1
|
Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
Collapse
Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| |
Collapse
|
2
|
Rossiter D, Arenas-Calle L, Urfels A, Nayak H, Sherpa S, McDonald A. Characterizing soil hydrology in the Indo-Gangetic plain of Bihar, India: Methods and preliminary results. GEODERMA REGIONAL 2024; 37:None. [PMID: 38887654 PMCID: PMC11181959 DOI: 10.1016/j.geodrs.2024.e00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 06/20/2024]
Abstract
In the Eastern Gangetic Plain (EGP) soil hydrology is a major determinant of land use and also governs the ecosystem services derived from cropping systems, particularly greenhouse gas (GHG) emissions from rice fields. To characterize patterns of soil hydrology in these, daily field monitoring of water levels was conducted during the monsoon (kharif) season in a comparatively wet (2021) and dry (2022) year with flooding depth and drainage tracked with field water tubes across 47 (2021) and 183 (2022) locations. Fields were clustered into hydrologic response types (HRT) which can then be used for land surface modelling, land use recommendations, and to target agronomic interventions that contribute to sustainable development outcomes. Clusters based on two methods of summarizing a single information source were compared. The information source was a time-series of field water-level observations, and the two methods were (1) the original time-series and their first differences and (2) a set of derived hydrologic descriptors that are conceptually related to greenhouse gas (GHG) emissions. Clustering was (1) by k-means with an optimization of cluster numbers and (2) by hierarchical clustering with the same number of clusters as identified by k-means. Hydrologic behaviour shifted dramatically between growing seasons, and it was not possible to identify consistent HRT's across years. The clusters had only a weak relation with soil properties, almost no relation with farmer perception of relative landscape position, and no relation with rice establishment method. Clusters based on time-series were moderately well predicted in the dry year 2022 by optimized random forest models, with the most important predictors being the number of irrigations, seasonal precipitation, pre-monsoon groundwater levels, seasonal groundwater level change, and pH, this latter as a surrogate for landscape position and other soil properties. In the wet year 2021 clusters were (poorly) predicted by just seasonal precipitation and pre-monsoon groundwater levels. This shows the complex relation of soil hydrology with landscape position and land management, as well as synoptic climate. By contrast, clusters based on the descriptors were not well-matched with those from the time-series, and could not be well predicted by random forest models. This shows that different clustering criteria may result in different interpretations of the landscape hydrology and thus different heuristics for anticipating the hydrology of a given field under different management choices.
Collapse
Affiliation(s)
- D.G. Rossiter
- Section of Soil & Crop Sciences, School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY 14853, USA
| | - Laura Arenas-Calle
- Section of Soil & Crop Sciences, School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY 14853, USA
| | - Anton Urfels
- International Rice Research Institute, Los Baños, Philippines
| | - Harishankar Nayak
- Section of Soil & Crop Sciences, School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY 14853, USA
| | | | - Andrew McDonald
- Section of Soil & Crop Sciences, School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
3
|
Lu H, Wang M, Zhou S, Chen K, Wang L, Yi Z, Bai L, Zhang Y. Chitosan Oligosaccharides Mitigate Flooding Stress Damage in Rice by Affecting Antioxidants, Osmoregulation, and Hormones. Antioxidants (Basel) 2024; 13:521. [PMID: 38790626 PMCID: PMC11117766 DOI: 10.3390/antiox13050521] [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: 03/28/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Rice (Oryza sativa L.) is one of the most important food crops worldwide. However, during direct seeding, rice is extremely vulnerable to flooding stress, which impairs rice's emergence and seedling growth and results in a significant yield loss. According to our research, chitosan oligosaccharides have the potential to be a chemical seed-soaking agent that greatly increases rice's resistance to flooding. Chitosan oligosaccharides were able to enhance seed energy supply, osmoregulation, and antioxidant capacity, according to physiological index assessments. Using transcriptome and metabolomic analysis, we discovered that important differential metabolites and genes were involved in the signaling pathway for hormone synthesis and antioxidant capacity. Exogenous chitosan oligosaccharides specifically and significantly inhibit genes linked to auxin, jasmonic acid, and abscisic acid. This suggested that applying chitosan oligosaccharides could stabilize seedling growth and development by controlling associated hormones and reducing flooding stress by enhancing membrane stability and antioxidant capacity. Finally, we verified the effectiveness of exogenous chitosan oligosaccharides imbibed in seeds by field validation, demonstrating that they can enhance rice seedling emergence and growth under flooding stress.
Collapse
Affiliation(s)
- Haoyu Lu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China;
| | - Mei Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China;
| | - Shangfeng Zhou
- Hunan Agricultural Biotechnology Research Institute, Changsha 410125, China;
| | - Ke Chen
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
| | - Lifeng Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
| | - Zhenxie Yi
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China;
| | - Lianyang Bai
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
- Hunan Agricultural Biotechnology Research Institute, Changsha 410125, China;
| | - Yuzhu Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China; (H.L.); (M.W.); (K.C.); (L.W.)
| |
Collapse
|
4
|
Thapa R, Tabien RE, Thomson MJ, Septiningsih EM. Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis. THE PLANT GENOME 2024; 17:e20261. [PMID: 36169134 DOI: 10.1002/tpg2.20261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The success of rice (Oryza sativa L.) germination and survival under submerged conditions is mainly determined by the rapid growth of the coleoptile to reach the water surface. Previous reports have shown the presence of genetic variability within rice accessions in the levels of flooding tolerance during germination or anaerobic germination (AG). Although many studies have focused on the physiological mechanisms of oxygen stress, few studies have explored the breadth of natural variation in AG tolerance-related traits in rice. In this study, we evaluated the coleoptile lengths of a geographically diverse rice panel of 241 accessions, including global accessions along with elite breeding lines and released cultivars from the United States, under the normal and flooded conditions in laboratory and greenhouse environments. A genome-wide association study (GWAS) was performed using a 7K single-nucleotide polymorphism (SNP) array and the phenotypic data of normal coleoptile length, flooded coleoptile length, flooding tolerance index, and survival at 14 d after seeding (DAS). Out of the 30 significant GWAS quantitative trait loci (QTL) regions identified, 14 colocalized with previously identified candidate genes of AG tolerance, whereas 16 were potentially novel. Two rice accessions showing contrasting phenotypic responses to AG stress were selected for the transcriptomics study. The combined approach of GWAS and transcriptomics analysis identified 77 potential candidate genes related to AG tolerance. The findings of our study may assist rice improvement programs in developing rice cultivars with robust tolerance under flooding stress during germination and the early seedling stage.
Collapse
Affiliation(s)
- Ranjita Thapa
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Michael J Thomson
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
| | | |
Collapse
|
5
|
Lin C, Zhang Z, Shen X, Liu D, Pedersen O. Flooding-adaptive root and shoot traits in rice. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23226. [PMID: 38167593 DOI: 10.1071/fp23226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Wetland plants, including rice (Oryza spp.), have developed multiple functional adaptive traits to survive soil flooding, partial submergence or even complete submergence. In waterlogged soils and under water, diffusion of O2 and CO2 is extremely slow with severe impacts on photosynthesis and respiration. As a response to shallow floods or rising floodwater, several rice varieties, including deepwater rice, elongate their stems to keep their leaves above the water surface so that photosynthesis can occur unhindered during partial submergence. In stark contrast, some other varieties hardly elongate even if they become completely submerged. Instead, their metabolism is reduced to an absolute minimum so that carbohydrates are conserved enabling fast regrowth once the floodwater recedes. This review focuses on the fascinating functional adaptive traits conferring tolerance to soil flooding, partial or complete submergence. We provide a general analysis of these traits focusing on molecular, anatomical and morphological, physiological and ecological levels. Some of these key traits have already been introgressed into modern high-yielding genotypes improving flood tolerance of several cultivars used by millions of farmers in Asia. However, with the ongoing changes in climate, we propose that even more emphasis should be placed on improving flood tolerance of rice by breeding for rice that can tolerate longer periods of complete submergence or stagnant flooding. Such tolerance could be achieved via additional tissues; i.e. aquatic adventitious roots relevant during partial submergence, and leaves with higher underwater photosynthesis caused by a longer gas film retention time.
Collapse
Affiliation(s)
- Chen Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; and Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, Kiel 24118, Germany
| | - Zhao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xuwen Shen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Dan Liu
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, Kiel 24118, Germany; and Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen 2100, Denmark
| | - Ole Pedersen
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen 2100, Denmark; and School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| |
Collapse
|
6
|
Mwakyusa L, Heredia MC, Kilasi NL, Madege RR, Herzog M, Dixit S. Screening of potential donors for anaerobic stress tolerance during germination in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1261101. [PMID: 38023850 PMCID: PMC10667690 DOI: 10.3389/fpls.2023.1261101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
The rising cost of transplanting rice has made direct seeding an affordable alternative for rice establishment, particularly in Africa. However, direct seeding, while cost-effective, faces crop establishment challenges due to flooding. Uncontrolled water, driven by erratic rains in low-lying areas or uneven fields, limit germination. Rice possesses the unique ability of anaerobic germination, enabling it to sprout and emerge in oxygen-deprived conditions. Understanding rice's response to anaerobic stress during germination is crucial for resilience breeding. Africa, although relying on direct seeding, has made limited progress in addressing flooding during germination compared to Asia. Anaerobic stress tolerance ensures successful crop emergence even in oxygen-limited environments and can help suppress weeds, a significant challenge in direct-seeded rice cultivation. This study aims to contribute by screening for potential rice donors exhibiting anaerobic stress tolerance. We screened 200 rice genotypes at Sokoine University of Agriculture (SUA) in Morogoro, Tanzania, primarily focusing on landraces with untapped potential. Using an alpha lattice design, we conducted two anaerobic experiments in September and October 2022, adding 7 cm of standing water immediately after dry seeding for flooded and maintaining a 2 cm water level after germination in the control for duration of 21 days. We identified potential donors based on selection index computed from genomic estimated breeding values (GEBVs) using eight variables: germination at 14 DAS, germination at 21 DAS, seedling height at 14 DAS, seedling height at 21 DAS, shoot dry matter at 21 DAS, root dry matter at 21 DAS, culm diameter at 21 DAS, and root length at 21DAS. Ten genotypes emerged as the most promising, exhibiting at least 70% germination in floodwater at 21 DAS and greater selection indices. These genotypes were like: Afaa Mwanza 1/159, Rojomena 271/10, Kubwa Jinga, Wahiwahi, Magongo ya Wayungu, Mpaka wa Bibi, Mwangaza, Tarabinzona, IB126-Bug 2013A, and Kanamalia with respective percentages of 75, 74, 71, 86, 75, 80, 71, 80, 70, and 73. These findings contribute to global efforts to mitigate the impacts of flooding during germination. These donors, will be potential to enrich the gene pool for anaerobic germination, providing valuable resources for breeding for flooding tolerance.
Collapse
Affiliation(s)
- Lupakisyo Mwakyusa
- Department of Crop Science and Horticulture, College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Research and Innovation, Tanzania Agricultural Research Institute, Kigoma, Tanzania
| | - Maria Cristina Heredia
- Rice Breeding Innovations Department, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Newton Lwiyiso Kilasi
- Department of Crop Science and Horticulture, College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Richard R. Madege
- Department of Crop Science and Horticulture, College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Max Herzog
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shalabh Dixit
- Rice Breeding Innovations Department, International Rice Research Institute, Los Baños, Laguna, Philippines
| |
Collapse
|
7
|
Yan W, Wang Z, Pei Y, Zhou B. How does ocean acidification affect Zostera marina during a marine heatwave? MARINE POLLUTION BULLETIN 2023; 194:115394. [PMID: 37598524 DOI: 10.1016/j.marpolbul.2023.115394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Extreme ocean events caused by global warming, such as marine heatwaves (MHWs) and ocean acidification (OA), are projected to intensify. A combination of extreme events may have severe consequences for marine ecosystems. Zostera marina was selected to understand how seagrass adapts to OA in extremely hot conditions. By combining morphology, transcriptomics, and metabolomics under mesoscale experimental conditions, we systematically investigated the response characteristics of Z. marina. Extremely high temperatures had a pronounced effect on growth, and the combined effect of OA mitigated the inhibitory effect of MHW. Both transcriptomic and metabolomic results showed that Z. marina resisted OA and MHW by upregulating the TCA cycle, glycolysis, amino acid metabolism, and relevant genes, as well as by activating the antioxidant system. The results of this study serve to improve our understanding of dual effects of factors of climate change on seagrass and may be used to direct future management and conservation efforts.
Collapse
Affiliation(s)
- Wenjie Yan
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China.
| | - Zhaohua Wang
- First Institute of Oceanography, MNR, Qingdao 266061, China
| | - Yanzhao Pei
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bin Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
8
|
Aung KM, Oo WH, Maung TZ, Min MH, Somsri A, Nam J, Kim KW, Nawade B, Lee CY, Chu SH, Park YJ. Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1225445. [PMID: 37560030 PMCID: PMC10407808 DOI: 10.3389/fpls.2023.1225445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.
Collapse
Affiliation(s)
- Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Win Htet Oo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Bhagwat Nawade
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| |
Collapse
|
9
|
Naithani S, Mohanty B, Elser J, D’Eustachio P, Jaiswal P. Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice ( Oryza sativa). PLANTS (BASEL, SWITZERLAND) 2023; 12:2146. [PMID: 37299125 PMCID: PMC10255735 DOI: 10.3390/plants12112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.
Collapse
Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Bijayalaxmi Mohanty
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore;
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| |
Collapse
|
10
|
Yin CC, Huang YH, Zhang X, Zhou Y, Chen SY, Zhang JS. Ethylene-mediated regulation of coleoptile elongation in rice seedlings. PLANT, CELL & ENVIRONMENT 2023; 46:1060-1074. [PMID: 36397123 DOI: 10.1111/pce.14492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Rice is an important food crop in the world and the study of its growth and plasticity has a profound influence on sustainable development. Ethylene modulates multiple agronomic traits of rice as well as abiotic and biotic stresses during its lifecycle. It has diverse roles, depending on the organs, developmental stages and environmental conditions. Compared to Arabidopsis (Arabidopsis thaliana), rice ethylene signalling pathway has its own unique features due to its special semiaquatic living environment and distinct plant structure. Ethylene signalling and responses are part of an intricate network in crosstalk with internal and external factors. This review will summarize the current progress in the mechanisms of ethylene-regulated coleoptile growth in rice, with a special focus on ethylene signaling and interaction with other hormones. Insights into these molecular mechanisms may shed light on ethylene biology and should be beneficial for the genetic improvement of rice and other crops.
Collapse
Affiliation(s)
- Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Yi-Hua Huang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Xun Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Zhou
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
11
|
Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches. Mol Biol Rep 2023; 50:2795-2812. [PMID: 36592290 DOI: 10.1007/s11033-022-07853-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 01/03/2023]
Abstract
Natural and man-made ecosystems worldwide are subjected to flooding, which is a form of environmental stress. Genetic variability in the plant response to flooding involves variations in metabolism, architecture, and elongation development that are related with a low oxygen escape strategy and an opposing quiescence scheme that enables prolonged submergence endurance. Flooding is typically associated with a decrease in O2 in the cells, which is especially severe when photosynthesis is absent or limited, leading to significant annual yield losses globally. Over the past two decades, considerable advancements have been made in understanding of mechanisms of rice adaptation and tolerance to flooding/submergence. The mapping and identification of Sub1 QTL have led to the development of marker-assisted selection (MAS) breeding approach to improve flooding-tolerant rice varieties in submergence-prone ecosystems. The Sub1 incorporated in rice varieties showed tolerance during flash flood, but not during stagnant conditions. Hence, gene pyramiding techniques can be applied to combine/stack multiple resistant genes for developing flood-resilient rice varieties for different types of flooding stresses. This review contains an update on the latest advances in understanding the molecular mechanisms, metabolic adaptions, and genetic factors governing rice flooding tolerance. A better understanding of molecular genetics and adaptation mechanisms that enhance flood-tolerant varieties under different flooding regimes was also discussed.
Collapse
|
12
|
Liang W, Du H, Pang B, Cheng J, He B, Hu F, Lv Y, Zhang Y. High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1076600. [PMID: 36618635 PMCID: PMC9822775 DOI: 10.3389/fpls.2022.1076600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.
Collapse
Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
13
|
Sun J, Zhang G, Cui Z, Kong X, Yu X, Gui R, Han Y, Li Z, Lang H, Hua Y, Zhang X, Xu Q, Tang L, Xu Z, Ma D, Chen W. Regain flood adaptation in rice through a 14-3-3 protein OsGF14h. Nat Commun 2022; 13:5664. [PMID: 36175427 PMCID: PMC9522936 DOI: 10.1038/s41467-022-33320-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Contemporary climatic stress seriously affects rice production. Unfortunately, long-term domestication and improvement modified the phytohormones network to achieve the production needs of cultivated rice, thus leading to a decrease in adaptation. Here, we identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance. OsGF14h acts as a signal switch to balance ABA signaling and GA biosynthesis by interacting with the transcription factors OsHOX3 and OsVP1, thereby boosting the seeding rate from 13.5% to 60.5% for anaerobic sensitive variety under flooded direct-seeded conditions. Meanwhile, OsGF14h co-inheritance with the Rc (red pericarp gene) promotes divergence between temperate japonica cultivated rice and temperate japonica weedy rice through artificial and natural selection. Our study retrieves a superior allele that has been lost during modern japonica rice improvement and provides a fine-tuning tool to improve flood adaptation for elite rice varieties.
Collapse
Affiliation(s)
- Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Guangchen Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ximan Kong
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaoyu Yu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rui Gui
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuqing Han
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhuan Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hong Lang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuchen Hua
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xuemin Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
| |
Collapse
|
14
|
Zhu Y, Li Z, Shen J, Wu K, Zhao P, Wu Z, Liu Z, Yang J, Liu H, Rensing C, Feng R. Toxicity of different forms of antimony to rice plants: Photosynthetic electron transfer, gas exchange, photosynthetic efficiency, and carbon assimilation combined with metabolome analysis. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129433. [PMID: 35897190 DOI: 10.1016/j.jhazmat.2022.129433] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/08/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Antimony (Sb) is a toxic metalloid, and excess Sb causes damage to the plant photosynthetic system. However, the underlying mechanisms of Sb toxicity in the plant photosynthetic system are not clear. Hydroponic culture experiments were conducted to illustrate the toxicity differences of antimonite [Sb(III)] and antimonate [Sb(V)] to the photosynthetic system in a rice plant (Yangdao No. 6). The results showed that Sb(III) showed a higher toxicity than Sb(V), judging from (1) lower shoot and root biomass, leaf water moisture content, water use efficiency, stomatal conductance, net photosynthetic rate, and transpiration rate; (2) higher water vapor deficit, soluble sugar content, starch content, and oligosaccharide content (sucrose, stachyose, and 1-kestose). To further analyze the direction of the photosynthetic products, we conducted a metabonomic analysis. More glycosyls were allocated to the synthesis pathways of oligosaccharides (sucrose, stachyose, and 1-kestose), anthocyanins, salicylic acid, flavones, flavonols, and lignin under Sb stress to quench excess oxygen free radicals (ROS), strengthen the cell wall structure, rebalance the cell membrane, and/or regulate cell permeability. This study provides a complete mechanism to elucidate the toxicity differences of Sb(III) and Sb(V) by exploring their effects on photosynthesis, saccharide synthesis, and the subsequent flow directions of glycosyls.
Collapse
Affiliation(s)
- YanMing Zhu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - ZengFei Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Jun Shen
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - KongYuan Wu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - PingPing Zhao
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - ZiHan Wu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - ZiQing Liu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - JiGang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Hong Liu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - RenWei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China.
| |
Collapse
|
15
|
Shiono K, Koshide A, Iwasaki K, Oguri K, Fukao T, Larsen M, Glud RN. Imaging the snorkel effect during submerged germination in rice: Oxygen supply via the coleoptile triggers seminal root emergence underwater. FRONTIERS IN PLANT SCIENCE 2022; 13:946776. [PMID: 35968087 PMCID: PMC9372499 DOI: 10.3389/fpls.2022.946776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Submergence during germination impedes aerobic metabolisms and limits the growth of most higher plants. However, some wetland plants including rice can germinate under submerged conditions. It has long been hypothesized that the first elongating shoot tissue, the coleoptile, acts as a snorkel to acquire atmospheric oxygen (O2) to initiate the first leaf elongation and seminal root emergence. Here, we obtained direct evidence for this hypothesis by visualizing the spatiotemporal O2 dynamics during submerged germination in rice using a planar O2 optode system. In parallel with the O2 imaging, we tracked the anatomical development of shoot and root tissues in real-time using an automated flatbed scanner. Three hours after the coleoptile tip reached the water surface, O2 levels around the embryo transiently increased. At this time, the activity of alcohol dehydrogenase (ADH), an enzyme critical for anaerobic metabolism, was significantly reduced, and the coleorhiza covering the seminal roots in the embryo was broken. Approximately 10 h after the transient burst in O2, seminal roots emerged. A transient O2 burst around the embryo was shown to be essential for seminal root emergence during submerged rice germination. The parallel application of a planar O2 optode system and automated scanning system can be a powerful tool for examining how environmental conditions affect germination in rice and other plants.
Collapse
Affiliation(s)
- Katsuhiro Shiono
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
| | - Akiko Koshide
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
| | - Kazunari Iwasaki
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
| | - Kazumasa Oguri
- HADAL and Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Research Institute of Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takeshi Fukao
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui, Japan
| | - Morten Larsen
- HADAL and Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Ronnie N. Glud
- HADAL and Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, Minato, Japan
- Danish Institute of Advanced Studies, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
16
|
Bispo TM, Vieira EA. Assimilatory deficit and energy regulation in young Handroanthus chrysotrichus plants under flooding stress. JOURNAL OF PLANT RESEARCH 2022; 135:323-336. [PMID: 35050423 DOI: 10.1007/s10265-022-01370-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Flooding negatively influences the growth and development of several plant species. Here, we show that the flood tolerance of young Handroanthus chrysotrichus plants involves growth deficit, carbon assimilation reductions, starch remobilization, and energy regulation. The effect of hypoxia was evaluated in a controlled experiment consisting of plants subjected to normoxia and water-logging, with later recovery. We measured morphological changes, gas exchange, photosynthetic pigments, soluble carbohydrates and starch contents, the activity of the enzymes alcohol dehydrogenase (ADH), and pyruvate decarboxylase (PDC), and ATP and ADP levels. While control plants showed normal appearance and growth, flooded plants exhibited a drastic decrease in growth, necrosis of some root tips, hypertrophic lenticels on the stems, and foliar chlorosis. Oxygen deprivation in root cells led to a significant decrease in stomatal conductance. The low Amax rates caused a decline in foliar soluble sugar content at 20 days and a subsequent increase in the leaves and roots, coinciding with starch degradation at 40 days. We also observed increases of 220.5% in ADH and 292% in PDC activities in the roots at 20 and 40 days of flooding. The activation of anaerobic metabolism in stressed plants was an essential mechanism for ATP regulation in both tissues used to maintain a minimal metabolism to cope with hypoxia to the detriment of growth. The post-stress recovery process in H. chrysotrichus occurred slowly, with gas exchange gradually resumed and anaerobic metabolism and sugar content maintained to improve energy regulation.
Collapse
Affiliation(s)
- Tailysa Morais Bispo
- Laboratory of Biology, State University of Mato Grosso do Sul-UEMS, Coxim, Brazil
| | - Evandro Alves Vieira
- Department of Plant Biology, Institute of Biology, State University of Campinas-UNICAMP, Campinas, Brazil.
| |
Collapse
|
17
|
Gómez-Álvarez EM, Pucciariello C. Cereal Germination under Low Oxygen: Molecular Processes. PLANTS (BASEL, SWITZERLAND) 2022; 11:460. [PMID: 35161441 PMCID: PMC8838265 DOI: 10.3390/plants11030460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Cereal crops can differ greatly in tolerance to oxygen shortage under germination and seedling establishment. Rice is able to germinate and elongate the coleoptile under submergence and anoxia. This capacity has been attributed to the successful use of starchy reserves through a molecular pathway activated by sugar starvation and low oxygen. This pathway culminates with the expression of α-amylases to provide sugars that fuel the sink organs. On the contrary, barley and wheat are unable to germinate under anoxia. The sensitivity of barley and wheat is likely due to the incapacity to use starch during germination. This review highlights what is currently known about the molecular mechanisms associated with cereal germination and seedling establishment under oxygen shortage with a special focus on barley and rice. Insights into the molecular mechanisms that support rice germination under low oxygen and into those that are associated with barley sensitivity may be of help for genetic improvement programs.
Collapse
|
18
|
Fernandes T, Melo F, Vieira MB, Lourenço TF, Pucciariello C, Saibo NJM, Abreu IA, Oliveira MM. Screening for Abiotic Stress Response in Rice. Methods Mol Biol 2022; 2494:161-194. [PMID: 35467207 DOI: 10.1007/978-1-0716-2297-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa L.) is the staple food for over half of the world population. However, most rice varieties are severely injured by abiotic stresses, with strong social and economic impacts. Understanding rice responses to stress may guide breeding for more tolerant varieties. However, the lack of consistency in the design of the stress experiments described in the literature limits comparative studies and output assessments. The use of identical setups is the only way to generate comparable data. This chapter comprises three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB NOVA to assess the response of rice plants to different abiotic stresses-high salinity, cold, drought, simulated drought, and submergence-and their recovery capacity when intended. All sections include a detailed description of the materials and methodology and useful notes gathered from our team experience. We use seedlings since rice plants at this stage show high sensitivity to abiotic stresses. For the salt, cold, and simulated drought (PEG, polyethylene glycol) stress assays, we grow rice seedlings in a hydroponic system, while for the drought assay, plants are grown in soil and subjected to water withholding. For submergence, we use water-filled Magenta boxes. All setups enable visual score determination and are suitable for sample collection during stress imposition and also recovery. The proposed methodologies are affordable and straightforward to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic levels.
Collapse
Affiliation(s)
- Telma Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Fredilson Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Maria Beatriz Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal.
| |
Collapse
|
19
|
Kong W, Li S, Zhang C, Qiang Y, Li Y. Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice. Food Energy Secur 2021. [DOI: 10.1002/fes3.354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
| | - Shuangmiao Li
- State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan China
| | - Yalin Qiang
- State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan China
| |
Collapse
|
20
|
Ma Y, Zhao J, Fu H, Yang T, Dong J, Yang W, Chen L, Zhou L, Wang J, Liu B, Zhang S, Edwards D. Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice. RICE (NEW YORK, N.Y.) 2021; 14:76. [PMID: 34417910 PMCID: PMC8380221 DOI: 10.1186/s12284-021-00519-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Direct seeding is an efficient rice cultivation practice. However, its application is often limited due to O2 deficiency following submergence, leading to poor seed germination, seedling establishment, and consequently yield loss. Identification of genes associated with tolerance to submergence and understanding their regulatory mechanisms is the fundamental way to address this problem. Unfortunately, the molecular mechanism of rice response to submergence stress is still not well understood. RESULTS Here, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice. We identified 29 FLZ genes in rice, and the expression analysis revealed that several genes actively responded to submergence stress. Eight OsFLZ proteins interact with SnRK1A. As a case study, we demonstrated that OsFLZ18 interacted with SnRK1A and inhibited the transcriptional activation activity of SnRK1A in modulating the expression of its target gene αAmy3, a positive regulator in rice flooding tolerance. In line with this, OsFLZ18-overexpression lines displayed retarded early seedling growth and shorter coleoptile following submergence. CONCLUSIONS These data provide the most comprehensive information of OsFLZ genes in rice, and highlight their roles in rice submergence response.
Collapse
Affiliation(s)
- Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Hua Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA Australia
| |
Collapse
|
21
|
León J, Castillo MC, Gayubas B. The hypoxia-reoxygenation stress in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5841-5856. [PMID: 33367851 PMCID: PMC8355755 DOI: 10.1093/jxb/eraa591] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/16/2020] [Indexed: 05/04/2023]
Abstract
Plants are very plastic in adapting growth and development to changing adverse environmental conditions. This feature will be essential for plants to survive climate changes characterized by extreme temperatures and rainfall. Although plants require molecular oxygen (O2) to live, they can overcome transient low-O2 conditions (hypoxia) until return to standard 21% O2 atmospheric conditions (normoxia). After heavy rainfall, submerged plants in flooded lands undergo transient hypoxia until water recedes and normoxia is recovered. The accumulated information on the physiological and molecular events occurring during the hypoxia phase contrasts with the limited knowledge on the reoxygenation process after hypoxia, which has often been overlooked in many studies in plants. Phenotypic alterations during recovery are due to potentiated oxidative stress generated by simultaneous reoxygenation and reillumination leading to cell damage. Besides processes such as N-degron proteolytic pathway-mediated O2 sensing, or mitochondria-driven metabolic alterations, other molecular events controlling gene expression have been recently proposed as key regulators of hypoxia and reoxygenation. RNA regulatory functions, chromatin remodeling, protein synthesis, and post-translational modifications must all be studied in depth in the coming years to improve our knowledge on hypoxia-reoxygenation transition in plants, a topic with relevance in agricultural biotechnology in the context of global climate change.
Collapse
Affiliation(s)
- José León
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia), Valencia, Spain
- Correspondence:
| | - Mari Cruz Castillo
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia), Valencia, Spain
| | - Beatriz Gayubas
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia), Valencia, Spain
| |
Collapse
|
22
|
Zhang G, Liu Y, Gui R, Wang Z, Li Z, Han Y, Guo X, Sun J. Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles. Genomics 2021; 113:3337-3348. [PMID: 34298069 DOI: 10.1016/j.ygeno.2021.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/04/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Hypoxic germination tolerance is an important trait for seedling establishment of direct-seeded rice. Our comparative metabolomics analysis revealed that weedy rice accumulated more sugar and amino acids than cultivated rice accumulated in the embryo and coleoptile tissues under hypoxic stress. At the transcriptional level, oxidative phosphorylation activity in weedy rice was higher than in cultivated rice that likely led to more efficient energy metabolism during hypoxic stress. Based on our comparative proteomics analysis, enriched proteins related to cell wall implied that the advantages in energy metabolism of weedy rice were ultimately reflected in the formation of tissue structures. In this study, we found that most of key hypoxic germination tolerance (HGT) genes shared the same genetic backgrounds with Oryza japonica, however, several of them genetically similar to other Oryza plant also play important roles. Our findings suggest weedy rice can serve as genetic resources for the improvement of direct-seeding rice.
Collapse
Affiliation(s)
- Guangchen Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Youhong Liu
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Molecular Design and Germplasm Innovation, Haerbin, 150086, China
| | - Rui Gui
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Ziming Wang
- College of forestry, Shenyang Agricultural University, Shenyang 110161, China
| | - Zhuan Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Yuqing Han
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
| | - Xiaojia Guo
- Jinzhou Institute of Science and Technology, Jinzhou, 121000, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China.
| |
Collapse
|
23
|
Castano-Duque L, Ghosal S, Quilloy FA, Mitchell-Olds T, Dixit S. An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. PLANT PHYSIOLOGY 2021; 186:1042-1059. [PMID: 33638990 PMCID: PMC8195528 DOI: 10.1093/plphys/kiab100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.
Collapse
Affiliation(s)
| | - Sharmistha Ghosal
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
| | - Fergie A Quilloy
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
| | | | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
| |
Collapse
|
24
|
Mason GA. Growing under water: DNA methylation may affect rice germination and establishment in anaerobic conditions. PLANT PHYSIOLOGY 2021; 186:824-826. [PMID: 33823033 PMCID: PMC8195502 DOI: 10.1093/plphys/kiab137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Grace Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| |
Collapse
|
25
|
Praharaj S, Skalicky M, Maitra S, Bhadra P, Shankar T, Brestic M, Hejnak V, Vachova P, Hossain A. Zinc Biofortification in Food Crops Could Alleviate the Zinc Malnutrition in Human Health. Molecules 2021; 26:molecules26123509. [PMID: 34207649 PMCID: PMC8230286 DOI: 10.3390/molecules26123509] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/21/2021] [Accepted: 06/04/2021] [Indexed: 12/02/2022] Open
Abstract
Micronutrient malnutrition is a global health issue and needs immediate attention. Over two billion people across the globe suffer from micronutrient malnutrition. The widespread zinc (Zn) deficiency in soils, poor zinc intake by humans in their diet, low bioavailability, and health consequences has led the research community to think of an economic as well as sustainable strategy for the alleviation of zinc deficiency. Strategies like fortification and diet supplements, though effective, are not economical and most people in low-income countries cannot afford them, and they are the most vulnerable to Zn deficiency. In this regard, the biofortification of staple food crops with Zn has been considered a useful strategy. An agronomic biofortification approach that uses crop fertilization with Zn-based fertilizers at the appropriate time to ensure grain Zn enrichment has been found to be cost-effective, easy to practice, and efficient. Genetic biofortification, though time-consuming, is also highly effective. Moreover, a Zn-rich genotype once developed can also be used for many years without any recurring cost. Hence, both agronomic and genetic biofortification can be a very useful tool in alleviating Zn deficiency.
Collapse
Affiliation(s)
- Subhashisa Praharaj
- Department of Agronomy, Centurion University of Technology and Management, Pralakhemundi 761211, India; (S.P.); (S.M.); (T.S.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.B.); (V.H.); (P.V.)
- Correspondence: (M.S.); (A.H.)
| | - Sagar Maitra
- Department of Agronomy, Centurion University of Technology and Management, Pralakhemundi 761211, India; (S.P.); (S.M.); (T.S.)
| | - Preetha Bhadra
- Department of Biotechnology, Centurion University of Technology and Management, Pralakhemundi 761211, India;
| | - Tanmoy Shankar
- Department of Agronomy, Centurion University of Technology and Management, Pralakhemundi 761211, India; (S.P.); (S.M.); (T.S.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.B.); (V.H.); (P.V.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.B.); (V.H.); (P.V.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.B.); (V.H.); (P.V.)
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh
- Correspondence: (M.S.); (A.H.)
| |
Collapse
|
26
|
Zhang Y, Zhao P, Yue S, Liu M, Qiao Y, Xu S, Gu R, Zhang X, Zhou Y. New insights into physiological effects of anoxia under darkness on the iconic seagrass Zostera marina based on a combined analysis of transcriptomics and metabolomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144717. [PMID: 33736305 DOI: 10.1016/j.scitotenv.2020.144717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Coastal hypoxia/anoxia is a major emerging threat to global coastal ecosystems. Macroalgae blooms of tens of kilometers are often observed in open waters. These blooms not only cause a lack of oxygen, but also benthic light limitation. We explored the physiological responses of Zostera marina L. to anoxia under darkness. After exposing Z. marina to anoxia under darkness for 72 h, we measured the elongation of leaves and the decrease in maximal quantum yield of photosystem II (Fv/Fm), and investigated the transcriptomic and metabolomic responses to anoxic stress based on RNA-sequencing and liquid chromatography-mass spectrometry (LC-MS) technology. The results showed that anoxic stress significantly reduced the leaf Fv/Fm, and had a significant negative effect on the photosynthesis and growth of Z. marina. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of up-regulated differentially expressed genes (DEGs) showed that glycolysis was the most significant enrichment pathway (p < 0.001), and most of the important products in glycolysis were significantly up-regulated. This indicated that the glycolysis process of anaerobic respiration is promoted under anoxia. The metabolite results also showed that glyceraldehyde 3-phosphate in the glycolysis pathway was significantly up-regulated. Moreover, three genes encoding sucrose synthase (gene-ZOSMA_310G00150, gene-ZOSMA_81G00980, and gene-ZOSMA_8G00730) and one gene encoding alpha-amylase (gene-ZOSMA_95G00270) were significantly up-regulated, providing the sugar basis for the subsequent increase in glycolysis. Furthermore, gene-encoding oxoglutarate dehydrogenase, the rate-limiting step of the tricarboxylic acid (TCA) cycle, was significantly down-regulated, indicating that this cycle was inhibited under anoxia. Metabolomic results showed that L-tryptophan, L-phenylalanine, and DL-leucine were significantly up-regulated. Only significantly decreased glutamate and non-significantly decreased glutamine, substances consumed in alanine and γ-aminobutyric acid (GABA) shunt mechanisms, were detected in the leaves, while GABA and alanine were not detected. The results of this study show that anoxic stress induces a programmed transcriptomic and metabolomic response in seagrass, most likely reflecting a complex strategy of acclimation and adaptation in seagrass to resist anoxic stress.
Collapse
Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Shidong Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingjie Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongliang Qiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Qingdao University of Science and Technology, Qingdao, 266000, China
| | - Shaochun Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruiting Gu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaomei Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
27
|
Panda D, Barik J, Sarkar RK. Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice. Curr Genomics 2021; 22:41-58. [PMID: 34045923 PMCID: PMC8142345 DOI: 10.2174/1389202922666210114104140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/16/2020] [Accepted: 12/26/2020] [Indexed: 12/16/2022] Open
Abstract
Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.
Collapse
Affiliation(s)
- Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Jijnasa Barik
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Ramani K Sarkar
- ICAR-National Rice Research Institute, Cuttack-753 006, Odisha, India
| |
Collapse
|
28
|
Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
Collapse
Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
| |
Collapse
|
29
|
Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice. PLANTS 2021; 10:plants10040705. [PMID: 33917499 PMCID: PMC8067528 DOI: 10.3390/plants10040705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/16/2022]
Abstract
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.
Collapse
|
30
|
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. Genes (Basel) 2021; 12:genes12020189. [PMID: 33525400 PMCID: PMC7912563 DOI: 10.3390/genes12020189] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/23/2021] [Indexed: 02/06/2023] Open
Abstract
Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.
Collapse
|
31
|
Su L, Yang J, Li D, Peng Z, Xia A, Yang M, Luo L, Huang C, Wang J, Wang H, Chen Z, Guo T. Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice. RICE (NEW YORK, N.Y.) 2021; 14:1. [PMID: 33409869 PMCID: PMC7788155 DOI: 10.1186/s12284-020-00444-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/06/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. RESULTS In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (-log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG. CONCLUSION The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.
Collapse
Affiliation(s)
- Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Dandan Li
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Ziai Peng
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Aoyun Xia
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Meng Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Lixin Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| |
Collapse
|
32
|
Yu SM, Lee HT, Lo SF, Ho THD. How does rice cope with too little oxygen during its early life? THE NEW PHYTOLOGIST 2021; 229:36-41. [PMID: 31880324 DOI: 10.1111/nph.16395] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/28/2019] [Indexed: 05/25/2023]
Abstract
Most crops cannot germinate underwater. Rice exhibits certain degrees of tolerance to oxygen deficiency for anaerobic germination (AG) and anaerobic seedling development (ASD). Direct rice seeding, whereby seeds are sown into soil rather than transplanting seedlings from the nursery, becomes an increasingly popular cultivation method due to labor shortages and opportunities for sustainable cultivation. Flooding is common under direct seeding, but most rice varieties have poor capability of AG/ASD, which is a major obstacle to broad adoption of direct seeding. A better understanding of the physiological basis and molecular mechanisms regulating AG/ASD should facilitate rice breeding for enhanced seedling vigor under flooding. This review highlights recent advances on molecular and physiological mechanisms and future breeding strategies of rice AG/ASD.
Collapse
Affiliation(s)
- Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Hsiang-Ting Lee
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan
| | - Shuen-Fang Lo
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
| | - Tuan-Hua David Ho
- Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan
| |
Collapse
|
33
|
The Molecular Regulatory Pathways and Metabolic Adaptation in the Seed Germination and Early Seedling Growth of Rice in Response to Low O 2 Stress. PLANTS 2020; 9:plants9101363. [PMID: 33066550 PMCID: PMC7602250 DOI: 10.3390/plants9101363] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022]
Abstract
As sessile organisms, flooding/submergence is one of the major abiotic stresses for higher plants, with deleterious effects on their growth and survival. Therefore, flooding/submergence is a large challenge for agriculture in lowland areas worldwide. Long-term flooding/submergence can cause severe hypoxia stress to crop plants and can result in substantial yield loss. Rice has evolved distinct adaptive strategies in response to low oxygen (O2) stress caused by flooding/submergence circumstances. Recently, direct seeding practice has been increasing in popularity due to its advantages of reducing cultivation cost and labor. However, establishment and growth of the seedlings from seed germination under the submergence condition are large obstacles for rice in direct seeding practice. The physiological and molecular regulatory mechanisms underlying tolerant and sensitive phenotypes in rice have been extensively investigated. Here, this review focuses on the progress of recent advances in the studies of the molecular mechanisms and metabolic adaptions underlying anaerobic germination (AG) and coleoptile elongation. Further, we highlight the prospect of introducing quantitative trait loci (QTL) for AG into rice mega varieties to ensure the compatibility of flooding/submergence tolerance traits and yield stability, thereby advancing the direct seeding practice and facilitating future breeding improvement.
Collapse
|
34
|
Kaspary TE, Roma-Burgos N, Merotto A. Snorkeling Strategy: Tolerance to Flooding in Rice and Potential Application for Weed Management. Genes (Basel) 2020; 11:genes11090975. [PMID: 32842571 PMCID: PMC7564916 DOI: 10.3390/genes11090975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 01/28/2023] Open
Abstract
Flooding is an important strategy for weed control in paddy rice fields. However, terrestrial weeds had evolved mechanisms of tolerance to flooding, resulting in new 'snorkeling' ecotypes. The aim of this review is to discuss the mechanisms of flooding tolerance in cultivated and weedy rice at different plant stages and the putative utility of this trait for weed management. Knowledge about flooding tolerance is derived primarily from crop models, mainly rice. The rice model informs us about the possible flooding tolerance mechanisms in weedy rice, Echinochloa species, and other weeds. During germination, the gene related to carbohydrate mobilization and energy intake (RAmy3D), and genes involved in metabolism maintenance under anoxia (ADH, PDC, and OsB12D1) are the most important for flooding tolerance. Flooding tolerance during emergence involved responses promoted by ethylene and induction of RAmy3D, ADH, PDC, and OsB12D1. Plant species tolerant to complete submersion also employ escape strategies or the ability to become quiescent during the submergence period. In weedy rice, the expression of PDC1, SUS3, and SUB1 genes is not directly related to flooding tolerance, contrary to what was learned in cultivated rice. Mitigation of flooding tolerance in weeds could be achieved with biotechnological approaches and genetic manipulation of flood tolerance genes through RNAi and transposons, providing a potential new tool for weed management.
Collapse
Affiliation(s)
- Tiago Edu Kaspary
- Instituto Nacional de Investigación Agropecuaria, INIA, La Estanzuela, Colonia 70006, Uruguay;
| | - Nilda Roma-Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre 90040-060, Brazil
- Correspondence:
| |
Collapse
|
35
|
Shimoyama N, Johnson M, Beaumont A, Schläppi M. Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci in Oryza sativa. RICE (NEW YORK, N.Y.) 2020; 13:57. [PMID: 32797316 PMCID: PMC7427827 DOI: 10.1186/s12284-020-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/29/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. RESULTS The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to "carbohydrate biosynthesis", "carbohydrate transmembrane transport", "small molecule protein modification", and "plasma membrane" were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to "Golgi apparatus", "stress response", "transmembrane transport", and "signal transduction". CONCLUSIONS Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.
Collapse
Affiliation(s)
- Naoki Shimoyama
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Melineeh Johnson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - André Beaumont
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Michael Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| |
Collapse
|
36
|
MacDonald JG, Rodriguez K, Quirk S. An Oxygen Delivery Polymer Enhances Seed Germination in a Martian-like Environment. ASTROBIOLOGY 2020; 20:846-863. [PMID: 32196355 PMCID: PMC7368388 DOI: 10.1089/ast.2019.2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
Critical to the success of establishing a sustainable human presence on Mars is the ability to economically grow crop plants. Several environmental factors make it difficult to fully rely on local resources for agriculture. These include nutrient sparse regolith, low and fluctuating temperatures, a high amount of ultraviolet radiation, and water trapped locally in the form of ice or metal oxides. While the 96% CO2 martian atmosphere is ideal to support photosynthesis, high CO2 concentrations inhibit germination. An added difficulty is the fact that a vast majority of crop plants require oxygen for germination. Here, we report the production of a polymer-based oxygen delivery system that supports the germination and growth of cress seeds (Lepidium sativum) in a martian regolith simulant under a martian atmosphere at 101 kPa. The oxygen-donating system is based on a low-density lightly cross-linked polyacrylate that is foamed and converted into a dry powder. It is lightweight, added in low amounts to regolith simulant, and efficiently donates enough oxygen throughout the volume of hydrated regolith simulant to fully support seed germination and plant growth. Germination rates, plant development, and plant mass are nearly identical for L. sativum grown in 100% CO2 in the presence of the oxygen-donating lightly cross-linked polyacrylate compared with plants grown in air. The polymer system also serves to protect root structures and better anchors plants in the regolith simulant.
Collapse
|
37
|
Mondal S, Khan MIR, Entila F, Dixit S, Sta Cruz PC, Panna Ali M, Pittendrigh B, Septiningsih EM, Ismail AM. Responses of AG1 and AG2 QTL introgression lines and seed pre-treatment on growth and physiological processes during anaerobic germination of rice under flooding. Sci Rep 2020; 10:10214. [PMID: 32576897 PMCID: PMC7311552 DOI: 10.1038/s41598-020-67240-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/29/2020] [Indexed: 01/24/2023] Open
Abstract
Rice seeds germinating in flooded soils encounter hypoxia or even anoxia leading to poor seed germination and crop establishment. Introgression of AG1 and AG2 QTLs associated with tolerance of flooding during germination, together with seed pre-treatment via hydro-priming or presoaking can enhance germination and seedling growth in anaerobic soils. This study assessed the performance of elite lines incorporating AG1, AG2 and their combination when directly seeded in flooded soils using dry seeds. The QTLs were in the background of two popular varieties PSB Rc82 and Ciherang-Sub1, evaluated along with the donors Kho Hlan On (AG1) and Ma-Zhan Red (AG2) and recipient parents PSB Rc82 and Ciherang-Sub1. In one set of experiments conducted in the greenhouse, seedling emergence, growth, and carbohydrate mobilization from seeds were assessed. Metabolites associated with reactive oxygen species (ROS) scavenging including malondialdehyde (MDA) as a measure of lipid peroxidation, ascorbate, total phenolic concentration (TPC), and activities of ROS scavenging enzymes were quantified in seeds germinating under control (saturated) and flooded (10 cm) soils. In another set of experiments conducted in a natural field with 3-5 cm flooding depths, control and pretreated seeds of Ciherang-Sub1 introgression lines and checks were used. Flooding reduced seedling emergence of all genotypes, though emergence of AG1 + AG2 introgression lines was greater than the other AG lines. Soluble sugars increased, while starch concentration decreased gradually under flooding especially in the tolerant checks and in AG1 + AG2 introgression lines. Less lipid peroxidation and higher α-amylase activity, higher ascorbate (RAsA) and TPC were observed in the tolerant checks and in the AG1 + AG2 introgression lines. Lipid peroxidation correlated negatively with ascorbate, TPC, and with ROS scavengers. Seed hydro-priming or pre-soaking increased emergence by 7-10% over that of dry seeds. Introgression of AG2 and AG1 + AG2 QTLs with seed pretreatment showed 101-153% higher emergence over dry seeds of intolerant genotypes in the field. Lines carrying AG1 + AG2 QTLs showed higher α-amylase activity, leading to rapid starch degradation and increase in soluble sugars, ascorbate, and TPC, together leading to higher germination and seedling growth in flooded soils. Seed hydro-priming or pre-soaking for 24 h also improved traits associated with flooding tolerance. Combining tolerance with seed management could therefore, improve crop establishment in flooded soils and encourage large-scale adoption of direct seeded rice system.
Collapse
Affiliation(s)
- Satyen Mondal
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. .,Bangladesh Rice Research Institute, Gazipur 1701, Bangladesh. .,University of the Philippines Los Baños, College 4031, Laguna, Philippines.
| | - M Iqbal R Khan
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.,Jamia Hamdard, New Delhi 110062, India
| | - Frederickson Entila
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Pompe C Sta Cruz
- University of the Philippines Los Baños, College 4031, Laguna, Philippines
| | - M Panna Ali
- Bangladesh Rice Research Institute, Gazipur 1701, Bangladesh
| | | | | | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| |
Collapse
|
38
|
Zayas-Santiago CC, Rivas-Ubach A, Kuo LJ, Ward ND, Zimmerman RC. Metabolic Profiling Reveals Biochemical Pathways Responsible for Eelgrass Response to Elevated CO 2 and Temperature. Sci Rep 2020; 10:4693. [PMID: 32170204 PMCID: PMC7070064 DOI: 10.1038/s41598-020-61684-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/25/2020] [Indexed: 11/17/2022] Open
Abstract
As CO2 levels in Earth’s atmosphere and oceans steadily rise, varying organismal responses may produce ecological losers and winners. Increased ocean CO2 can enhance seagrass productivity and thermal tolerance, providing some compensation for climate warming. However, the metabolic shifts driving the positive response to elevated CO2 by these important ecosystem engineers remain unknown. We analyzed whole-plant performance and metabolic profiles of two geographically distinct eelgrass (Zostera marina L.) populations in response to CO2 enrichment. In addition to enhancing overall plant size, growth and survival, CO2 enrichment increased the abundance of Calvin Cycle and nitrogen assimilation metabolites while suppressing the abundance of stress-related metabolites. Overall metabolome differences between populations suggest that some eelgrass phenotypes may be better suited than others to cope with an increasingly hot and sour sea. Our results suggest that seagrass populations will respond variably, but overall positively, to increasing CO2 concentrations, generating negative feedbacks to climate change.
Collapse
Affiliation(s)
- Carmen C Zayas-Santiago
- Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University, Norfolk, VA, 23429, USA.
| | - Albert Rivas-Ubach
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA, 99352, USA
| | - Li-Jung Kuo
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 W. Sequim Bay Rd., Sequim, WA, 98382, USA
| | - Nicholas D Ward
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 W. Sequim Bay Rd., Sequim, WA, 98382, USA.,School of Oceanography, University of Washington, Seattle, WA, 98105, USA
| | - Richard C Zimmerman
- Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University, Norfolk, VA, 23429, USA
| |
Collapse
|
39
|
Wu YS, Yang CY. Comprehensive Transcriptomic Analysis of Auxin Responses in Submerged Rice Coleoptile Growth. Int J Mol Sci 2020; 21:E1292. [PMID: 32075118 PMCID: PMC7072898 DOI: 10.3390/ijms21041292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
Cultivating rice in wet or water direct seeding systems is simple and time and labor efficient. Rice (Oryza sativa) seeds are a unique cereal that can germinate not only when submerged, but also in anoxic conditions. Many complicated hormone signals interact in submerged seed germination. Ethylene is involved in rice coleoptile elongation, but little is known regarding the role of auxin signaling under submergence. This study demonstrated that the coleoptile is shorter and curlier when submerged with 2,3,5-triiodobenzoic acid (TIBA). In transcriptomic analysis, 3448 of the 31,860 genes were upregulated, and 4360 genes were downregulated with submergence and TIBA treatment. The Gene Ontology function classification results demonstrated that upregulated differentially expressed genes (DEGs) were mainly involved in redox, stress, and signal transduction, whereas the down-regulated DEGs were mainly involved in RNA transcription, stress, and development. Furthermore, auxin signaling involved in the carbohydrate metabolism pathway was demonstrated while using transcriptomic analysis and confirmed in a quantitative real-time polymerase chain reaction. In addition, the transcript levels of development-related genes and mitochondria-electron- transport-related genes were regulated by auxin signaling under submergence. Auxin signaling was not only involved in regulating rice coleoptile elongation and development, but also regulated secondary metabolism, carbohydrate metabolism, and mitochondria electron transport under submergence. Our results presented that auxin signaling plays an important role during rice coleoptile elongation upon the submergence condition and improving the advance of research of direct rice seeding system.
Collapse
Affiliation(s)
- Yu-Sian Wu
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Chin-Ying Yang
- Department of Agronomy, National Chung Hsing University, Taichung 40227, Taiwan;
- Pervasive AI Research (PAIR) Labs, Hsinchu 30010, Taiwan
| |
Collapse
|
40
|
Kuya N, Sun J, Iijima K, Venuprasad R, Yamamoto T. Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections. BREEDING SCIENCE 2019; 69:633-639. [PMID: 31988627 PMCID: PMC6977445 DOI: 10.1270/jsbbs.19003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Direct seeding saves time and labour in the cultivation of rice. However, seedling establishment is often unstable, and yields are lower than in transplanting. Anaerobic germination (AG) is a key trait for improvement of direct seeding of rice. We established a simple and reliable method of evaluating AG in rice breeding. We germinated seeds in distilled water or deoxygenated water and measured coleoptile length several days later; compared the results of each method with survival rate in flooded soil; and used the anoxic water method for QTL analysis and for testing cultivars. Coleoptile elongation in anoxic water and survival rate in flooded soil were significantly correlated (r = 0.879, P < 0.01). A significant QTL, likely to be a major gene (AG1), was found in chromosome segment substitution lines and in a backcrossed F2 population derived from tolerant and sensitive lines. Diverse rice genetic resources were classified into tolerant or sensitive accession groups reflecting their ecotypes. Our study revealed that anoxic water evaluation method saves space and time in a stable environment compared with flooded soil evaluation. It is applicable to QTL analysis and isolation of genes underlying anaerobic germination.
Collapse
Affiliation(s)
- Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Jian Sun
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Rice Research Institute of Shenyang Agricultural University,
Shenyang 110161,
China
| | - Ken Iijima
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | | | - Toshio Yamamoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Institute of Plant Science and Resources, Okayama University,
2-20-1 Chuo, Kurashiki, Okayama 710-0046,
Japan
| |
Collapse
|
41
|
Nghi KN, Tondelli A, Valè G, Tagliani A, Marè C, Perata P, Pucciariello C. Dissection of coleoptile elongation in japonica rice under submergence through integrated genome-wide association mapping and transcriptional analyses. PLANT, CELL & ENVIRONMENT 2019; 42:1832-1846. [PMID: 30802973 DOI: 10.1111/pce.13540] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Accepted: 02/10/2019] [Indexed: 05/23/2023]
Abstract
Rice is unique among cereals for its ability to germinate not only when submerged but also under anoxic conditions. Rice germination under submergence or anoxia is characterized by a longer coleoptile and delay in radicle emergence. A panel of temperate and tropical japonica rice accessions showing a large variability in coleoptile length was used to investigate genetic factors involved in this developmental process. The ability of the Khao Hlan On rice landrace to vigorously germinate when submerged has been previously associated with the presence of the trehalose 6 phosphate phosphatase 7 (TPP7) gene. In this study, we found that, in the presence of TPP7, polymorphisms and transcriptional variations of the gene in coleoptile tissue were not related to differences in the final coleoptile length under submergence. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome-wide association study analysis on a panel of 273 japonica rice accessions. We discovered 11 significant marker-trait associations and identified candidate genes potentially involved in coleoptile length. Candidate gene expression analyses indicated that japonica rice genotypes possess complex genetic elements that control final coleoptile length under low oxygen.
Collapse
Affiliation(s)
- Khac Nhu Nghi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Giampiero Valè
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Andrea Tagliani
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Caterina Marè
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| |
Collapse
|
42
|
Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq. BMC Genomics 2019; 20:355. [PMID: 31072298 PMCID: PMC6506967 DOI: 10.1186/s12864-019-5741-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
Background Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. Results In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination. Conclusions Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5741-y) contains supplementary material, which is available to authorized users.
Collapse
|
43
|
Huang YC, Yeh TH, Yang CY. Ethylene signaling involves in seeds germination upon submergence and antioxidant response elicited confers submergence tolerance to rice seedlings. RICE (NEW YORK, N.Y.) 2019; 12:23. [PMID: 30972510 PMCID: PMC6458221 DOI: 10.1186/s12284-019-0284-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/02/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Flooding has negative impact on agriculture. The plant hormone ethylene is involved in plant growth and stress responses, which are important role in tolerance and adaptation regulatory mechanisms during submergence stress. Ethylene signaling crosstalk with gibberellin signaling enhances tolerance in lowland rice (Flood Resistant 13A) through a quiescence strategy or in deepwater rice through an escape strategy when rice is submerged. Information regarding ethylene-mediated priming in submergence stress tolerance in rice is scant. Here, we used 1-aminocyclopropane-1-carboxylic acid, an ethylene precursor, to evaluate the response in submerged rice seedlings. RESULTS The germination rate and mean germination times of rice seeds was higher in seedlings under submergence only when ethylene signaling was inhibited by supplemented with silver nitrate (AgNO3). Reduced leaf chlorophyll contents and induced senescence-associated genes in rice seedlings under submergence were relieved by pretreatment with an ethylene precursor. The ethylene-mediated priming by pretreatment with an ethylene precursor enhanced the survival rate and hydrogen peroxide (H2O2) and superoxide (O2-) anion accumulation and affected antioxidant response in rice seedlings. CONCLUSIONS Pretreatment with an ethylene precursor leads to reactive oxygen species generation, which in turn triggered the antioxidant response system, thus improving the tolerance of rice seedlings to complete submergence stress. Thus, H2O2 signaling may contribute to ethylene-mediated priming to submergence stress tolerance in rice seedlings.
Collapse
Affiliation(s)
- Yi-Chun Huang
- Department of Agronomy, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Tsun-Hao Yeh
- Department of Agronomy, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chin-Ying Yang
- Department of Agronomy, National Chung Hsing University, Taichung, 40227, Taiwan.
| |
Collapse
|
44
|
Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. FRONTIERS IN PLANT SCIENCE 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
Collapse
Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
| |
Collapse
|
45
|
Chen MX, Zhu FY, Wang FZ, Ye NH, Gao B, Chen X, Zhao SS, Fan T, Cao YY, Liu TY, Su ZZ, Xie LJ, Hu QJ, Wu HJ, Xiao S, Zhang J, Liu YG. Alternative splicing and translation play important roles in hypoxic germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:817-833. [PMID: 30535157 PMCID: PMC6363088 DOI: 10.1093/jxb/ery393] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/27/2018] [Indexed: 05/04/2023]
Abstract
Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.
Collapse
Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Feng-Zhu Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
| | - Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd, Wuhan, China
| | - Shan-Shan Zhao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Yun-Ying Cao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Tie-Yuan Liu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ze-Zhuo Su
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li-Juan Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Juan Hu
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hui-Jie Wu
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Correspondence: or
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Correspondence: or
| |
Collapse
|
46
|
Takenaka S, Yamamoto R, Nakamura C. Differential and interactive effects of cytoplasmic substitution and seed ageing on submergence stress response in wheat ( Triticum aestivum L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1549960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shotaro Takenaka
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Ryohei Yamamoto
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Chiharu Nakamura
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Japan
| |
Collapse
|
47
|
The role of the NADH-dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification. Arch Microbiol 2018; 201:519-530. [PMID: 30406295 DOI: 10.1007/s00203-018-1590-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/17/2018] [Accepted: 10/24/2018] [Indexed: 10/27/2022]
Abstract
Nitrate and nitrite reduction are of paramount importance for nitrogen assimilation and anaerobic metabolism, and understanding the specific roles of each participating reductase is necessary to describe the biochemical balance that dictates cellular responses to their environments. The soluble, cytoplasmic siroheme NADH-nitrite reductase (Nir) in Escherichia coli is necessary for nitrate/nitrite assimilation but has also been reported to either "detoxify" nitrite, or to carry out fermentative ammonification in support of anaerobic catabolism. Theoretically, nitrite detoxification would be important for anaerobic growth on nitrate, during which excess nitrite would be reduced to ammonium. Fermentative ammonification by Nir would be important for maximization of non-respiratory ATP production during anaerobic growth in the presence of nitrite. Experiments reported here were designed to test the potential role of Nir in fermentative ammonification directly by growing E. coli along with mutant strains lacking Nir or the respiratory nitrite reductase (Nrf) under anaerobic conditions in defined media while monitoring nitrogen utilization and fermentation metabolites. To focus on the role of Nir in fermentative ammonification, pH control was used in most experiments to eliminate nitrite toxicity due to nitric acid formation. Our results demonstrate that Nir confers a significant benefit during fermentative growth that reflects fermentative ammonification rather than detoxification. We conclude that fermentative ammonification by Nir allows for the energetically favorable fermentation of glucose to formate and acetate. These results and conclusions are discussed in light of the roles of Nir in other bacteria and in plants.
Collapse
|
48
|
Takenaka S, Yamamoto R, Nakamura C. Genetic diversity of submergence stress response in cytoplasms of the Triticum-Aegilops complex. Sci Rep 2018; 8:16267. [PMID: 30390041 PMCID: PMC6214928 DOI: 10.1038/s41598-018-34682-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
Genetic diversity in cytoplasmic and nuclear genomes and their interaction affecting adaptive traits is an attractive research subject in plants. We addressed submergence stress response of wheat that has become increasingly important but remained largely uninvestigated. Our primary aim was to disclose cytoplasmic diversity using nucleus-cytoplasm (NC) hybrids possessing a series of heterologous cytoplasms in a common nuclear background. Effects of submergence on seedling emergence and growth from imbibed seeds were studied and compared with euplasmic lines. Marked phenotypic variabilities were observed among both lines, demonstrating divergent cytoplasmic and nuclear effects on submergence response. NC hybrids with cytoplasm of Aegilops mutica showed a less inhibition, indicative of their positive contribution to submergence tolerance, whereas cytoplasms of Aegilops umbellulata and related species caused a greater inhibition. Superoxide dismutase (SOD) activity showed a marked increase accompanied by retardation of seedling growth in a susceptible NC hybrid. The observation suggested that the elevated SOD activity was resulted from a high level of reactive oxygen species accumulated and remained in susceptible seedlings. Taken together, our results point to the usefulness of NC hybrids in further studies needed to clarify molecular mechanisms underlying the nucleus-cytoplasm interaction regulating submergence stress response in wheat.
Collapse
Affiliation(s)
- Shotaro Takenaka
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Ohe-cho, Seta, Otsu, 520-2194, Japan
| | - Ryohei Yamamoto
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Ohe-cho, Seta, Otsu, 520-2194, Japan
| | - Chiharu Nakamura
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Ohe-cho, Seta, Otsu, 520-2194, Japan.
| |
Collapse
|
49
|
Lee HY, Yoon GM. Regulation of Ethylene Biosynthesis by Phytohormones in Etiolated Rice ( Oryza sativa L.) Seedlings. Mol Cells 2018; 41:311-319. [PMID: 29463069 PMCID: PMC5935104 DOI: 10.14348/molcells.2018.2224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 11/27/2022] Open
Abstract
The gaseous hormone ethylene influences many aspects of plant growth, development, and responses to a variety of stresses. The biosynthesis of ethylene is tightly regulated by various internal and external stimuli, and the primary target of the regulation is the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), which catalyzes the rate-limiting step of ethylene biosynthesis. We have previously demonstrated that the regulation of ethylene biosynthesis is a common feature of most of the phytohormones in etiolated Arabidopsis seedlings via the modulation of the protein stability of ACS. Here, we show that various phytohormones also regulate ethylene biosynthesis from etiolated rice seedlings in a similar manner to those in Arabidopsis. Cytokinin, brassinosteroids, and gibberellic acid increase ethylene biosynthesis without changing the transcript levels of neither OsACS nor ACC oxidases (OsACO), a family of enzymes catalyzing the final step of the ethylene biosynthetic pathway. Likewise, salicylic acid and abscisic acid do not alter the gene expression of OsACS, but both hormones downregulate the transcript levels of a subset of ACO genes, resulting in a decrease in ethylene biosynthesis. In addition, we show that the treatment of the phytohormones results in distinct etiolated seedling phenotypes, some of which resemble ethylene-responsive phenotypes, while others display ethylene-independent morphologies, indicating a complicated hormone crosstalk in rice. Together, our study brings a new insight into crosstalk between ethylene biosynthesis and other phytohormones, and provides evidence that rice ethylene biosynthesis could be regulated by the post-transcriptional regulation of ACS proteins.
Collapse
Affiliation(s)
- Han Yong Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Gyeong Mee Yoon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|