substitution Lines in Rice. Genes (Basel) 2022; 13:genes13122248. [PMID: 36553515 PMCID: PMC9777623 DOI: 10.3390/genes13122248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
High temperature is a major stress in rice production. Although considerable progress has been made in investigating heat tolerance (HT) in rice, the genetic basis of HT at the heading stage remains largely unknown. In this study, a novel set of chromosome segment substitution lines (CSSLs) consisting of 113 lines derived from a heat-resistant indica variety N22 and a heat-sensitive indica variety 9311 was developed and used for the analysis of the genetic basis of HT. The heat sensitivity index (HSI) calculated based on seed-setting rates under natural and high-temperature environments was used to evaluate the influence of HT at the rice heading stage. In total, five quantitative trait loci (QTLs) associated with HT were detected based on seed-setting rate (SSR) evaluation; these were named qSSR6-1, qSSR7-1, qSSR8-1, qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11, respectively. Heat-tolerant alleles of the QTLs were all derived from N22. Among them, qSSR9-1 overlapped with QTLs identified previously, while the remaining QTLs were found novel. In particular, qSSR7-1 explained a high phenotypic variation of 26.35% with a LOD score of 10.75, thus deserved to be further validated. These findings will increase our understanding of the genetic mechanism underlying HT and facilitate the breeding of heat-tolerant rice varieties.
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Kumar R, Bahuguna RN, Tiwari M, Pal M, Chinnusamy V, Sreeman S, Muthurajan R, Krishna Jagadish SV. Walking through crossroads-rice responses to heat and biotic stress interactions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4065-4081. [PMID: 35713657 DOI: 10.1007/s00122-022-04131-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Rice, the most important source of calories for humans is prone to severe yield loss due to changing climate including heat stress. Additionally, rice encounters biotic stresses in conjunction with heat stress, which exacerbates the adverse effects, and exponentially increase such losses. Several investigations have identified biotic and heat stress-related quantitative trait loci (QTLs) that may contribute to improved tolerance to these stresses. However, a significant knowledge gap exists in identifying the genomic regions imparting tolerance against combined biotic and heat stress. Hereby, we are presenting a conceptual meta-analysis identifying genomic regions that may be promising candidates for enhancing combined biotic and heat stress tolerance in rice. Fourteen common genomic regions were identified along chromosomes 1, 2, 3, 4, 6, 10 and 12, which harbored 1265 genes related to heat stress and defense responses in rice. Further, the meta expression analysis revealed 24 differentially expressed genes (DEGs) involved in calcium-mediated stress signaling including transcription factors Myb, bHLH, ROS signaling, molecular chaperones HSP110 and pathogenesis related proteins. Additionally, we also proposed a hypothetical model based on GO and MapMan analysis representing the pathways intersecting heat and biotic stresses. These DEGs can be potential candidate genes for improving tolerance to combined biotic and heat stress in rice. We present a framework highlighting plausible connecting links (QTLs/genes) between rice response to heat stress and different biotic factors associated with yield, that can be extended to other crops.
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Affiliation(s)
- Ritesh Kumar
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Rajeev N Bahuguna
- Center for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, India
| | - Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India.
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
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11
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Villalobos-López MA, Arroyo-Becerra A, Quintero-Jiménez A, Iturriaga G. Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:12053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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Affiliation(s)
- Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Anareli Quintero-Jiménez
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
| | - Gabriel Iturriaga
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
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12
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Hu C, Jiang J, Li Y, Song S, Zou Y, Jing C, Zhang Y, Wang D, He Q, Dang X. QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.). Front Genet 2022; 13:983525. [PMID: 36186421 PMCID: PMC9520461 DOI: 10.3389/fgene.2022.983525] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice accessions were investigated in two environments and showed abundant variations. We performed a genome-wide association study on RSF using 1.2 million single nucleotide polymorphisms (SNPs). Five QTLs were significantly associated with RSF were identified, four were found in previously reported QTLs/genes, and one was novel. The novel QTL qRSF9.2 was mapped into the 22,059,984-22,259,984 bp region, which had 38 positional candidate genes. By combining the linkage disequilibrium analysis, the QTL region was narrowed to 22,110,508–22,187,677 bp, which contained 16 candidate genes. Among them, only gene LOC_Os09g38500 contained nonsynonymous SNPs that were significantly associated with RSF. In addition, accessions with large and small RSF values had corresponding respective high and low gene expression levels. Furthermore, the RSF of the CC allele was significantly higher than that of the TT allele. Hap 2 and Hap 3 can increase heat tolerance by 7.9 and 11.3%, respectively. Our results provide useful information that recommends further cloning of qRSF9.2 and breeding heat-tolerant rice varieties by marker-assisted selection.
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Affiliation(s)
- Changmin Hu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yulong Li
- Institute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shaojie Song
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu Zou
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Chunyu Jing
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ying Zhang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dezheng Wang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- *Correspondence: Qiang He, ; Xiaojing Dang,
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- *Correspondence: Qiang He, ; Xiaojing Dang,
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13
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Cao Z, Tang H, Cai Y, Zeng B, Zhao J, Tang X, Lu M, Wang H, Zhu X, Wu X, Yuan L, Wan J. Natural variation of HTH5 from wild rice, Oryza rufipogon Griff., is involved in conferring high-temperature tolerance at the heading stage. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1591-1605. [PMID: 35514030 PMCID: PMC9342620 DOI: 10.1111/pbi.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/24/2022] [Accepted: 04/28/2022] [Indexed: 05/13/2023]
Abstract
Global warming is a major abiotic stress factor, which limit rice production. Exploiting the genetic basis of the natural variation in heat resistance at different reproductive stages among diverse exotic Oryza germplasms can help breeding heat-resistant rice cultivars. Here, we identified a stable quantitative trait locus (QTL) for heat tolerance at the heading stage on chromosome 5 (qHTH5) in O. rufipogon Griff. The corresponding gene, HTH5, pertains to the pyridoxal phosphate-binding protein PLPBP (formerly called PROSC) family, which is predicted to encode pyridoxal phosphate homeostasis protein (PLPHP) localized to the mitochondrion. Overexpression of HTH5 increased the seed-setting rate of rice plants under heat stress at the heading stage, whereas suppression of HTH5 resulted in greater susceptibility to heat stress. Further investigation indicated that HTH5 reduces reactive oxygen species accumulation at high temperatures by increasing the heat-induced pyridoxal 5'-phosphate (PLP) content. Moreover, we found that two SNPs located in the HTH5 promoter region are involved with its expression level and associated with heat tolerance diversity. These findings suggest that the novel gene HTH5 might have great potential value for heightening rice tolerance to heat stress to the on-going threat of global warming.
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Affiliation(s)
- Zhibin Cao
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Huiwu Tang
- College of Agriculture and BiologyZhongkai University of Agriculture and EngineeringGuangzhouChina
| | - Yaohui Cai
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Bohong Zeng
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Jialiang Zhao
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Xiuying Tang
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Ming Lu
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Huimin Wang
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Xuejing Zhu
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Xiaofeng Wu
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Linfeng Yuan
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
| | - Jianlin Wan
- Rice National Engineering Research Center (Nanchang)Jiangxi Research and Development Center of Super RiceJiangxi Academy of Agricultural SciencesNanchangChina
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14
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Identification of Heat-Tolerant Genes in Non-Reference Sequences in Rice by Integrating Pan-Genome, Transcriptomics, and QTLs. Genes (Basel) 2022; 13:genes13081353. [PMID: 36011264 PMCID: PMC9407402 DOI: 10.3390/genes13081353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 01/04/2023] Open
Abstract
The availability of large-scale genomic data resources makes it very convenient to mine and analyze genes that are related to important agricultural traits in rice. Pan-genomes have been constructed to provide insight into the genome diversity and functionality of different plants, which can be used in genome-assisted crop improvement. Thus, a pan-genome comprising all genetic elements is crucial for comprehensive variation study among the heat-resistant and -susceptible rice varieties. In this study, a rice pan-genome was firstly constructed by using 45 heat-tolerant and 15 heat-sensitive rice varieties. A total of 38,998 pan-genome genes were identified, including 37,859 genes in the reference and 1141 in the non-reference contigs. Genomic variation analysis demonstrated that a total of 76,435 SNPs were detected and identified as the heat-tolerance-related SNPs, which were specifically present in the highly heat-resistant rice cultivars and located in the genic regions or within 2 kbp upstream and downstream of the genes. Meanwhile, 3214 upregulated and 2212 downregulated genes with heat stress tolerance-related SNPs were detected in one or multiple RNA-seq datasets of rice under heat stress, among which 24 were located in the non-reference contigs of the rice pan-genome. We then mapped the DEGs with heat stress tolerance-related SNPs to the heat stress-resistant QTL regions. A total of 1677 DEGs, including 990 upregulated and 687 downregulated genes, were mapped to the 46 heat stress-resistant QTL regions, in which 2 upregulated genes with heat stress tolerance-related SNPs were identified in the non-reference sequences. This pan-genome resource is an important step towards the effective and efficient genetic improvement of heat stress resistance in rice to help meet the rapidly growing needs for improved rice productivity under different environmental stresses. These findings provide further insight into the functional validation of a number of non-reference genes and, especially, the two genes identified in the heat stress-resistant QTLs in rice.
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15
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Radha B, Sunitha NC, Sah RP, T P MA, Krishna GK, Umesh DK, Thomas S, Anilkumar C, Upadhyay S, Kumar A, Ch L N M, S B, Marndi BC, Siddique KHM. Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:996514. [PMID: 36714754 PMCID: PMC9874338 DOI: 10.3389/fpls.2022.996514] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/05/2022] [Indexed: 05/12/2023]
Abstract
Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.
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Affiliation(s)
- Beena Radha
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, India
| | | | - Rameswar P Sah
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Md Azharudheen T P
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - G K Krishna
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Thrissur, Kerala, India
| | - Deepika Kumar Umesh
- Mulberry Breeding & Genetics Section, Central Sericultural Research and Training Institute-Berhampore, Central Silk Board, Murshidabad, West Bengal, India
| | - Sini Thomas
- Department of Plant Physiology, Kerala Agricultural University-Regional Agricultural Research Station, Kumarakom, Kerala, India
| | - Chandrappa Anilkumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Sameer Upadhyay
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Awadhesh Kumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Manikanta Ch L N
- Department of Plant Physiology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Behera S
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Bishnu Charan Marndi
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Kadambot H M Siddique
- The University of Western Australia Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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16
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Huang S, Gali KK, Lachagari RVB, Chakravartty N, Bueckert RA, Tar’an B, Warkentin TD. Identification of heat responsive genes in pea stipules and anthers through transcriptional profiling. PLoS One 2021; 16:e0251167. [PMID: 34735457 PMCID: PMC8568175 DOI: 10.1371/journal.pone.0251167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Field pea (Pisum sativum L.), a cool-season legume crop, is known for poor heat tolerance. Our previous work identified PR11-2 and PR11-90 as heat tolerant and susceptible lines in a recombinant inbred population. CDC Amarillo, a Canadian elite pea variety, was considered as another heat tolerant variety based on its similar field performance as PR11-2. This study aimed to characterize the differential transcription. Plants of these three varieties were stressed for 3 h at 38°C prior to self-pollination, and RNAs from heat stressed anthers and stipules on the same flowering node were extracted and sequenced via the Illumina NovaSeq platform for the characterization of heat responsive genes. In silico results were further validated by qPCR assay. Differentially expressed genes (DEGs) were identified at log2 |fold change (FC)| ≥ 2 between high temperature and control temperature, the three varieties shared 588 DEGs which were up-regulated and 220 genes which were down-regulated in anthers when subjected to heat treatment. In stipules, 879 DEGs (463/416 upregulation/downregulation) were consistent among varieties. The above heat-induced genes of the two plant organs were related to several biological processes i.e., response to heat, protein folding and DNA templated transcription. Ten gene ontology (GO) terms were over-represented in the consistently down-regulated DEGs of the two organs, and these terms were mainly related to cell wall macromolecule metabolism, lipid transport, lipid localization, and lipid metabolic processes. GO enrichment analysis on distinct DEGs of individual pea varieties suggested that heat affected biological processes were dynamic, and variety distinct responses provide insight into molecular mechanisms of heat-tolerance response. Several biological processes, e.g., cellular response to DNA damage stimulus in stipule, electron transport chain in anther that were only observed in heat induced PR11-2 and CDC Amarillo, and their relevance to field pea heat tolerance is worth further validation.
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Affiliation(s)
- Shaoming Huang
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Krishna K. Gali
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | | | - Bunyamin Tar’an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thomas D. Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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17
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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18
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Kumar N, Chhokar RS, Meena RP, Kharub AS, Gill SC, Tripathi SC, Gupta OP, Mangrauthia SK, Sundaram RM, Sawant CP, Gupta A, Naorem A, Kumar M, Singh GP. Challenges and opportunities in productivity and sustainability of rice cultivation system: a critical review in Indian perspective. CEREAL RESEARCH COMMUNICATIONS 2021; 50:573-601. [PMID: 34642509 PMCID: PMC8498983 DOI: 10.1007/s42976-021-00214-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/22/2021] [Indexed: 06/12/2023]
Abstract
Abstract Rice-wheat cropping system, intensively followed in Indo-Gangetic plains (IGP), played a prominent role in fulfilling the food grains demand of the increasing population of South Asia. In northern Indian plains, some practices such as intensive rice cultivation with traditional method for long-term have been associated with severe deterioration of natural resources, declining factor productivity, multiple nutrients deficiencies, depleting groundwater, labour scarcity and higher cost of cultivation, putting the agricultural sustainability in question. Varietal development, soil and water management, and adoption of resource conservation technologies in rice cultivation are the key interventions areas to address these challenges. The cultivation of lesser water requiring crops, replacing rice in light-textured soil and rainfed condition, should be encouraged through policy interventions. Direct seeding of short duration, high-yielding and stress tolerant rice varieties with water conservation technologies can be a successful approach to improve the input use efficiency in rice cultivation under medium-heavy-textured soils. Moreover, integrated approach of suitable cultivars for conservation agriculture, mechanized transplanting on zero-tilled/unpuddled field and need-based application of water, fertilizer and chemicals might be a successful approach for sustainable rice production system in the current scenario. In this review study, various challenges in productivity and sustainability of rice cultivation system and possible alternatives and solutions to overcome such challenges are discussed in details. Graphic abstract
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Affiliation(s)
- Neeraj Kumar
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - R. S. Chhokar
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - R. P. Meena
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - A. S. Kharub
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - S. C. Gill
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - S. C. Tripathi
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - O. P. Gupta
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - S. K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - C. P. Sawant
- ICAR- Central Institute of Agricultural Engineering, Bhopal, Madhya Pradesh 462038 India
| | - Ajita Gupta
- ICAR- Central Institute of Agricultural Engineering, Bhopal, Madhya Pradesh 462038 India
| | - Anandkumar Naorem
- ICAR- Central Arid Zone Research Institute, Regional Research Station-Kukma, Bhuj, Gujarat 370105 India
| | - Manoj Kumar
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Indian Institute of Soil and Water Conservation, Regional Centre, Chandigarh, 160019 India
| | - G. P. Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
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19
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Bineau E, Diouf I, Carretero Y, Duboscq R, Bitton F, Djari A, Zouine M, Causse M. Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1213-1227. [PMID: 34160103 DOI: 10.1111/tpj.15379] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 05/15/2023]
Abstract
Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.
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Affiliation(s)
- Estelle Bineau
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
- GAUTIER Semences, route d'Avignon, Eyragues, 13630, France
| | - Isidore Diouf
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
| | - Yolande Carretero
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
| | - Renaud Duboscq
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
| | - Frédérique Bitton
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
| | - Anis Djari
- Laboratory of Genomics and Biotechnology of Fruit, University of Toulouse, INPT, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- UMR990 Génomique et Biotechnologie des Fruits, INRAE, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Mohamed Zouine
- Laboratory of Genomics and Biotechnology of Fruit, University of Toulouse, INPT, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- UMR990 Génomique et Biotechnologie des Fruits, INRAE, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Mathilde Causse
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, Domaine Saint Maurice, 67 Allée des Chênes, CS60094, Montfavet, 84143, France
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20
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Sun J, Wang J, Guo W, Yin T, Zhang S, Wang L, Xie D, Zou D. Identification of alkali-tolerant candidate genes using the NGS-assisted BSA strategy in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:44. [PMID: 37309384 PMCID: PMC10236117 DOI: 10.1007/s11032-021-01228-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/03/2021] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa L.) is a saline-alkali-sensitive crop. Saline-alkali environments can seriously affect the growth, development, and yield of rice. The mechanisms of salt tolerance and alkali tolerance in rice are different; thus, it is very important to study and explore the alkali-tolerant gene loci to improve the saline-alkali tolerance of rice varieties. In this study, the japonica rice varieties Dongnong 425 (DN425) and Changbai 10 (CB10) and a hybridized recombinant inbred line (RIL) population were used as materials to be irrigated with Na2CO3 solution under field test conditions. A resistant pool (R-pool) and a sensitive pool (S-pool) were constructed by selecting the lines with extremely high and extremely low 1000-grain weight (TGW), respectively, from the RIL population under alkali treatment. Four candidate TGW regions on chromosomes (Chr.) 2 and 3 were associated using the bulked segregant analysis (BSA) strategy assisted by next-generation sequencing (NGS) technology (NGS-assisted BSA). Using the linkage analysis, QTL-qATGW2-2 in the candidate region was mapped within a range of 116 Kb between the SSR marker RM13592 and the Indel marker Indel3 of Chr. 2, which contained 18 predictive genes. The BSA sequencing results showed that Os02g39884 contained a nonsynonymous substitution mutation SNP (nsSNP), leading to the transformation of a residue from arginine (cGg) to glutamine (cAg); thus, Os02g39884 was inferred to be the candidate gene of qATGW2-2. The results of the qRT-PCR analysis also confirmed this. This paper provides important information for the rapid and accurate identification of the alkali-tolerant gene loci in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01228-x.
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Affiliation(s)
- Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Wei Guo
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Tianjiao Yin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Shuli Zhang
- Biotechnology Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Liang Wang
- Kunming Tobacco Company of Yunnan Province, Kunming, 650051 China
| | - Dongwei Xie
- School of Life Sciences, Nantong University, Nantong, 226019 China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
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21
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Sevanthi AM, Sinha SK, V S, Rani M, Saini MR, Kumari S, Kaushik M, Prakash C, K V, Singh GP, Mohapatra T, Mandal PK. Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice. RICE (NEW YORK, N.Y.) 2021; 14:49. [PMID: 34089405 PMCID: PMC8179884 DOI: 10.1186/s12284-021-00487-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/05/2021] [Indexed: 05/19/2023]
Abstract
We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology.
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Affiliation(s)
| | - Subodh Kumar Sinha
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sureshkumar V
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manju Rani
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manish Ranjan Saini
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sapna Kumari
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Megha Kaushik
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Chandra Prakash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Venkatesh K
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Trilochan Mohapatra
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India
| | - Pranab Kumar Mandal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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22
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Rabara RC, Msanne J, Basu S, Ferrer MC, Roychoudhury A. Coping with inclement weather conditions due to high temperature and water deficit in rice: An insight from genetic and biochemical perspectives. PHYSIOLOGIA PLANTARUM 2021; 172:487-504. [PMID: 33179306 DOI: 10.1111/ppl.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Climatic fluctuations, temperature extremes, and water scarcity are becoming increasingly unpredictable with the passage of time. Such environmental atrocities have been the scourge of agriculture over the ages, bringing with them poor harvests and threat of famine. Rice production, owing to its high-water requirement for cultivation, is highly vulnerable to the threat of changing climate, particularly prolonged drought and high temperature, individually or in combination. Amidst all the abiotic stresses, heat and drought are considered as the most important concurrent stressors, largely affecting rice yield and productivity under the current scenario. Such threats heighten the need for new breeding and cultivation strategies in generating abiotic stress-resilient rice varieties with better yield potential. Responses of rice to these stresses can be categorized at the morphological, physiological and biochemical levels. This review examines the physiological and molecular mechanism, in the form of up regulation of several defense machineries of rice varieties to cope with drought stress (DS), high temperature stress (HTS), and their combination (DS-HTS). Genotypic differences among rice varieties in their tolerance ability have also been addressed. The review also appraises research studies conducted in rice regarding various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for improved tolerance to DS and HTS, singly or in combination. The review also encompasses the gene regulatory networks and transcription factors, and their cross-talks in mediating tolerance to such stresses. Understanding the epigenetic regulation, involving DNA methylation and histone modification during such hostile situations, will also play a crucial role in our comprehensive understanding of combinatorial stress responses. Taken together, this review consolidates current research and available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to DS-HTS-induced abiotic stress.
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Affiliation(s)
- Roel C Rabara
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Supratim Basu
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Marilyn C Ferrer
- Genetic Resources Division, Philippine Rice Research Institute, Science City of Muñoz, Nueva Ecija, Philippines
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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23
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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice. Sci Rep 2021; 11:6747. [PMID: 33762605 PMCID: PMC7991035 DOI: 10.1038/s41598-021-85921-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.
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24
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Chen L, Wang Q, Tang M, Zhang X, Pan Y, Yang X, Gao G, Lv R, Tao W, Jiang L, Liang T. QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice. Front Genet 2021; 11:621871. [PMID: 33552136 PMCID: PMC7862774 DOI: 10.3389/fgene.2020.621871] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/29/2020] [Indexed: 01/21/2023] Open
Abstract
High-temperature stress can cause serious abiotic damage that limits the yield and quality of rice. Heat tolerance (HT) during the flowering stage of rice is a key trait that can guarantee a high and stable yield under heat stress. HT is a complex trait that is regulated by multiple quantitative trait loci (QTLs); however, few underlying genes have been fine mapped and cloned. In this study, the F2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant cultivar, and 9311, a heat-sensitive variety, was used to map HT QTLs during the flowering stage in rice. A new major QTL, qHTT8, controlling HT was identified on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was mapped into the 3,555,000–4,520,000 bp, which had a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes, and 10 putative predicted genes were found to be associated with abiotic stress tolerance. Furthermore, qRT-PCR was performed to analyze the differential expression of these 10 genes between HHZ and 9311 under high temperature conditions. LOC_Os08g07010 and LOC_Os08g07440 were highly induced in HHZ compared with 9311 under heat stress. Orthologous genes of LOC_Os08g07010 and LOC_Os08g07440 in plants played a role in abiotic stress, suggesting that they may be the candidate genes of qHTT8. Generally, the results of this study will prove useful for future efforts to clone qHTT8 and breed heat-tolerant varieties of rice using marker-assisted selection.
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Affiliation(s)
- Lei Chen
- Key Laboratory of Crop Cultivation and Farming System, College of Agriculture, Guangxi University, Nanning, China.,Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Qiang Wang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Maoyan Tang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Xiaoli Zhang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yinghua Pan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Xinghai Yang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Guoqing Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Ronghua Lv
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Wei Tao
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Ligeng Jiang
- Key Laboratory of Crop Cultivation and Farming System, College of Agriculture, Guangxi University, Nanning, China
| | - Tianfeng Liang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
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25
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Song H, Huang Y, Gu B. QTL-Seq identifies quantitative trait loci of relative electrical conductivity associated with heat tolerance in bottle gourd (Lagenaria siceraria). PLoS One 2020; 15:e0227663. [PMID: 33170849 PMCID: PMC7654804 DOI: 10.1371/journal.pone.0227663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 10/23/2020] [Indexed: 12/20/2022] Open
Abstract
Heat is a major abiotic stress that seriously affects watermelon (Citrullus lanatus) production. However, its effects may be mitigated through grafting watermelon to heat tolerant bottle gourd (Lagenaria siceraria) rootstocks. Understanding the genetic basis of heat tolerance and development of reliable DNA markers to indirectly select for the trait are necessary in breeding for new varieties with heat tolerance. The objectives of this study were to investigate the inheritance of heat tolerance and identify molecular markers associated with heat tolerance in bottle gourd. A segregating F2 population was developed from a cross between two heat tolerant and sensitive inbred lines. The population was phenotyped for relative electrical conductivity (REC) upon high temperature treatment which was used as an indicator for heat tolerance. QTL-seq was performed to identify regions associated with heat tolerance. We found that REC-based heat tolerance in this population exhibited recessive inheritance. Seven heat-tolerant quantitative trait loci (qHT1.1, qHT2.1, qHT2.2, qHT5.1, qHT6.1, qHT7.1, and qHT8.1) were identified with qHT2.1 being a promising major-effect QTL. In the qHT2.1 region, we identified three non-synonymous SNPs that were potentially associated with heat tolerance. These SNPs were located in the genes that may play roles in pollen sterility, intracellular transport, and signal recognition. Association of the three SNPs with heat tolerance was verified in segregating F2 populations, which could be candidate markers for marker assisted selection for heat tolerance in bottle gourd. The qHT2.1 region is an important finding that may be used for fine mapping and discovery of novel genes associated with heat tolerance in bottle gourd.
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Affiliation(s)
- Hui Song
- Key Lab of Cucurbit Vegetable Breeding, Ningbo Academy of Agricultural Sciences, Ningbo, Zhejiang, China
- * E-mail:
| | - Yunping Huang
- Key Lab of Cucurbit Vegetable Breeding, Ningbo Academy of Agricultural Sciences, Ningbo, Zhejiang, China
| | - Binquan Gu
- Key Lab of Cucurbit Vegetable Breeding, Ningbo Academy of Agricultural Sciences, Ningbo, Zhejiang, China
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26
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Raza Q, Riaz A, Bashir K, Sabar M. Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars. PLANT MOLECULAR BIOLOGY 2020; 104:97-112. [PMID: 32643113 DOI: 10.1007/s11103-020-01027-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars. Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan.
| | - Awais Riaz
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, Center for Sustainable Resource Science, RIKEN, Yokohama Campus, Yokohama, Japan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku, Lahore, Punjab, Pakistan
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27
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Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom ®CicerSNP Array in Chickpea. Int J Mol Sci 2020; 21:ijms21145058. [PMID: 32709160 PMCID: PMC7404205 DOI: 10.3390/ijms21145058] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.
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28
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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29
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Calleja-Cabrera J, Boter M, Oñate-Sánchez L, Pernas M. Root Growth Adaptation to Climate Change in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:544. [PMID: 32457782 PMCID: PMC7227386 DOI: 10.3389/fpls.2020.00544] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 05/05/2023]
Abstract
Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.
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Affiliation(s)
| | | | | | - M. Pernas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Zafar SA, Hameed A, Ashraf M, Khan AS, Qamar ZU, Li X, Siddique KHM. Agronomic, physiological and molecular characterisation of rice mutants revealed the key role of reactive oxygen species and catalase in high-temperature stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:440-453. [PMID: 32209204 DOI: 10.1071/fp19246] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 12/09/2019] [Indexed: 05/20/2023]
Abstract
Climatic variations have increased the occurrence of heat stress during critical growth stages, which negatively affects grain yield in rice. Plants adapt to harsh environments, and particularly high-temperature stress, by regulating their physiological and biochemical processes, which are key tolerance mechanisms. The identification of heat-tolerant rice genotypes and reliable selection indices are crucial for rice improvement programs. Here, we evaluated the response of a rice mutant population for high-temperature stress at the seedling and reproductive stages based on agronomic, physiological and molecular indices. Estimates of variance components revealed significant differences (P < 0.001) among genotypes, treatments and their interactions for almost all traits. The principal component analysis showed significant diversity among genotypes and traits under high-temperature stress. The mutant HTT-121 was identified as the most heat-tolerant mutant with higher grain yield, panicle fertility, cell membrane thermo-stability (CMTS) and antioxidant enzyme levels under heat stress. Various seedling-based morpho-physiological traits (leaf fresh weight, relative water contents, malondialdehyde, CMTS) and biochemical traits (superoxide dismutase, catalase and hydrogen peroxide) explained variations in grain yield that could be used as selection indices for heat tolerance in rice during early growth. Notably, heat-sensitive mutants accumulated reactive oxygen species, reduced catalase activity and upregulated OsSRFP1 expression under heat stress, suggesting their key roles in regulating heat tolerance in rice. The heat-tolerant mutants identified in this study could be used in breeding programs and to develop mapping populations to unravel the underlying genetic architecture for heat-stress adaptability.
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Affiliation(s)
- Syed Adeel Zafar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan; and Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan; and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Amjad Hameed
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan; and Corresponding authors. ;
| | - Muhammad Ashraf
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan
| | - Abdus Salam Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zia-Ul- Qamar
- Nuclear Institute for Agriculture and Biology (NIAB), PO Box 128, Faisalabad, Pakistan
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; and Corresponding authors. ;
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Cao Z, Li Y, Tang H, Zeng B, Tang X, Long Q, Wu X, Cai Y, Yuan L, Wan J. Fine mapping of the qHTB1-1QTL, which confers heat tolerance at the booting stage, using an Oryza rufipogon Griff. introgression line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1161-1175. [PMID: 31989206 DOI: 10.1007/s00122-020-03539-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/07/2020] [Indexed: 05/27/2023]
Abstract
The qHTB1-1 QTL, controlling heat tolerance at the booting stage in rice, was fine mapped to a 47.1 kb region containing eight candidate genes. Two positional candidate genes showed significant changes in expression levels under heat stress. High-temperature stress at the booting stage has the potential to significantly limit rice production. An interspecific advanced backcrossed population between the Oryza sativa L. cultivar R53 and the wild Oryza rufipogon Griff accession HHT4 was used as the source material to develop a set of chromosome segment introgression lines to elucidate the genetic mechanism of the qHTB1-1 QTL in heat tolerance. A single-chromosome-segment introgression line, IL01-15, was used to develop secondary populations for the mapping of qHTB1-1 on chromosome 1 for heat tolerance at the booting stage. Using the BC5F2, BC5F3, and BC5F4 populations, we first confirmed qHTB1-1 and validated the phenotypic effect. The qHTB1-1 QTL explained 13.1%, 16.9%, and 17.8% of the phenotypic variance observed in the BC5F2, BC5F3, and BC5F4 generations, respectively. Using homozygous recombinants screened from larger BC6F2 and BC6F3 populations, qHTB1-1 was fine mapped within a 47.1 kb region between markers RM11633 and RM11642. Eight putative predicted genes were annotated in the region, and six genes were predicted to encode expressed proteins. The expression patterns of these six genes demonstrated that LOC_Os01g53160 and LOC_Os01g53220 were highly induced by heat stress in IL01-15 compared to R53. Sequence comparison of the gene-coding regions of LOC_Os01g53160 and LOC_Os01g53220 between R53 and IL01-15 revealed one synonymous and two nonsynonymous SNPs in exons, respectively. Our results provide a basis for identifying the genes underlying qHTB1-1 and indicate that markers linked to the qHTB1-1 locus can be used to improve the heat tolerance of rice at the booting stage by marker-assisted selection.
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Affiliation(s)
- Zhibin Cao
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yao Li
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
- Institute of Soil Fertilizer and Resource Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Huiwu Tang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510550, China
| | - Bohong Zeng
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xiuying Tang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Qizhang Long
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xiaofeng Wu
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yaohui Cai
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Linfeng Yuan
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
| | - Jianlin Wan
- Rice National Engineering Laboratory (Nanchang), Jiangxi Research and Development Center of Super Rice, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
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Biswal AK, Mangrauthia SK, Reddy MR, Yugandhar P. CRISPR mediated genome engineering to develop climate smart rice: Challenges and opportunities. Semin Cell Dev Biol 2019; 96:100-106. [DOI: 10.1016/j.semcdb.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
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Khan S, Anwar S, Ashraf MY, Khaliq B, Sun M, Hussain S, Gao ZQ, Noor H, Alam S. Mechanisms and Adaptation Strategies to Improve Heat Tolerance in Rice. A Review. PLANTS (BASEL, SWITZERLAND) 2019; 8:E508. [PMID: 31731732 PMCID: PMC6918131 DOI: 10.3390/plants8110508] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 02/05/2023]
Abstract
The incidence of short episodes of high temperature in the most productive rice growing region is a severe threat for sustainable rice production. Screening for heat tolerance and breeding to increase the heat tolerance of rice is major objective in the situation of recent climate change. Replacing sensitive genotypes with heat tolerant cultivars, modification in sowing time, and use of growth regulators are some of the adaptive strategies for the mitigation of yield reduction by climate change. Different strategies could be adopted to enhance the thermos-tolerance of rice by (1) the modification of agronomic practices i.e., adjusting sowing time or selecting early morning flowering cultivars; (2) induction of acclimation by using growth regulators and fertilizers; (3) selecting the genetically heat resistant cultivars by breeding; and, (4) developing genetic modification. Understanding the differences among the genotypes could be exploited for the identification of traits that are responsible for thermo-tolerance for breeding purpose. The selection of cultivars that flowers in early morning before the increase of temperature, and having larger anthers with long basal pore, higher basal dehiscence, and pollen viability could induce higher thermo-tolerance. Furthermore, the high expression of heat shock proteins could impart thermo-tolerance by protecting structural proteins and enzymes. Thus, these traits could be considered for breeding programs to develop resistant cultivars under a changing climate.
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Affiliation(s)
- Shahbaz Khan
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; (S.K.); (M.S.); (H.N.); (S.A.)
| | - Sumera Anwar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (M.Y.A.); (B.K.)
- China National Rice Research Institute, Hangzhou 311400, China;
| | - M. Yasin Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (M.Y.A.); (B.K.)
| | - Binish Khaliq
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (M.Y.A.); (B.K.)
| | - Min Sun
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; (S.K.); (M.S.); (H.N.); (S.A.)
| | - Sajid Hussain
- China National Rice Research Institute, Hangzhou 311400, China;
| | - Zhi-qiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; (S.K.); (M.S.); (H.N.); (S.A.)
| | - Hafeez Noor
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; (S.K.); (M.S.); (H.N.); (S.A.)
| | - Sher Alam
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; (S.K.); (M.S.); (H.N.); (S.A.)
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QTLian breeding for climate resilience in cereals: progress and prospects. Funct Integr Genomics 2019; 19:685-701. [PMID: 31093800 DOI: 10.1007/s10142-019-00684-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/05/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
Abstract
The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change.
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35
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Kilasi NL, Singh J, Vallejos CE, Ye C, Jagadish SVK, Kusolwa P, Rathinasabapathi B. Heat Stress Tolerance in Rice ( Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:1578. [PMID: 30443261 PMCID: PMC6221968 DOI: 10.3389/fpls.2018.01578] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/10/2018] [Indexed: 05/21/2023]
Abstract
Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to identify quantitative trait loci (QTL) for vegetative stage tolerance to heat stress in rice and the corresponding candidate genes. We used genotyping-by-sequencing to generate single nucleotide polymorphic (SNP) markers and genotype 150 F8 recombinant inbred lines (RILs) obtained by crossing heat tolerant "N22" and heat susceptible "IR64" varieties. A linkage map was constructed using 4,074 high quality SNP markers that corresponded to 1,638 recombinationally unique events in this mapping population. Six QTL for root length and two for shoot length under control conditions with 2.1-12% effect were identified. One QTL rlht5.1 was identified for "root length under heat stress," with 20.4% effect. Four QTL were identified for "root length under heat stress as percent of control" that explained the total phenotypic variation from 5.2 to 8.6%. Three QTL with 5.3-10.2% effect were identified for "shoot length under heat stress," and seven QTL with 6.6-19% effect were identified for "shoot length under heat stress expressed as percentage of control." Among the QTL identified six were overlapping between those identified using shoot traits and root traits: two were overlapping between QTL identified for "shoot length under heat stress" and "root length expressed as percentage of control" and two QTL for "shoot length as percentage of control" were overlapping a QTL each for "root length as percentage of control" and "shoot length under heat stress." Genes coding 1,037 potential transcripts were identified based on their location in 10 QTL regions for vegetative stage heat stress tolerance. Among these, 213 transcript annotations were reported to be connected to stress tolerance in previous research in the literature. These putative candidate genes included transcription factors, chaperone proteins (e.g., alpha-crystallin family heat shock protein 20 and DNAJ homolog heat shock protein), proteases, protein kinases, phospholipases, and proteins related to disease resistance and defense and several novel proteins currently annotated as expressed and hypothetical proteins.
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Affiliation(s)
- Newton Lwiyiso Kilasi
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jugpreet Singh
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | | | - Changrong Ye
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Paul Kusolwa
- Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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36
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Fujino K, Hirayama Y, Obara M, Ikegaya T. Colocalization of QTLs for hull-cracked rice and grain size in elite rice varieties in Japan. BREEDING SCIENCE 2018; 68:449-454. [PMID: 30369819 PMCID: PMC6198905 DOI: 10.1270/jsbbs.18024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/05/2018] [Indexed: 05/20/2023]
Abstract
The control of insects that consume cereal grains is important for the production and storage of grains. Hull-cracked rice, which has splits in the hull, becomes more susceptible to insects both in the paddy field and during storage. The development of varieties with a low frequency of hull-cracked rice is the most economical and effective strategy to avoid insect damage and the environmental risks from agricultural chemical entering rice grains. In this study, we identified that QTLs for the frequency of hull-cracked rice and for grain width are located on the same chromosome using recombinant inbred lines derived from a cross between the elite rice varieties in Hokkaido, Japan, which are from the same pedigree and are genetically closely related. These QTLs were detected close to different molecular markers, which were separated by 1,101,675 bp, on chromosome 5 in the reference Nipponbare genome. In addition, low coefficient values of the phenotype were found between hull-cracked rice and grain size. These results suggested that the ratio of hull-cracked rice is independent of grain size. Using these QTLs, new varieties with low hull-cracked rice could be developed regardless of grain size.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
- Corresponding author (e-mail: )
| | - Yuji Hirayama
- Rice breeding group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Pippu, Hokkaido 078-0397,
Japan
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
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Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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38
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Unraveling Field Crops Sensitivity to Heat Stress:Mechanisms, Approaches, and Future Prospects. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8070128] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The astonishing increase in temperature presents an alarming threat to crop production worldwide. As evident by huge yield decline in various crops, the escalating drastic impacts of heat stress (HS) are putting global food production as well as nutritional security at high risk. HS is a major abiotic stress that influences plant morphology, physiology, reproduction, and productivity worldwide. The physiological and molecular responses to HS are dynamic research areas, and molecular techniques are being adopted for producing heat tolerant crop plants. In this article, we reviewed recent findings, impacts, adoption, and tolerance at the cellular, organellar, and whole plant level and reported several approaches that are used to improve HS tolerance in crop plants. Omics approaches unravel various mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward HS. Our review about physiological and molecular mechanisms may enlighten ways to develop thermo-tolerant cultivars and to produce crop plants that are agriculturally important in adverse climatic conditions.
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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40
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Sevanthi AMV, Kandwal P, Kale PB, Prakash C, Ramkumar MK, Yadav N, Mahato AK, Sureshkumar V, Behera M, Deshmukh RK, Jeyaparakash P, Kar MK, Manonmani S, Muthurajan R, Gopala KS, Neelamraju S, Sheshshayee MS, Swain P, Singh AK, Singh NK, Mohapatra T, Sharma RP. Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type. FRONTIERS IN PLANT SCIENCE 2018; 9:1179. [PMID: 0 PMCID: PMC6132179 DOI: 10.3389/fpls.2018.01179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/24/2018] [Indexed: 05/07/2023]
Abstract
The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).
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Affiliation(s)
- Amitha M. V. Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- *Correspondence: Amitha M. V. Sevanthi,
| | - Prashant Kandwal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Prashant B. Kale
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - M. K. Ramkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Neera Yadav
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ajay K. Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - V. Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | | | - Meera K. Kar
- ICAR-National Rice Research Institute, Cuttack, India
| | - S. Manonmani
- Tamil Nadu Agricultural University, Coimbatore, India
| | | | - K. S. Gopala
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - P. Swain
- ICAR-National Rice Research Institute, Cuttack, India
| | - Ashok K. Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - N. K. Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - R. P. Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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