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Phukan UJ, Jindal S, Laldinsangi C, Singh PK, Longchar B. A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice. PLANTA 2023; 259:9. [PMID: 38030751 DOI: 10.1007/s00425-023-04285-y] [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: 09/01/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
MAIN CONCLUSION Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.
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Affiliation(s)
- Ujjal J Phukan
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Sunita Jindal
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic
| | - C Laldinsangi
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India
- Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Center, 68 HaMacabim Road, 7505101, Rishon Lezion, Israel
| | - Bendangchuchang Longchar
- Department of Life Sciences, Pachhunga University College, Mizoram University, Aizawl, 796001, Mizoram, India.
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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Nagai K, Ashikari M. Molecular mechanism of internode elongation in rice. BREEDING SCIENCE 2023; 73:108-116. [PMID: 37404350 PMCID: PMC10316307 DOI: 10.1270/jsbbs.22086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 07/06/2023]
Abstract
Rice plants that form ventilated tissues, such as aerenchyma in the leaves, stems, and roots, allow for growth in waterlogged conditions (paddy fields), but they cannot breathe and drown in flooded environments where the whole plant body is submerged. However, deepwater rice plants grown in flood-prone areas of Southeast Asia survive in prolonged flooded environments by taking in air through an elongated stem (internode) and leaves that emerge above the water surface, even if the water level is several meters high and flooding continues for several months. Although it has been known that plant hormones, such as ethylene and gibberellins, promote internode elongation in deepwater rice plants, the genes that control rapid internode elongation during submergence have not been identified. We recently identified several genes responsible for the quantitative trait loci involved in internode elongation in deepwater rice. Identification of the the genes revealed a molecular gene network from ethylene to gibberellins in which internode elongation is promoted by novel ethylene-responsive factors and enhances gibberellin responsiveness at the internode. In addition, elucidation of the molecular mechanism of internode elongation in deepwater rice will help our understanding of the internode elongation mechanism in normal paddy rice and contribute to improving crops through the regulation of internode elongation.
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Affiliation(s)
- Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
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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: 0] [Impact Index Per Article: 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.
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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: 2] [Impact Index Per Article: 0.7] [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.
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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
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Antagonistic regulation of the gibberellic acid response during stem growth in rice. Nature 2020; 584:109-114. [PMID: 32669710 DOI: 10.1038/s41586-020-2501-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/04/2020] [Indexed: 12/24/2022]
Abstract
The size of plants is largely determined by growth of the stem. Stem elongation is stimulated by gibberellic acid1-3. Here we show that internode stem elongation in rice is regulated antagonistically by an 'accelerator' and a 'decelerator' in concert with gibberellic acid. Expression of a gene we name ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1), which encodes a protein of unknown function, confers cells of the intercalary meristematic region with the competence for cell division, leading to internode elongation in the presence of gibberellic acid. By contrast, upregulation of DECELERATOR OF INTERNODE ELONGATION 1 (DEC1), which encodes a zinc-finger transcription factor, suppresses internode elongation, whereas downregulation of DEC1 allows internode elongation. We also show that the mechanism of internode elongation that is mediated by ACE1 and DEC1 is conserved in the Gramineae family. Furthermore, an analysis of genetic diversity suggests that mutations in ACE1 and DEC1 have historically contributed to the selection of shorter plants in domesticated populations of rice to increase their resistance to lodging, and of taller plants in wild species of rice for adaptation to growth in deep water. Our identification of these antagonistic regulatory factors enhances our understanding of the gibberellic acid response as an additional mechanism that regulates internode elongation and environmental fitness, beyond biosynthesis and gibberellic acid signal transduction.
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Submergence Tolerance in Rice: Review of Mechanism, Breeding and, Future Prospects. SUSTAINABILITY 2020. [DOI: 10.3390/su12041632] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Flooding or submergence is one of the major environmental stressors affecting many man-made and natural ecosystems worldwide. The increase in the frequency and duration of heavy rainfall due to climate change has negatively affected plant growth and development, which eventually causes the death of plants if it persists for days. Most crops, especially rice, being a semi-aquatic plant, are greatly affected by flooding, leading to yield losses each year. Genetic variability in the plant response to flooding includes the quiescence scheme, which allows underwater endurance of a prolonged period, escape strategy through stem elongation, and alterations in plant architecture and metabolism. Investigating the mechanism for flooding survival in wild species and modern rice has yielded significant insight into developmental, physiological, and molecular strategies for submergence and waterlogging survival. Significant progress in the breeding of submergence tolerant rice varieties has been made during the last decade following the successful identification and mapping of a quantitative trait locus for submergence tolerance, designated as SUBMERGENCE 1 (SUB1) from the FR13A landrace. Using marker-assisted backcrossing, the SUB1 QTL (quantitative trait locus) has been incorporated into many elite varieties within a short time and with high precision as compared with conventional breeding methods. Despite the advancement in submergence tolerance, for future studies, there is a need for practical approaches exploring genome-wide association studies (GWA) and QTL in combination with specific tolerance traits, such as drought, salinity, disease and insect resistance.
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Makumbi D, Alvarado G, Crossa J, Burgueño J. SASHAYDIALL: A SAS Program for Hayman's Diallel Analysis. CROP SCIENCE 2018; 58:1605-1615. [PMID: 33343012 PMCID: PMC7680942 DOI: 10.2135/cropsci2018.01.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/17/2018] [Indexed: 05/18/2023]
Abstract
Different methods of diallel crossing are commonly used in plant breeding. The diallel cross analysis method proposed by Hayman is particularly useful because it provides information, among others, on additive and dominance effects of genes, average degree of dominance, proportion of dominance, direction of dominance, distribution of genes, maternal and reciprocal effects, number of groups of genes that control a trait and exhibit dominance, ratio of dominant to recessive alleles in all the parents, and broad-sense and narrow-sense heritability. In this paper, we fully describe a SAS-based software SASHAYDIALL for performing a complete diallel cross analysis based on Hayman's model with or without reciprocals. We demonstrate the use of SASHAYDIALL with two data sets; one is a published diallel cross data set with reciprocals in cabbage (Brassica oleracea L.), and the second is a data set from a multilocation diallel cross trial in maize (Zea mays L.) without reciprocals. With SASHAYDIALL, diallel experiments conducted in single sites can be analyzed to estimate various genetic parameters, and this analysis is extended over locations or environments to assess genetic effect × environment interaction. SASHAYDIALL is user-friendly software that provides detailed genetic information from diallel crosses involving any number of parents and locations.
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Affiliation(s)
- Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041-00621, Nairobi, Kenya
- Corresponding author (). Assigned to Associate Editor Natalia de Leon
| | - Gregorio Alvarado
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico DF, Mexico
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico DF, Mexico
| | - Juan Burgueño
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico DF, Mexico
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Singh A, Septiningsih EM, Balyan HS, Singh NK, Rai V. Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativa L.). PLANT & CELL PHYSIOLOGY 2017; 58:185-197. [PMID: 28069894 DOI: 10.1093/pcp/pcw206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Flooding of rice fields is a serious problem in the river basins of South and South-East Asia where about 15 Mha of lowland rice cultivation is regularly affected. Flooding creates hypoxic conditions resulting in poor germination and seedling establishment. Flash flooding, where rice plants are completely submerged for 10-15 d during their vegetative stage, causes huge losses. Water stagnation for weeks to months also leads to substantial yield losses when large parts of rice aerial tissues are inundated. The low-yielding traditional varieties and landraces of rice adapted to these flooding conditions have been replaced by flood-sensitive high-yielding rice varieties. The 'FR13A' rice variety and the Submergence 1A (SUB1A) gene were identified for flash flooding and subsequently introgressed to high-yielding rice varieties. The challenge is to find superior alleles of the SUB1A gene, or even new genes that may confer greater tolerance to submergence. Similarly, genes have been identified in tolerant landraces of rice for their ability to survive by rapid stem elongation (SNORKEL1 and SNORKEL2) during deep-water flooding, and for anaerobic germination ability (TPP7). Research on rice genotypes and novel genes that are tolerant to prolonged water stagnation is in progress. These studies will greatly assist in devising more efficient and precise molecular breeding strategies for developing climate-resilient high-yielding rice varieties for flood-prone regions. Here we review the state of our knowledge of flooding tolerance in rice and its application in varietal improvement.
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Affiliation(s)
- Anuradha Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Endang M Septiningsih
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Harendra S Balyan
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
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Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize. Sci Rep 2017; 7:40239. [PMID: 28071695 PMCID: PMC5223130 DOI: 10.1038/srep40239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
Various types of populations have been used in genetics, genomics and crop improvement, including bi- and multi-parental populations and natural ones. The latter has been widely used in genome-wide association study (GWAS). However, inbred-based GWAS cannot be used to reveal the mechanisms involved in hybrid performance. We developed a novel maize population, multiple-hybrid population (MHP), consisting of 724 hybrids produced using 28 temperate and 23 tropical inbreds. The hybrids can be divided into three subpopulations, two diallels and NC (North Carolina Design) II. Significant genetic differences were identified among parents, hybrids and heterotic groups. A cluster analysis revealed heterotic groups existing in the parental lines and the results showed that MHPs are well suitable for GWAS in hybrid crops. MHP-based GWAS was performed using 55 K SNP array for flowering time traits, days to tassel, days to silk, days to anthesis and anthesis-silking interval. Two independent methods, PEPIS developed for hybrids and TASSEL software designed for inbred line populations, revealed highly consistent results with five overlapping chromosomal regions identified and used for discovery of candidate genes and quantitative trait nucleotides. Our results indicate that MHPs are powerful in GWAS for hybrid-related traits with great potential applications in the molecular breeding era.
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Ayano M, Kani T, Kojima M, Sakakibara H, Kitaoka T, Kuroha T, Angeles-Shim RB, Kitano H, Nagai K, Ashikari M. Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice. PLANT, CELL & ENVIRONMENT 2014; 37:2313-24. [PMID: 24891164 PMCID: PMC4282320 DOI: 10.1111/pce.12377] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 05/15/2014] [Accepted: 05/21/2014] [Indexed: 05/17/2023]
Abstract
Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice.
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Affiliation(s)
- Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601
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Nagai K, Kondo Y, Kitaoka T, Noda T, Kuroha T, Angeles-Shim RB, Yasui H, Yoshimura A, Ashikari M. QTL analysis of internode elongation in response to gibberellin in deepwater rice. AOB PLANTS 2014; 6:plu028. [PMID: 24946943 PMCID: PMC4086424 DOI: 10.1093/aobpla/plu028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/19/2014] [Indexed: 05/21/2023]
Abstract
Gibberellin (GA) is a plant hormone that has important roles in numerous plant developmental phases. Rice plants known as deepwater rice respond to flooding by elongating their internodes to avoid anoxia. Previous studies reported that GA is essential for internode elongation in deepwater rice. Quantitative trait locus (QTL) analyses identified QTLs regulating internode elongation in response to deepwater conditions. However, the interaction between internode elongation and regulators of GA sensitivity in deepwater rice is unknown. In this study, we applied GA to recombinant inbred lines of T65 (non-deepwater rice) and Bhadua (deepwater rice), and performed a QTL analysis of internode elongation in response to GA. GA-induced internode elongation was detected only in deepwater rice. Our QTL analysis revealed two major QTLs on chromosomes 3 and 9 regulating total internode length, lowest elongated internode and number of elongated internodes. Furthermore, the QTL on chromosome 3 acted as an enhancer of other QTLs (e.g. the QTL on chromosome 12). Nearly isogenic lines of deepwater rice carrying the QTL regions from chromosomes 3 and 12 of the deepwater rice C9285 showed internode elongation in response to GA. Thus, these QTLs may regulate GA responsiveness in deepwater rice. This study furthers our understanding of the mechanism of internode elongation in rice.
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Affiliation(s)
- Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yuma Kondo
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Takuya Kitaoka
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Tomonori Noda
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rosalyn B Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Kyushu University, 6-10-1 Hakozaki-ku, Higashi, Fukuoka 812-8581, Japan
| | - Atsushi Yoshimura
- Plant Breeding Laboratory, Kyushu University, 6-10-1 Hakozaki-ku, Higashi, Fukuoka 812-8581, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
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Nagai K, Kuroha T, Ayano M, Kurokawa Y, Angeles-Shim RB, Shim JH, Yasui H, Yoshimura A, Ashikari M. Two novel QTLs regulate internode elongation in deepwater rice during the early vegetative stage. BREEDING SCIENCE 2012; 62:178-85. [PMID: 23136529 PMCID: PMC3405962 DOI: 10.1270/jsbbs.62.178] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 04/04/2012] [Indexed: 05/20/2023]
Abstract
Deepwater rice possesses internode elongation ability to avoid drowning under deepwater conditions. Previous studies identified three QTLs regulating internode elongation ability on chromosomes 1, 3 and 12 using different populations. However, these QTLs only induce internode elongation in response to deepwater conditions from the 7-leaf stage and not during the early leaf stage. In this study, we detected two novel QTLs, qTIL2 and qTIL4 regulating deepwater response at the early leaf stage using an F(2) population derived from the cross between NIL1-3-12 carrying the three QTLs regulating deepwater response in T65 (O. sativa ssp. japonica) genetic background and C9285 (O. sativa ssp. indica, deepwater rice). Plants of the BC(2)F(2) population derived from NIL1-3-12/C9285 and the RILs of T65/Bhadua (O. sativa ssp. indica, deepwater rice) possessing these QTLs as well as the three QTLs previously identified also showed internode elongation during the early leaf stage. These results indicate that qTIL2 and qTIL4 regulate early internode elongation and function in coordination with the three major QTLs under deepwater conditions. The results presented here would not only help define the mechanism of deepwater response in rice but also contribute in the breeding of deepwater tolerant rice that is adapted to various water depths.
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Affiliation(s)
- Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yusuke Kurokawa
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rosalyn B. Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Jung-Hyun Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka 812-8581, Japan
| | - Atsushi Yoshimura
- Plant Breeding Laboratory, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka 812-8581, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, Aichi 464-8601, Japan
- Corresponding author (e-mail: )
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Sakagami JI, Sone C, Nakazono M. Injury to Rice Plants by Floods and Resistance to Submergence. ACTA ACUST UNITED AC 2012. [DOI: 10.1626/jcs.81.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hattori Y, Nagai K, Ashikari M. Rice growth adapting to deepwater. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:100-5. [PMID: 20934370 DOI: 10.1016/j.pbi.2010.09.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/02/2010] [Accepted: 09/10/2010] [Indexed: 05/24/2023]
Abstract
Flooding is one of the most hazardous natural disasters, and there are several levels of flooding. Recently, research on flood-tolerant rice plants revealed that some rice varieties have evolved to overcome two different flood types, 'flash flood' and 'deepwater flood', using two different mechanisms, and their molecular mechanisms were determined. During flash flooding, the tolerant plants that are fully submerged for a few weeks stop elongating and thus avoid energy consumption that will be needed to restart growth when the water recedes. On the contrary, during deepwater flooding, with water depth up to several meters for several months, the deepwater-flood-tolerant rice plants promote elongation of internodes to keep the foliage above the water surface and thus allow respiration and photosynthesis.
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Affiliation(s)
- Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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16
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Hao W, Lin HX. Toward understanding genetic mechanisms of complex traits in rice. J Genet Genomics 2010; 37:653-66. [DOI: 10.1016/s1673-8527(09)60084-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 08/26/2010] [Indexed: 10/18/2022]
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17
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Nagai K, Hattori Y, Ashikari M. Stunt or elongate? Two opposite strategies by which rice adapts to floods. JOURNAL OF PLANT RESEARCH 2010; 123:303-9. [PMID: 20354754 DOI: 10.1007/s10265-010-0332-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 03/05/2010] [Indexed: 05/20/2023]
Abstract
Expansion of habitat is important for the perpetuation of species. In particular, plants which are sedentary must evolve specialized functions to adapt itself to new environment. Deepwater rice is cultivated mainly in the lowland areas of South and Southeast Asia that are flooded during the rainy season. The internodes of deepwater rice elongates in response to increasing water level to keep its leaves above the water surface and avoid anoxia. This elongation is stimulated by ethylene-regulated genes, Snorkel1 and Snorkel2. In contrast, when a flash flood occurs at the seedling stage, submergence-tolerant rice, which carries Submergence-1A, remains stunted and survives in water for a few weeks to avoid the energy consumption associated with plant elongation, and restarts its growth using its conserved energy after the water recedes. Interestingly, both Snorkel genes and Submergence-1A encode ethylene-responsive factor-type transcription factor and are connected to gibberellin biosynthesis or signal transduction. However, deepwater and submergence-tolerant rice seem to have opposite flooding response; namely, escape by elongation or remain stunted under water until flood recedes.
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Affiliation(s)
- Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
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18
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The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 2009; 460:1026-30. [DOI: 10.1038/nature08258] [Citation(s) in RCA: 668] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 06/30/2009] [Indexed: 01/07/2023]
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19
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Kawano R, Doi K, Yasui H, Mochizuki T, Yoshimura A. Mapping of QTLs for floating ability in rice. BREEDING SCIENCE 2008. [PMID: 0 DOI: 10.1270/jsbbs.58.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Ritsuko Kawano
- Plant Breeding Laboratory, Kyushu University
- Japan Society for the Promotion of Science
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