1
|
Sowadan O, Xu S, Li Y, Muleke EM, Sitoe HM, Dang X, Jiang J, Dong H, Hong D. Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice ( Oryza sativa L.). Genes (Basel) 2024; 15:105. [PMID: 38254994 PMCID: PMC10815206 DOI: 10.3390/genes15010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.
Collapse
Affiliation(s)
- Ognigamal Sowadan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Shanbin Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Yulong Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Institute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Everlyne Mmbone Muleke
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Department of Agriculture and Land Use Management, School of Agriculture, Veterinary Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega P.O. Box 190-50100, Kenya
| | - Hélder Manuel Sitoe
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
- Faculty of Agronomy and Biological Sciences, Púngue University, P.O. Box 323, Manica 2202, Mozambique
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (X.D.); (J.J.)
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| | - Delin Hong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (O.S.); (S.X.); (Y.L.); (E.M.M.); (H.M.S.); (H.D.)
| |
Collapse
|
2
|
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
|
3
|
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.
Collapse
|
4
|
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.
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
|
5
|
Ejiri M, Fukao T, Miyashita T, Shiono K. A barrier to radial oxygen loss helps the root system cope with waterlogging-induced hypoxia. BREEDING SCIENCE 2021; 71:40-50. [PMID: 33762875 PMCID: PMC7973497 DOI: 10.1270/jsbbs.20110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Internal aeration is crucial for root growth under waterlogged conditions. Many wetland plants have a structural barrier that impedes oxygen leakage from the basal part of roots called a radial oxygen loss (ROL) barrier. ROL barriers reduce the loss of oxygen transported via the aerenchyma to the root tips, enabling long-distance oxygen transport for cell respiration at the root tip. Because the root tip does not have an ROL barrier, some of the transferred oxygen is released into the waterlogged soil, where it oxidizes and detoxifies toxic substances (e.g., sulfate and Fe2+) around the root tip. ROL barriers are located at the outer part of roots (OPRs). Their main component is thought to be suberin. Suberin deposits may block the entry of potentially toxic compounds in highly reduced soils. The amount of ROL from the roots depends on the strength of the ROL barrier, the length of the roots, and environmental conditions, which causes spatiotemporal changes in the root system's oxidization pattern. We summarize recent achievements in understanding how ROL barrier formation is regulated and discuss opportunities for breeding waterlogging-tolerant crops.
Collapse
Affiliation(s)
- Masato Ejiri
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Fukui 910-1195,
Japan
| | - Takeshi Fukao
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Fukui 910-1195,
Japan
| | - Tomoki Miyashita
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Fukui 910-1195,
Japan
| | - Katsuhiro Shiono
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Fukui 910-1195,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
6
|
Yang J, Li D, Liu H, Liu Y, Huang M, Wang H, Chen Z, Guo T. Identification of QTLs involved in cold tolerance during the germination and bud stages of rice ( Oryza sativa L.) via a high-density genetic map. BREEDING SCIENCE 2020; 70:292-302. [PMID: 32714051 PMCID: PMC7372033 DOI: 10.1270/jsbbs.19127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Low-temperature tolerance during the germination and bud stages is an important characteristic of direct-seeded rice (DSR). Recombinant inbred lines (RILs) derived from indica rice H335, which is highly tolerant to low temperature, and indica rice CHA-1, which is sensitive to low temperature, were used to identify quantitative trait loci (QTLs) associated with low-temperature tolerance during the germination and bud stages. a total of 11 QTLs were detected based on a high-density genetic map; among these, six QTLs explained 5.13-9.42% of the total phenotypic variation explained (PVE) during the germination stage, and five QTLs explained 4.17-6.42% of the total PVE during the bud stage. All QTLs were distributed on chromosome 9, and all favourable alleles originated from H335. The physical position of each QTL was determined, and 11 QTLs were combined into five genetic loci; three of these loci are involved during the germination stage (loci 1, 2, and 3), and three are involved during the bud stage (loci 3, 4, and 5). Loci 2, 4 and 5 were repeatedly detected in the wet season (WS) and dry season (DS). Notably, loci 3 was detected during both the germination and bud stages. These loci are good candidates for future studies of gene function and could serve as highly valuable genetic factors for improving cold tolerance during the germination and bud stages of rice.
Collapse
Affiliation(s)
- 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
| | - Hong Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Ming Huang
- 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
- Corresponding author (e-mail: )
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Fukushima A, Kuroha T, Nagai K, Hattori Y, Kobayashi M, Nishizawa T, Kojima M, Utsumi Y, Oikawa A, Seki M, Sakakibara H, Saito K, Ashikari M, Kusano M. Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress. Metabolites 2020; 10:metabo10020068. [PMID: 32075002 PMCID: PMC7074043 DOI: 10.3390/metabo10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.
Collapse
Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Correspondence:
| |
Collapse
|
9
|
Yang J, Yang G, Yang M, Su L, Xia A, Li D, Huang C, Zhou D, Liu Y, Wang H, Chen Z, Guo T. Quantitative Trait Locus Analysis of Seed Germination and Early Seedling Growth in Rice. FRONTIERS IN PLANT SCIENCE 2019; 10:1582. [PMID: 31921238 PMCID: PMC6923285 DOI: 10.3389/fpls.2019.01582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/12/2019] [Indexed: 05/13/2023]
Abstract
Seed germination and early seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice (DSR). To investigate the genetic mechanisms underlying seed germination and early seedling growth in rice, 275 recombinant inbred lines (RILs) were genotyped in this study via the genotyping-by-sequencing (GBS) approach to construct a high-density linkage bin map based on the parent-independent genotyping method. Quantitative trait loci (QTLs) for 12 traits related to seed germination and early seedling growth were analyzed. Totally, 22 additive loci were detected, after analysis of the interaction between additive QTLs and environments, five stable additive loci were obtained. Among them, loci 4, 5, 12 and 14 exhibited clear pleiotropic effects that were associated with multiple traits. Analysis of the effects of the five additive stable loci showed that a single locus increased the corresponding phenotypic value. Ten of the 275 RILs pyramided the excellent alleles of the five stable genetic loci. Most phenotypic values of the ten RILs were greater than the average values. Four RILs (G260, G342, G371, and G401) with more excellent phenotypic values were subsequently selected; these RILs could serve as donor parents of favorable alleles in the breeding process. Due to the existence of pleiotropy, the use of these genetic loci for pyramid breeding can further increase the efficiency to reach breeding goals. In addition, these five stable loci have an average physical interval of only 170 kb, we also further identified five promising candidate genes by qRT-PCR, which provides us with a basis for future cloning of these genes. Overall, this work will help broaden our understanding of the genetic control of seed germination and early seedling growth, and this study provides both a good theoretical basis and a new genetic resource for the breeding of direct-seeded rice.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tao Guo
- *Correspondence: Zhiqiang Chen, ; Tao Guo,
| |
Collapse
|
10
|
Kurokawa Y, Nagai K, Huan PD, Shimazaki K, Qu H, Mori Y, Toda Y, Kuroha T, Hayashi N, Aiga S, Itoh JI, Yoshimura A, Sasaki-Sekimoto Y, Ohta H, Shimojima M, Malik AI, Pedersen O, Colmer TD, Ashikari M. Rice leaf hydrophobicity and gas films are conferred by a wax synthesis gene (LGF1) and contribute to flood tolerance. THE NEW PHYTOLOGIST 2018; 218:1558-1569. [PMID: 29498045 DOI: 10.1111/nph.15070] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/14/2018] [Indexed: 06/08/2023]
Abstract
Floods impede gas (O2 and CO2 ) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown. We used a rice mutant (dripping wet leaf 7, drp7) which does not retain gas films on leaves, and its wild-type (Kinmaze), in gene discovery for this trait. Gene complementation was tested in transgenic lines. Functional properties of leaves as related to gas film retention and underwater photosynthesis were evaluated. Leaf Gas Film 1 (LGF1) was identified as the gene determining leaf gas films. LGF1 regulates C30 primary alcohol synthesis, which is necessary for abundant epicuticular wax platelets, leaf hydrophobicity and gas films on submerged leaves. This trait enhanced underwater photosynthesis 8.2-fold and contributes to submergence tolerance. Gene function was verified by a complementation test of LGF1 expressed in the drp7 mutant background, which restored C30 primary alcohol synthesis, wax platelet abundance, leaf hydrophobicity, gas film retention, and underwater photosynthesis. The discovery of LGF1 provides an opportunity to better understand variation amongst rice genotypes for gas film retention ability and to target various alleles in breeding for improved submergence tolerance for yield stability in flood-prone areas.
Collapse
Affiliation(s)
- Yusuke Kurokawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Phung Danh Huan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
- Crops Research and Development Institute, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Ha Noi, Vietnam
| | - Kousuke Shimazaki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Huangqi Qu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Yoshinao Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Yosuke Toda
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Takeshi Kuroha
- Graduate School of Life Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai, Miyagi, 980-8578, Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Saori Aiga
- Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka, 812-8581, Japan
| | - Yuko Sasaki-Sekimoto
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8503, Japan
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, Copenhagen, 2100, Denmark
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Timothy David Colmer
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| |
Collapse
|
11
|
Minami A, Yano K, Gamuyao R, Nagai K, Kuroha T, Ayano M, Nakamori M, Koike M, Kondo Y, Niimi Y, Kuwata K, Suzuki T, Higashiyama T, Takebayashi Y, Kojima M, Sakakibara H, Toyoda A, Fujiyama A, Kurata N, Ashikari M, Reuscher S. Time-Course Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding. PLANT PHYSIOLOGY 2018; 176:3081-3102. [PMID: 29475897 PMCID: PMC5884608 DOI: 10.1104/pp.17.00858] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/15/2018] [Indexed: 05/29/2023]
Abstract
Water submergence is an environmental factor that limits plant growth and survival. Deepwater rice (Oryza sativa) adapts to submergence by rapidly elongating its internodes and thereby maintaining its leaves above the water surface. We performed a comparative RNA sequencing transcriptome analysis of the shoot base region, including basal nodes, internodes, and shoot apices of seedlings at two developmental stages from two varieties with contrasting deepwater growth responses. A transcriptomic comparison between deepwater rice cv C9285 and nondeepwater rice cv Taichung 65 revealed both similar and differential expression patterns between the two genotypes during submergence. The expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factors was significantly different between the varieties. Interestingly, in both varieties, the jasmonic acid content at the shoot base decreased during submergence, while exogenous jasmonic acid inhibited submergence-induced internode elongation in cv C9285, suggesting that jasmonic acid plays a role in the submergence response of rice. Furthermore, a targeted de novo transcript assembly revealed transcripts that were specific to cv C9285, including submergence-induced biotic stress-related genes. Our multifaceted transcriptome approach using the rice shoot base region illustrates a differential response to submergence between deepwater and nondeepwater rice. Jasmonic acid metabolism appears to participate in the submergence-mediated internode elongation response of deepwater rice.
Collapse
Affiliation(s)
- Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kenji Yano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masanari Nakamori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masaya Koike
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuma Kondo
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoko Niimi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Takamasa Suzuki
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya Aichi 464-8601, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Nori Kurata
- Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Motoyuki Ashikari
- Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| |
Collapse
|
12
|
Positive interactions of major-effect QTLs with genetic background that enhances rice yield under drought. Sci Rep 2018; 8:1626. [PMID: 29374240 PMCID: PMC5786057 DOI: 10.1038/s41598-018-20116-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/08/2018] [Indexed: 12/19/2022] Open
Abstract
To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY 2.2 + qDTY 4.1 in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY 1.1 + qDTY 2.1 + qDTY 3.1 + qDTY 11.1 ) and two QTLs (qDTY 1.1 + qDTY 11.1 ) yielded higher than PLs with other qDTY combinations. The selected PLs showed a yield advantage of 0.3-2.0 t ha-1 under RS. An allelic profile of MAS PLs having same qDTY combination but with different yields under drought was studied. Hierarchical clustering grouped together the selected lines with high yield under drought. Epistasis test showed the interaction of qDTY 4.1 and qDTY 9.1 loci with qDTY 7.1 significantly increased yield under drought and all the lines with higher yield under drought possessed the conserved region of qDTY 7.1 on chromosome 7. The positive interactions among QTLs, effectiveness of QTLs in different backgrounds, introgression of DTY QTLs together with resistance to biotic stresses shall help enhance grain yield under RS.
Collapse
|
13
|
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Kuroha T, Nagai K, Kurokawa Y, Nagamura Y, Kusano M, Yasui H, Ashikari M, Fukushima A. eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1753. [PMID: 29081784 PMCID: PMC5645499 DOI: 10.3389/fpls.2017.01753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 05/09/2023]
Abstract
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.
Collapse
Affiliation(s)
- Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yusuke Kurokawa
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Yoshiaki Nagamura
- Genome Resource Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Takeshi Kuroha, Atsushi Fukushima,
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
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. [PMID: 24891164 DOI: 10.1111/pce.12377.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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.
Collapse
Affiliation(s)
- Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Vergara GV, Nugraha Y, Esguerra MQ, Mackill DJ, Ismail AM. Variation in tolerance of rice to long-term stagnant flooding that submerges most of the shoot will aid in breeding tolerant cultivars. AOB PLANTS 2014; 6:plu055. [PMID: 25202124 PMCID: PMC4196555 DOI: 10.1093/aobpla/plu055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/27/2014] [Indexed: 05/04/2023]
Abstract
Stagnant flooding (SF) is a major problem in rainfed lowlands where floodwater of 25-50 cm stagnates in the field for most of the season. We aimed to establish a system for phenotyping SF tolerance and identifying tolerant germplasm through screening of landraces. A total of 626 rice accessions were evaluated over 3 years under control conditions and two levels of SF. Floodwater was raised to 20 cm at 25 or 30 days after transplanting (DAT). In one trial, the depth was increased subsequently by 5 cm a week and in another (severe stress), it was increased to 40 cm at 37 DAT and to 50 cm at 42 DAT. In both trials, water depth was maintained at 50-60 cm until maturity. In all cases, no plant was completely submerged. Plant height, elongation rate and yield were measured at maturity. Genotypes best suited to SF showed moderate elongation of 1.3-2.3 cm day(-1) under SF. In contrast, semi-dwarf and fast-elongating types performed poorly. Subsequent trials using 18 genotypes, including six pairs of near isogenic lines (NILs) with or without SUB1 showed that all SUB1 NILs were sensitive to SF. Five of the other six genotypes contained SUB1 and were SF tolerant, suggesting the possibility of combining tolerances to complete submergence (SUB1) and SF. Stem starch and soluble sugar concentrations were similar under control conditions among the 18 genotypes, but starch was depleted by 37 % under SF, with less depletion in tolerant genotypes. SUB1 NILs contained similar concentrations of starch and sugars under SF. We conclude that survival and yield under SF are dependent on moderate elongation, high tillering, lesser carbohydrate depletion and higher fertility. The tolerant genotypes identified here performed strongly in both wet and dry seasons and will be used to identify tolerance mechanisms and alleles for use in marker-assisted breeding.
Collapse
Affiliation(s)
- Georgina V Vergara
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | - Manuel Q Esguerra
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J Mackill
- Mars, Inc., Department of Plant Sciences, University of California, Davis, CA, USA
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| |
Collapse
|
19
|
Htun TM, Inoue C, Chhourn O, Ishii T, Ishikawa R. Effect of quantitative trait loci for seed shattering on abscission layer formation in Asian wild rice Oryza rufipogon. BREEDING SCIENCE 2014; 64:199-205. [PMID: 25320554 PMCID: PMC4154608 DOI: 10.1270/jsbbs.64.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/23/2014] [Indexed: 05/29/2023]
Abstract
Asian cultivated rice Oryza sativa L. was domesticated from its wild ancestor, O. rufipogon. During domestication, the cultivated rice lost its seed-shattering behaviour. Previous studies have shown that two major quantitative trait loci (QTLs; qSH1 and sh4) are responsible for the seed-shattering degree. Here, we produced introgression lines carrying non-functional alleles from O. sativa 'Nipponbare' at the two major QTLs in the genetic background of wild rice O. rufipogon W630, and examined the effects of the two QTLs on seed shattering and abscission layer formation. The introgression lines, with Nipponbare alleles at either or both loci, showed complete or partial abscission layer formation, respectively, indicating that other unknown loci might be involved in enhancing seed shattering in wild rice. We detected a single QTL named qSH3 regulating seed-shattering degree using an F2 population between Nipponbare and the introgression line carrying Nipponbare alleles at the two QTLs. Although we generated an introgression line for qSH3 alone, no effects on seed shattering were observed. However, a significant effect on seed-shattering degree was observed for the introgression line carrying Nipponbare alleles at qSH3 and the two QTLs, suggesting an important role of qSH3 on seed shattering in coordination with the two QTLs.
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Doust AN, Lukens L, Olsen KM, Mauro-Herrera M, Meyer A, Rogers K. Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication. Proc Natl Acad Sci U S A 2014; 111:6178-83. [PMID: 24753598 PMCID: PMC4035984 DOI: 10.1073/pnas.1308940110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.
Collapse
Affiliation(s)
- Andrew N. Doust
- Botany Department, Oklahoma State University, Stillwater, OK 74078
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G2W1; and
| | - Kenneth M. Olsen
- Department of Biology, Washington University, St. Louis, MO 63130
| | | | - Ann Meyer
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G2W1; and
| | - Kimberly Rogers
- Botany Department, Oklahoma State University, Stillwater, OK 74078
| |
Collapse
|
22
|
Shinada H, Iwata N, Sato T, Fujino K. QTL pyramiding for improving of cold tolerance at fertilization stage in rice. BREEDING SCIENCE 2014; 63:483-8. [PMID: 24757388 PMCID: PMC3949585 DOI: 10.1270/jsbbs.63.483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 12/19/2013] [Indexed: 05/20/2023]
Abstract
Vigorous cold tolerance at the fertilization stage (CTF) is a very important characteristic for stable rice production in cold temperature conditions. Because CTF is a quantitatively inherited trait, pyramiding quantitative trait loci (QTLs) using marker-assisted selection (MAS) is effective for improving CTF levels in rice breeding programs. We previously identified three QTLs controlling CTF, qCTF7, qCTF8 and qCTF12, using backcrossed inbred lines derived from a cross between rice cultivar Eikei88223 (vigorous CTF) and Suisei (very weak CTF). However, pyramiding of these QTLs for the application of MAS in practical rice breeding programs have not yet been elucidated. In this study, we examined the effect of pyramiding QTLs for improvement of CTF level using eight possible genotype classes from the 152 F3 population derived from a cross between Eikei88223 and Suisei. Increasing of CTF levels in combinations between qCTF7 and qCTF12 and between qCTF8 and qCTF12 were detected. Furthermore, we compared the haplotype pattern around the QTLs for CTF among the rice cultivars from Hokkaido. These results are useful for improvement of new cultivars with high CTF levels using MAS and identification of genetic resources with the novel QTL(s) for CTF.
Collapse
Affiliation(s)
- Hiroshi Shinada
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
- Present address: Beans Breeding Group, Tokachi Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, Shinsei minami 9-2, Memuro, Hokkaido 082-0071, Japan
- Corresponding author (e-mail: )
| | - Natsuko Iwata
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives,
Naganuma, Hokkaido 069-1317,
Japan
| | - Takashi Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Kenji Fujino
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| |
Collapse
|
23
|
Colmer TD, Armstrong W, Greenway H, Ismail AM, Kirk GJD, Atwell BJ. Physiological Mechanisms of Flooding Tolerance in Rice: Transient Complete Submergence and Prolonged Standing Water. PROGRESS IN BOTANY 2014. [DOI: 10.1007/978-3-642-38797-5_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
24
|
Bin Rahman ANMR, Zhang J. Rayada specialty: the forgotten resource of elite features of rice. RICE (NEW YORK, N.Y.) 2013; 6:41. [PMID: 24359642 PMCID: PMC3903441 DOI: 10.1186/1939-8433-6-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/17/2013] [Indexed: 05/06/2023]
Abstract
Crop domestication and thereafter gradual selection or directional breeding have narrowed the genetic diversity of elite varieties and even promoted gathering of deleterious mutations in their stress response mechanisms, whereas local ecotypes, landraces and wild relatives still growing on native environment and preferences keep the genetic diversities for features like stress tolerance. Rayada is such an exceptional ecotype, variant of typical deepwater rice, completely endemic to certain areas of Madhumati river tracts of Bangladesh and still shares some features of wild rices. Multiple physiological features of Rayadas are distinctly different from typical deepwater rice. Tolerance to prolonged flood, submergence and cold are special features along with strong photoperiod sensitivity and lack of dormancy. Moreover, longer root system and prompt recovery capacity make it as an elite resource of stress tolerance. However, it has long been neglected because of mainly its long life cycle and poor yield. This review examines the specialty of Rayada rice and the potential use of its unique traits.
Collapse
Affiliation(s)
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| |
Collapse
|