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Sakashita Y, Kurashima H, Fukuda M, Hirano H, Lamsal S, Katayama N, Fukao T. Possible Roles of Carbohydrate Management and Cytokinin in the Process of Defoliation-Regrowth Cycles in Rice. Int J Mol Sci 2024; 25:5070. [PMID: 38791109 PMCID: PMC11120658 DOI: 10.3390/ijms25105070] [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: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Defoliation is an inevitable abiotic stress for forage and turf grasses because harvesting, grazing, and mowing are general processes for their production and management. Vegetative regrowth occurs upon defoliation, a crucial trait determining the productivity and persistence of these grasses. However, the information about the molecular regulation of this trait is limited because it is still challenging to perform molecular analyses in forage and turf grasses. Here, we used rice as a model to investigate vegetative regrowth upon defoliation at physiological and molecular levels. This study analyzed stubble and regrown leaves following periodic defoliation using two rice varieties with contrasting regrowth vigor. Vigorous regrowth was associated with maintained chlorophyll content and photosystem II performance; a restricted and promoted mRNA accumulation of sucrose synthase (SUS) I and III subfamilies, respectively; and reduced enzymatic activity of SUS. These results suggest that critical factors affecting vegetative regrowth upon defoliation are de novo carbohydrate synthesis by newly emerged leaves and proper carbohydrate management in leaves and stubble. Physiological and genetic analyses have demonstrated that the reduced sensitivity to and inhibited biosynthesis of cytokinin enhance regrowth vigor. Proper regulation of these metabolic and hormonal pathways identified in this study can lead to the development of new grass varieties with enhanced regrowth vigor following defoliation.
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Affiliation(s)
| | | | | | | | | | | | - Takeshi Fukao
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan
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Takahashi K, Kohno H, Okuda M. Spatial Distribution and Characteristics of Protein Content and Composition in Japonica Rice Grains: Implications for Sake Quality. RICE (NEW YORK, N.Y.) 2024; 17:26. [PMID: 38607500 PMCID: PMC11014839 DOI: 10.1186/s12284-024-00708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024]
Abstract
The quantity and composition of rice proteins play a crucial role in determining taste quality of sake, Japanese rice wine. However, the spatial distribution of proteins within rice grains, especially in endosperm tissue, and the differences between rice varieties remain unclear. Here, we analyzed the crude protein contents and composition ratios of table (Nipponbare and Koshihikari) and genuine sake rice varieties (Yamadanishiki, Gohyakumangoku, Dewasansan, Dewanosato, and Yumenokaori) to elucidate their spatial distribution within the Japonica rice grain endosperm. Seven sake rice varieties were polished over five harvest years using a brewer's rice-polishing machine. We obtained fractions at 90-70% (the outermost endosperm fraction), 70-50%, 50-30%, and 30-0% (the central region of the endosperm fraction). Yamadanishiki and Dewanosato exhibited considerably lower crude protein contents than the other cultivars. After applying SDS-PAGE, the protein composition, comprising glutelin/total protein (G/TP), prolamin/TP (P/TP), and G/P ratios of these fractions was determined. In white rice (at a 90% rice-polishing ratio), the average ratio of the major protein composition was G/TP 41%, P/TP 21%, and G/P ratios of 1.97. Gohyakumangoku and Yamadanishiki had higher G/TP ratio, while Dewanosato had a lower value. Despite having lower crude protein contents, Yamadanishiki and Dewanosato exhibited significantly varying G/TP ratios. The G/TP ratio markedly varied among rice varieties, particularly in the rice grains' central region. The 50-30% fraction had the highest P/TP ratio among all tested rice varieties, suggesting spatial differences in P/TP within rice grains. Koshihikari had the lowest P/TP ratio. In addition, the 50-30% fraction had the lowest G/P ratio among all tested rice varieties, with Gohyakumangoku having the highest G/P ratio. Dewanosato had the lowest G/P value, and this value significantly differed from that of Yamadanishiki in the 30-0% fraction. We found substantial differences in protein composition within distinct spatial regions of rice grains, and larger differences among rice varieties were observed in the rice grain's central region.
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Affiliation(s)
- Kei Takahashi
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan.
| | - Hiromi Kohno
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan
| | - Masaki Okuda
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-0046, Japan
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3
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Zhang C, Wang H, Tian X, Lin X, Han Y, Han Z, Sha H, Liu J, Liu J, Zhang J, Bu Q, Fang J. A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination. Nat Commun 2024; 15:2211. [PMID: 38480722 PMCID: PMC10937917 DOI: 10.1038/s41467-024-46420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.
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Affiliation(s)
- Chuanzhong Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Xinyan Lin
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Yunfei Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Zhongmin Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Hanjing Sha
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jianfeng Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China.
- Yazhouwan National Laboratory, Sanya, 572024, China.
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4
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Wakasa Y, Kawakatsu T, Ishimaru K, Ozawa K. Generation of major glutelin-deficient (GluA, GluB, and GluC) semi-dwarf Koshihikari rice line. PLANT CELL REPORTS 2024; 43:51. [PMID: 38308138 DOI: 10.1007/s00299-023-03131-5] [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: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 02/04/2024]
Abstract
KEY MESSAGE We generated a new Koshihikari rice line with a drastically reduced content of glutelin proteins and higher lodging resistance by using new and conventional plant breeding techniques. Using CRISPR/Cas9-mediated genome editing, we generated mutant rice with drastically decreased contents of major glutelins. A Koshihikari rice mutant line, a123, lacking four glutelins (GluA1, GluA2, GluB4, and GluB5) was used as a host, and another five major glutelin genes (GluA3, GluB1a, GluB1b, GluB2, and GluC) were knocked out through two iterations of Agrobacterium-mediated transformation. Mutant seeds were deficient in the GluA family, GluB family, and GluC, and the line obtained was named GluABC KO. Glutelin content was much lower in GluABC KO than in the existing low-glutelin rice mutant LGC-1. A null segregant of GluABC KO was selected using new-generation sequencing and backcrossing, and the sd-1 allele for the semi-dwarf trait was introduced to increase lodging resistance.
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Affiliation(s)
- Yuhya Wakasa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki, 305-8604, Japan.
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki, 305-8604, Japan
| | - Ken Ishimaru
- Institute of Crop Sciences, NARO, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Kenjirou Ozawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki, 305-8604, Japan
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5
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Dou Z, Yang Q, Guo H, Zhou Y, Xu Q, Gao H. A comparative study of grain quality and physicochemical properties of premium japonica rice from three typical production regions. FRONTIERS IN PLANT SCIENCE 2024; 15:1270388. [PMID: 38332770 PMCID: PMC10850325 DOI: 10.3389/fpls.2024.1270388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
Grain quality indicates rice commodity value. This research compared grain quality and physicochemical properties of premium japonica rice from three production regions, Yangtze River downstream of China (YRDCN), Northeast region of China (NECN) and Japan. Results showed that there were distinct quality and physicochemical characteristics variance among the three groups of japonica rice, while CVs of most quality parameters from low to high was Japan, YRDCN and NECN. YRDCN rice presented obvious lower apparent amylose content (AAC) and ratio of each chain-length sections of amylopectin, and showed higher protein contents especially glutelin and ratio in short and intermediate amylopectin molecules. Among three rice groups, YRDCN rice presented weaker appearance, whereas did not show inferior cooking and eating properties, which was primarily linked to lower AAC. Rice AAC and starch fine structure significantly correlated with pasting parameters, swelling power and solubility, while protein content had close relation with taste analyzer parameters. Results of this study indicated improvement direction for japonica rice of YRDCN, and also provided reference for consumers' rice purchasing selection in accordance with individual taste preference.
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Affiliation(s)
- Zhi Dou
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qian Yang
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Halun Guo
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yicheng Zhou
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiang Xu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Hui Gao
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
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6
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Shi S, Ma Y, Zhao D, Li L, Cao C, Jiang Y. The differences in metabolites, starch structure, and physicochemical properties of rice were related to the decrease in taste quality under high nitrogen fertilizer application. Int J Biol Macromol 2023; 253:126546. [PMID: 37643670 DOI: 10.1016/j.ijbiomac.2023.126546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/30/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Nitrogen fertilizer application is one of the key cultivation practices to improve rice yields. However, the application of high nitrogen fertilizers often leads to a reduction in the stickiness of the rice after cooking, thus reducing the taste quality of rice. Moreover, there are differences in taste quality among rice varieties, and the mechanism has not been studied in depth. In this study, two rice varieties (Meixiangzhan2hao and Exiang2hao) were planted under two nitrogen fertilizer levels. The physicochemical properties and taste quality of the rice were determined after maturity. Our results showed that high nitrogen fertilizer level alters tryptophan metabolism in rice, increasing most amino acid content and protein content in rice. The high content of protein and the higher short-range ordered structure of starch inhibited the gelatinization characteristics of starch and reduced the taste quality of rice. Under high nitrogen fertilizer application, Exiang2hao showed smaller increases in protein content, lower level of amylose and relative crystallinity, and higher content of lipid metabolites. These differences in chemical substances resulted in a less pronounced reduction in the taste quality of Exiang2hao. In this study, the taste quality of different rice varieties under different levels of nitrogen fertilizer application was analyzed, providing new ideas for future improvement of rice taste quality.
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Affiliation(s)
- Shijie Shi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yingying Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Dan Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lina Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cougui Cao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China.
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7
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Pezzotti G, Tsubota Y, Zhu W, Marin E, Masumura T, Kobayashi T, Nakazaki T. Raman Multi-Omic Snapshots of Koshihikari Rice Kernels Reveal Important Molecular Diversities with Potential Benefits in Healthcare. Foods 2023; 12:3771. [PMID: 37893662 PMCID: PMC10606906 DOI: 10.3390/foods12203771] [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: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman "multi-omic snapshots" of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Yusuke Tsubota
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, 2-5-1 Shinmachi, Osaka Prefecture, Hirakata 573-1010, Japan;
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa 619-0218, Japan;
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8
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Sato NK, Tsuji T, Iijima Y, Sekiya N, Watanabe K. Predicting Rice Lodging Risk from the Distribution of Available Nitrogen in Soil Using UAS Images in a Paddy Field. SENSORS (BASEL, SWITZERLAND) 2023; 23:6466. [PMID: 37514768 PMCID: PMC10383411 DOI: 10.3390/s23146466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Rice lodging causes a loss of yield and leads to lower-quality rice. In Japan, Koshihikari is the most popular rice variety, and it has been widely cultivated for many years despite its susceptibility to lodging. Reducing basal fertilizer is recommended when the available nitrogen in soil (SAN) exceeds the optimum level (80-200 mg N kg-1). However, many commercial farmers prefer to simultaneously apply one-shot basal fertilizer at transplant time. This study investigated the relationship between the rice lodging and SAN content by assessing their spatial distributions from unmanned aircraft system (UAS) images in a Koshihikari paddy field where one-shot basal fertilizer was applied. We analyzed the severity of lodging using the canopy height model and spatially clarified a heavily lodged area and a non-lodged area. For the SAN assessment, we selected green and red band pixel digital numbers from multispectral images and developed a SAN estimating equation by regression analysis. The estimated SAN values were rasterized and compiled into a 1 m mesh to create a soil fertility map. The heavily lodged area roughly coincided with the higher SAN area. A negative correlation was observed between the rice inclination angle and the estimated SAN, and rice lodging occurred even within the optimum SAN level. These results show that the amount of one-shot basal fertilizer applied to Koshihikari should be reduced when absorbable nitrogen (SAN + fertilizer nitrogen) exceeds 200 mg N kg-1.
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Affiliation(s)
- Nozomi Kaneko Sato
- Graduate School of Bioresources, Mie University, Tsu 5148507, Japan
- Office SoilCares, Yokkaichi 5100035, Japan
| | | | - Yoshihiro Iijima
- Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Hachioji 1920397, Japan
| | - Nobuhito Sekiya
- Graduate School of Bioresources, Mie University, Tsu 5148507, Japan
| | - Kunio Watanabe
- Graduate School of Bioresources, Mie University, Tsu 5148507, Japan
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9
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Hasan M, Quan NV, Anh LH, Khanh TD, Xuan TD. Salinity Treatments Promote the Accumulations of Momilactones and Phenolic Compounds in Germinated Brown Rice. Foods 2023; 12:2501. [PMID: 37444239 DOI: 10.3390/foods12132501] [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: 05/28/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
This is the first investigation, conducted in a completely randomized design (CRD), to determine the effects of different salinity levels (75 and 150 mM) and germination periods (3, 4, and 5 days) on momilactone and phenolic accumulations in germinated brown rice (GBR) var. Koshihikari. Particularly, the identification of bioactive compounds was confirmed using electrospray ionization-mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) spectroscopy (1H and 13C). Momilactone A (MA) and momilactone B (MB) amounts were determined by ultra-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS), whereas other compounds were quantified by spectrophotometry and high-performance liquid chromatography (HPLC). Accordingly, GBR under B2 treatment (75 mM salinity for 4 days) showed the greatest total phenolic and flavonoid contents (14.50 mg gallic acid and 11.06 mg rutin equivalents, respectively, per g dry weight). GBR treated with B2 also accumulated the highest quantities of MA, MB, ρ-coumaric, ferulic, cinnamic, salicylic acids, and tricin (18.94, 41.00, 93.77, 139.03, 46.05, 596.26, and 107.63 µg/g DW, respectively), which were consistent with the strongest antiradical activities in DPPH and ABTS assays (IC50 = 1.58 and 1.78 mg/mL, respectively). These findings have implications for promoting the value of GBR consumption and rice-based products that benefit human health.
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Affiliation(s)
- Mehedi Hasan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
| | - Nguyen Van Quan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
| | - La Hoang Anh
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
| | - Tran Dang Khanh
- Agricultural Genetics Institute, Pham Van Dong Street, Hanoi 122000, Vietnam
- Center for Agricultural Innovation, Vietnam National University of Agriculture, Hanoi 131000, Vietnam
| | - Tran Dang Xuan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-5-1 Kagamiyama, Higashi-Hiroshima 739-8529, Japan
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10
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Takai T, Taniguchi Y, Takahashi M, Nagasaki H, Yamamoto E, Hirose S, Hara N, Akashi H, Ito J, Arai-Sanoh Y, Hori K, Fukuoka S, Sakai H, Tokida T, Usui Y, Nakamura H, Kawamura K, Asai H, Ishizaki T, Maruyama K, Mochida K, Kobayashi N, Kondo M, Tsuji H, Tsujimoto Y, Hasegawa T, Uga Y. MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO 2 levels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:729-742. [PMID: 36974032 DOI: 10.1111/tpj.16143] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/06/2023] [Indexed: 05/27/2023]
Abstract
Improving crop yield potential through an enhanced response to rising atmospheric CO2 levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO2 levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO2 enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO2 levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO2 levels.
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Affiliation(s)
- Toshiyuki Takai
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Yojiro Taniguchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Megumu Takahashi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki, 305-8519, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Eiji Yamamoto
- Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Sakiko Hirose
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Naho Hara
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroko Akashi
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Jun Ito
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Yumiko Arai-Sanoh
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Kiyosumi Hori
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Hidemitsu Sakai
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Takeshi Tokida
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yasuhiro Usui
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, 305-8666, Japan
| | | | - Kensuke Kawamura
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Hidetoshi Asai
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Takuma Ishizaki
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Kyonoshin Maruyama
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Keiichi Mochida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Information and Data Sciences, Nagasaki University, Nagasaki, Nagasaki, 852-8521, Japan
| | - Nobuya Kobayashi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
| | - Motohiko Kondo
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yasuhiro Tsujimoto
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Toshihiro Hasegawa
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8518, Japan
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11
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Yamashita K, Kato N, Sakakibara K, Seguchi A, Kobayashi A, Miyagawa S, Uchimura T. Characterization of Cooked Nonglutinous Rice Cultivars Based on Flavor Volatiles and Their Change during Storage. ACS OMEGA 2023; 8:14823-14829. [PMID: 37125109 PMCID: PMC10134245 DOI: 10.1021/acsomega.3c01276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Characterizing fleshly cooked rice cultivars according to the volatile aroma compounds helps consumers select a favorite and is useful for the development of new cultivars that will have a pleasant aroma. In the present study, six Japanese nonglutinous cultivars, which were freshly harvested in 2021, were characterized based on their flavor volatiles after being freshly cooked. In order to extract the volatile compounds just after cooking, the vaporized compounds were extracted for 5 min using a solid-phase microextraction (SPME) fiber and were measured via gas chromatography/mass spectrometry (GC/MS). Multiple comparison tests statistically detected four volatile aroma compounds: 2-pentylfuran, nonanal, 4-vinylphenol, and indole. From among the six rice cultivars tested, the proportions of the latter two compounds showed significant differences, and in principal component analysis of cooked rice, these two best characterized freshly harvested and freshly cooked Japanese nonglutinous rice cultivars; indole was indicative of Nipponbare, and 4-vinylphenol was indicative of Koshihikari and Ichihomare. In the present study, changes in the volatile aroma compounds of the freshly cooked rice cultivars were found to slightly differentiate according to storage times: 2-pentylfuran tended to increase, nonanal first increased and then decreased, and 4-vinylphenol and indole either remained almost unchanged or were only slightly decreased during storage. Therefore, establishing the differences in rice cultivar types revealed that the characteristics of the flavor volatiles of freshly cooked rice after long-term storage significantly depend on how the rice cultivar is stored.
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Affiliation(s)
- Keishi Yamashita
- Department
of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Nanako Kato
- Department
of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Kento Sakakibara
- Department
of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Aki Seguchi
- Department
of Materials Science and Biotechnology, School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Asako Kobayashi
- Fukui
Agricultural Experiment Station, 52-21 Ryomachi, Fukui 918-8215, Japan
| | - Shinobu Miyagawa
- Department
of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Tomohiro Uchimura
- Department
of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
- . Phone: +81-776-27-8610
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12
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Fekih R, Ishimaru Y, Okada S, Maeda M, Miyagi R, Obana T, Suzuki K, Inamori M, Enoki H, Yamasaki M. High-Density Linkage Maps from Japanese Rice japonica Recombinant Inbred Lines Using Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040929. [PMID: 36840276 PMCID: PMC9959243 DOI: 10.3390/plants12040929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 05/14/2023]
Abstract
The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.
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Affiliation(s)
- Rym Fekih
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai 675-2103, Japan
- Correspondence: (R.F.); (M.Y.)
| | - Yohei Ishimaru
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai 675-2103, Japan
| | - Satoshi Okada
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai 675-2103, Japan
- Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan
| | - Michihiro Maeda
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai 675-2103, Japan
| | | | | | | | | | | | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai 675-2103, Japan
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Correspondence: (R.F.); (M.Y.)
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13
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Cheng B, Shi S, Pan K, Nie J, Xing J, Wang X, Li L, Tang J, Liu J, Cao C, Jiang Y. Untargeted metabolomics based on UHPLC-Q-Exactive-MS reveals metabolite and taste quality differences between Koshihikari rice from China and Japan. Int J Gastron Food Sci 2023. [DOI: 10.1016/j.ijgfs.2023.100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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14
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Chigira K, Yamasaki M, Adachi S, Nagano AJ, Ookawa T. Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi. RICE (NEW YORK, N.Y.) 2023; 16:4. [PMID: 36705856 PMCID: PMC9883377 DOI: 10.1186/s12284-023-00621-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F2 population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.
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Affiliation(s)
- Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-Ku, Niigata City, Niigata 950-2181 Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017 Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
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15
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Jin SK, Xu LN, Yang QQ, Zhang MQ, Wang SL, Wang RA, Tao T, Hong LM, Guo QQ, Jia SW, Song T, Leng YJ, Cai XL, Gao JP. High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing. FRONTIERS IN PLANT SCIENCE 2023; 13:1050882. [PMID: 36714703 PMCID: PMC9878556 DOI: 10.3389/fpls.2022.1050882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits-the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness-of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%-61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.
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Affiliation(s)
- Su-Kui Jin
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Na Xu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qing-Qing Yang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Ming-Qiu Zhang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shui-Lian Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruo-An Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Tao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Lian-Min Hong
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qian-Qian Guo
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shu-Wen Jia
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Jia Leng
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiu-Ling Cai
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ji-Ping Gao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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16
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Lee YK, Lee Y, Jang S, Lee T, Woo MO, Seo J, Kim B, Koh HJ. Sequencing and de novo assembly of the Koshihikari genome and identification of the genomic region related to the eating quality of cooked rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:65. [PMID: 37309489 PMCID: PMC10248671 DOI: 10.1007/s11032-022-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/02/2022] [Indexed: 06/14/2023]
Abstract
The japonica rice (Oryza sativa L.) cultivar Koshihikari is considered an important breeding material with good eating quality (EQ). To effectively utilize Koshihikari in molecular breeding programs, determining its whole genome sequence including cultivar-specific segment is crucial. Here, the Koshihikari genome was sequenced using Nanopore and Illumina platforms, and de novo assembly was performed. A highly contiguous Koshihikari genome sequence was compared with Nipponbare, the reference genome of japonica. Genome-wide synteny was observed, as expected, without large structural variations. However, several gaps in alignment were detected on chromosomes 3, 4, 9, and 11. It was notable that previously identified EQ-related QTLs were found in these gaps. Moreover, sequence variations were identified in chromosome 11 at a region flanking the P5 marker, one of the significant markers of good EQ. The Koshihikari-specific P5 region was found to be transmitted through the lineage. High EQ cultivars derived from Koshihikari possessed P5 sequences; on the other hand, Koshihikari-derived low EQ cultivars didn't contain the P5 region, which implies that the P5 genomic region affects the EQ of Koshihikari progenies. The EQ of near-isogenic lines (NILs) of Samnam (a low EQ cultivar) genetic background harboring the P5 segment was improved compared to that of Samnam in Toyo taste value. The structure of the Koshihikari-specific P5 genomic region associated with good EQ was analyzed, which is expected to facilitate the molecular breeding of rice cultivars with superior EQ. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01335-3.
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Affiliation(s)
- Yoon Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Su Jang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc, Seoul, 08511 Republic of Korea
| | - Mi-Ok Woo
- Science & Technology Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong, South Korea
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, 55365 Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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17
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Alam MS, Maina AW, Feng Y, Wu LB, Frei M. Interactive effects of tropospheric ozone and blast disease (Magnaporthe oryzae) on different rice genotypes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:48893-48907. [PMID: 35201578 PMCID: PMC9252976 DOI: 10.1007/s11356-022-19282-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/14/2022] [Indexed: 05/06/2023]
Abstract
Rising tropospheric ozone concentrations can cause rice yield losses and necessitate the breeding of ozone-tolerant rice varieties. However, ozone tolerance should not compromise the resistance to important biotic stresses such as the rice blast disease. Therefore, we investigated the interactive effects of ozone and rice blast disease on nine different rice varieties in an experiment testing an ozone treatment, blast inoculation, and their interaction. Plants were exposed to an ozone concentration of 100 ppb for 7 h per day or ambient air throughout the growth period. Half of the plants were simultaneously infected with rice blast inoculum. Grain yield was significantly reduced in the blast treatment (17%) and ozone treatment (37%), while the combination of both stresses did not further decrease grain yields compared to ozone alone. Similar trends occurred for physiological traits such as vegetation indices, normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), Lichtenthaler index 2 (Lic2), and anthocyanin reflectance index 1 (ARI1), as well as stomatal conductance and lipid peroxidation. Ozone exposure mitigated the formation of visible blast symptoms, while blast inoculation did not significantly affect visible ozone symptoms. Although different genotypes showed contrasting responses to the two types of stresses, no systematic pattern was observed regarding synergies or trade-offs under the two types of stresses. Therefore, we conclude that despite the similarities in physiological stress responses to ozone and blast, the tolerance to these stresses does not appear to be genetically linked in rice.
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Affiliation(s)
- Muhammad Shahedul Alam
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, 35390, Giessen, Germany
| | | | - Yanru Feng
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, 35390, Giessen, Germany
- Institute for Crop Science and Resource Conservation (INRES), Crop Science, University of Bonn, 53115, Bonn, Germany
| | - Lin-Bo Wu
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, 35390, Giessen, Germany
| | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding, Justus-Liebig University Giessen, 35390, Giessen, Germany.
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18
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Teramoto S, Yamasaki M, Uga Y. Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies. BREEDING SCIENCE 2022; 72:222-231. [PMID: 36408322 PMCID: PMC9653191 DOI: 10.1270/jsbbs.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/10/2022] [Indexed: 06/16/2023]
Abstract
To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo 675-2103, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
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Yang X, Gu X, Ding J, Yao L, Gao X, Zhang M, Meng Q, Wei S, Fu J. Gene expression analysis of resistant and susceptible rice cultivars to sheath blight after inoculation with Rhizoctonia solani. BMC Genomics 2022; 23:278. [PMID: 35392815 PMCID: PMC8991730 DOI: 10.1186/s12864-022-08524-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rice sheath blight, caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris), is one of the most severe diseases in rice (Oryza sativa L.) worldwide. Studies on resistance genes and resistance mechanisms of rice sheath blight have mainly focused on indica rice. Rice sheath blight is a growing threat to rice production with the increasing planting area of japonica rice in Northeast China, and it is therefore essential to explore the mechanism of sheath blight resistance in this rice subspecies. RESULTS In this study, RNA-seq technology was used to analyse the gene expression changes of leaf sheath at 12, 24, 36, 48, and 72 h after inoculation of the resistant cultivar 'Shennong 9819' and susceptible cultivar 'Koshihikari' with R. solani. In the early stage of R. solani infection of rice leaf sheaths, the number of differentially expressed genes (DEGs) in the inoculated leaf sheaths of resistant and susceptible cultivars showed different regularity. After inoculation, the number of DEGs in the resistant cultivar fluctuated, while the number of DEGs in the susceptible cultivar increased first and then decreased. In addition, the number of DEGs in the susceptible cultivar was always higher than that in the resistant cultivar. After inoculation with R. solani, the overall transcriptome changes corresponding to multiple biological processes, molecular functions, and cell components were observed in both resistant and susceptible cultivars. These included metabolic process, stimulus response, biological regulation, catalytic activity, binding and membrane, and they were differentially regulated. The phenylalanine metabolic pathway; tropane, piperidine, and pyridine alkaloid biosynthesis pathways; and plant hormone signal transduction were significantly enriched in the early stage of inoculation of the resistant cultivar Shennong 9819, but not in the susceptible cultivar Koshihikari. This indicates that the response of the resistant cultivar Shennong 9819 to pathogen stress was faster than that of the susceptible cultivar. The expression of plant defense response marker PR1b gene, transcription factor OsWRKY30 and OsPAL1 and OsPAL6 genes that induce plant resistance were upregulated in the resistant cultivar. These data suggest that in the early stage of rice infection by R. solani, there is a pathogen-induced defence system in resistant rice cultivars, involving the expression of PR genes, key transcription factors, PAL genes, and the enrichment of defence-related pathways. CONCLUSION The transcriptome data revealed the molecular and biochemical differences between resistant and susceptible cultivars of rice after inoculation with R. solani, indicating that resistant cultivars have an immune response mechanism in the early stage of pathogen infection. Disease resistance is related to the overexpression of PR genes, key transcriptome factors, and PAL genes, which are potential targets for crop improvement.
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Affiliation(s)
- Xiaohe Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.,Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Xin Gu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Qingying Meng
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, Heilongjiang, China
| | - Songhong Wei
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.
| | - Junfan Fu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110161, Liaoning, China.
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20
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Shah S, Tsuneyoshi H, Ichitani K, Taura S. QTL Analysis Revealed One Major Genetic Factor Inhibiting Lesion Elongation by Bacterial Blight (Xanthomonas oryzae pv. oryzae) from a japonica Cultivar Koshihikari in Rice. PLANTS 2022; 11:plants11070867. [PMID: 35406847 PMCID: PMC9003242 DOI: 10.3390/plants11070867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/19/2022]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen that has ravaged the rice industry as the causal agent of bacterial blight (BB) diseases in rice. Koshihikari (KO), an elite japonica cultivar, and ARC7013 (AR), an indica cultivar, are both susceptible to Xoo. Their phenotypic characteristics reveal that KO has shorter lesion length than that of AR. The F2 population from KO × AR results in continuous distribution of lesion length by inoculation of an Xoo race (T7147). Consequently, quantitative trait loci (QTL) mapping of the F2 population is conducted, covering 12 chromosomes with 107 simple sequence repeat (SSR) and insertion/deletion (InDel) genetic markers. Three QTLs are identified on chromosomes 2, 5, and 10. Of them, qXAR5 has the strongest resistance variance effect of 20.5%, whereas qXAR2 and qXAR10 have minor QTL effects on resistance variance, with 3.9% and 2.3%, respectively, for a total resistance variance of 26.7%. The QTLs we examine for this study differ from the loci of BB resistance genes from earlier studies. Our results can help to facilitate understanding of genetic and morphological fundamentals for use in rice breeding programs that are more durable against evolving Xoo pathogens and uncertain climatic temperature.
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Affiliation(s)
- Shameel Shah
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
| | - Hiroaki Tsuneyoshi
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan;
| | - Katsuyuki Ichitani
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan;
- The United Graduate School of Agriculture Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Satoru Taura
- Graduate School of Agriculture Science Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; (S.S.); (K.I.)
- Division of Gene Research, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: ; Tel.: +81-0992853590
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21
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Genome sequencing and genetic analysis of recombinant inbred lines reveals important agronomic traits related loci under different nitrogen fertilization. Mol Biol Rep 2022; 49:4545-4553. [PMID: 35262821 DOI: 10.1007/s11033-022-07298-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND The intensive application of inorganic nitrogen has contributed to increasing the crop yield with the risk of environmental damage. High nitrogen fertilizer requirements are a long-standing problem in japonica cultivation. MATERIALS AND METHODS In the present study, 200 recombinant inbred lines derived from two representative japonica varieties of Japanese and Chinese varieties, Akitakomachi and Liaogeng5, respectively, were planted under different nitrogen fertilization conditions. The relationships among nitrogen fertilization, genetic background, and important agronomic traits were surveyed through the phenotypic investigation and next-generation sequencing. RESULTS The results showed that the yield components of Akitakomachi dramatically decreased along with the nitrogen reduction, whereas those of Liaogeng5 exhibited a slight decrease. The appearance quality and milling quality of both Akitakomachi and Liaogeng5 were improved, especially Liaogeng5. The recombinant inbred lines (RILs) showed similar trends to their parental lines. The QTLs analysis of important agronomic traits detected 17 loci, one QTL clustering located on chromosome 9 that corresponded to the plant height, panicle angle, grain number per panicle, harvest index, and taste value was identified to be synonymous with a previously reported gene, DEP1. The function of DEP1 was verified by a knock-out mutant constructed by CRISPR/Cas9. The dep1 mutant exhibited improved grain quality without severe yield penalty under nitrogen reduction conditions. CONCLUSION The results of the present study provide useful information for the improvement of food security by enhancing nitrogen use efficiency.
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Hori K, Okunishi T, Nakamura K, Iijima K, Hagimoto M, Hayakawa K, Shu K, Ikka T, Yamashita H, Yamasaki M, Takeuchi Y, Koyama S, Tsujii Y, Kayano T, Ishii T, Kumamaru T, Kawagoe Y, Yamamoto T. Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. RICE (NEW YORK, N.Y.) 2022; 15:13. [PMID: 35247122 PMCID: PMC8898210 DOI: 10.1186/s12284-022-00560-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 05/18/2023]
Abstract
Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.
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Affiliation(s)
- Kiyosumi Hori
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan.
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Tomoya Okunishi
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Kenji Nakamura
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Ken Iijima
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Masahiro Hagimoto
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Katsuyuki Hayakawa
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc, Tsukuba, 300-2611, Japan
| | - Koka Shu
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Takashi Ikka
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroto Yamashita
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Kobe University, Kasai, 675-2103, Japan
| | - Yoshinobu Takeuchi
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Shota Koyama
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Yoshimasa Tsujii
- Department of Agricultural Chemistry, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Toshiaki Kayano
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Takuro Ishii
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | | | - Yasushi Kawagoe
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Toshio Yamamoto
- National Agricultural and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
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23
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Physicochemical properties of novel artificial rice produced from sago, arrowroot, and mung bean flour using hot extrusion technology. Heliyon 2022; 8:e08969. [PMID: 35243089 PMCID: PMC8861402 DOI: 10.1016/j.heliyon.2022.e08969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/22/2021] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
Due to high rice consumption, food insecurity can negatively impact health; hence, food diversification is considered an appropriate solution for achieving national food security. Artificial rice production using local natural resources will support food sustainability in Indonesia. Sago, arrowroot tuber, and mung bean flours were the main ingredients for producing artificial rice using the hot extrusion method. The effects of composite flour composition and extrusion temperatures on the nutritional value (carbohydrate, protein, fat, and fiber), morphological structure (scanning electron microscopy analysis), thermal stability (differential scanning calorimetry analysis), and acceptability of artificial rice were investigated in this study. The results showed that the best composition was obtained when using a combination of 50% (w/w) sago flour, 30% (w/w) arrowroot tuber flour, and 20% (w/w) mung bean flour. The results of chemical analysis showed that the best artificial rice in this study contained 11.18% water content, 80.27% carbohydrates, 5.14% protein, 0.46% fat, and 5.14% crude fiber. The product contained sufficient fiber and carbohydrate content to be an appropriate staple food. The best extrusion temperature was 85 °C. Moreover, the differential scanning calorimetry profiles showed that artificial rice began undergoing physical changes at approximately 100 °C. Importantly, the color, texture, aroma, and taste of the cooked artificial rice were accepted by consumers. Sago, arrowroot, and mung bean flour are the suitable material for artificial rice. Extrusion temperature influences the artificial nutritional rice significantly. The consumers reported that artificial rice product has been accepted as rice substitution.
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Kiriyama H, Matsuda H, Kamiji Y, Morita S. Nitrogen stock and farmer behaviour under rice policy change in Japan. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113438. [PMID: 34481376 DOI: 10.1016/j.jenvman.2021.113438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/08/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Mitigating the environmental impact of nitrogen (N) derived from agricultural production is a significant issue in our progression towards a sustainable society. This study aims to estimate the N stock (i.e., as the accumulation of N input into farmland that is neither taken up by the crops nor discharged into the environment, but rather remains in the soil) related to rice production in Japan and to identify the relationship between the economic behaviour of rice farmers and N stock. The results indicate a persistent reduction in N stock since the early 1990s, caused mainly by the change in N input by a change in government policy away from production subsidies to more extensive use of market mechanisms. It seems clear that production subsidy policies provide little incentive for farmers to reduce their N input; however, even if the introduction of market mechanisms, farmers may not properly evaluate the contribution of N stock to agricultural production. Consequently, it may be difficult to achieve the optimal level of N stock from an environmental impact perspective. To achieve the optimal N stock, the relationship between farmer behaviour and N stock needs to be better understood.
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Affiliation(s)
- Hiroki Kiriyama
- Tokyo University of Agriculture, Graduate School of Agriculture, 1737 Funako, Atugi-shi, Kanagawa, 243-0034, Japan
| | - Hirotaka Matsuda
- Tokyo University of Agriculture, Department of Agricultural Innovation for Sustainability Faculty of Agriculture, 1737 Funako, Atugi-shi, Kanagawa, 243-0034, Japan.
| | - Yoshiaki Kamiji
- Tokyo University of Agriculture, Graduate School of Agriculture, 1737 Funako, Atugi-shi, Kanagawa, 243-0034, Japan
| | - Shigenori Morita
- Tokyo University of Agriculture, Department of Agricultural Innovation for Sustainability Faculty of Agriculture, 1737 Funako, Atugi-shi, Kanagawa, 243-0034, Japan
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25
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Pezzotti G, Zhu W, Hashimoto Y, Marin E, Masumura T, Sato YI, Nakazaki T. Raman Fingerprints of Rice Nutritional Quality: A Comparison between Japanese Koshihikari and Internationally Renowned Cultivars. Foods 2021; 10:foods10122936. [PMID: 34945487 PMCID: PMC8701134 DOI: 10.3390/foods10122936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Raman spectroscopy was applied to characterize at the molecular scale the nutritional quality of the Japanese Koshihikari rice cultivar in comparison with other renowned rice cultivars including Carnaroli from Italy, Calrose from the USA, Jasmine rice from Thailand, and Basmati from both India and Pakistan. For comparison, two glutinous (mochigome) cultivars were also investigated. Calibrated and validated Raman analytical algorithms allowed quantitative determinations of: (i) amylopectin and amylose concentrations, (ii) fractions of aromatic amino acids, and (iii) protein content and secondary structure. The Raman assessments non-destructively linked the molecular composition of grains to key nutritional parameters and revealed a complex intertwine of chemical properties. The Koshihikari cultivar was rich in proteins (but with low statistical relevance as compared to other investigated cultivars) and aromatic amino acids. However, it also induced a clearly higher glycemic impact as compared to long-grain cultivars from Asian countries. Complementary to genomics and wet-chemistry analyses, Raman spectroscopy makes non-destructively available factual and data-driven information on rice nutritional characteristics, thus providing customers, dietitian nutritionists, and producers with a solid science-consolidated platform.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita 565-0854, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Correspondence:
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
| | - Yuuki Hashimoto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Yo-Ichiro Sato
- Research Center for Japanese Food Culture, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa 619-0218, Japan;
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Lee C, Chung CT, Hong WJ, Lee YS, Lee JH, Koh HJ, Jung KH. Transcriptional Changes in the Developing Rice Seeds Under Salt Stress Suggest Targets for Manipulating Seed Quality. FRONTIERS IN PLANT SCIENCE 2021; 12:748273. [PMID: 34819939 PMCID: PMC8606889 DOI: 10.3389/fpls.2021.748273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Global sea-level rise, the effect of climate change, poses a serious threat to rice production owing to saltwater intrusion and the accompanying increase in salt concentration. The reclaimed lands, comprising 22.1% of rice production in Korea, now face the crisis of global sea-level rise and a continuous increase in salt concentration. Here, we investigated the relationship between the decrease in seed quality and the transcriptional changes that occur in the developing rice seeds under salt stress. Compared to cultivation on normal land, the japonica rice cultivar, Samgwang, grown on reclaimed land showed a greatly increased accumulation of minerals, including sodium, magnesium, potassium, and sulfur, in seeds and a reduced yield, delayed heading, decreased thousand grain weight, and decreased palatability and amylose content. Samgwang showed phenotypical sensitivity to salt stress in the developing seeds. Using RNA-seq technology, we therefore carried out a comparative transcriptome analysis of the developing seeds grown on reclaimed and normal lands. In the biological process category, gene ontology enrichment analysis revealed that the upregulated genes were closely associated with the metabolism of biomolecules, including amino acids, carboxylic acid, lignin, trehalose, polysaccharide, and chitin, and to stress responses. MapMan analysis revealed the involvement of upregulated genes in the biosynthetic pathways of abscisic acid and melatonin and the relationship of trehalose, raffinose, and maltose with osmotic stress. Interestingly, many seed storage protein genes encoding glutelins and prolamins were upregulated in the developing seeds under salt stress, indicating the negative effect of the increase of storage proteins on palatability. Transcription factors upregulated in the developing seeds under salt stress included, in particular, bHLH, MYB, zinc finger, and heat shock factor, which could act as potential targets for the manipulation of seed quality under salt stress. Our study aims to develop a useful reference for elucidating the relationship between seed response mechanisms and decreased seed quality under salt stress, providing potential strategies for the improvement of seed quality under salt stress.
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Affiliation(s)
- Choonseok Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Chong-Tae Chung
- Crop Research Division, Chungcheongnam-do Agricultural Research and Extension Services, Yesan, South Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Yang-Seok Lee
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jong-Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Miryang, South Korea
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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27
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Chidambaram SB, Essa MM, Rathipriya AG, Bishir M, Ray B, Mahalakshmi AM, Tousif AH, Sakharkar MK, Kashyap RS, Friedland RP, Monaghan TM. Gut dysbiosis, defective autophagy and altered immune responses in neurodegenerative diseases: Tales of a vicious cycle. Pharmacol Ther 2021; 231:107988. [PMID: 34536490 DOI: 10.1016/j.pharmthera.2021.107988] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/16/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023]
Abstract
The human microbiota comprises trillions of symbiotic microorganisms and is involved in regulating gastrointestinal (GI), immune, nervous system and metabolic homeostasis. Recent observations suggest a bidirectional communication between the gut microbiota and the brain via immune, circulatory and neural pathways, termed the Gut-Brain Axis (GBA). Alterations in gut microbiota composition, such as seen with an increased number of pathobionts and a decreased number of symbionts, termed gut dysbiosis or microbial intestinal dysbiosis, plays a prominent role in the pathogenesis of central nervous system (CNS)-related disorders. Clinical reports confirm that GI symptoms often precede neurological symptoms several years before the development of neurodegenerative diseases (NDDs). Pathologically, gut dysbiosis disrupts the integrity of the intestinal barrier leading to ingress of pathobionts and toxic metabolites into the systemic circulation causing GBA dysregulation. Subsequently, chronic neuroinflammation via dysregulated immune activation triggers the accumulation of neurotoxic misfolded proteins in and around CNS cells resulting in neuronal death. Emerging evidence links gut dysbiosis to the aggravation and/or spread of proteinopathies from the peripheral nervous system to the CNS and defective autophagy-mediated proteinopathies. This review summarizes the current understanding of the role of gut microbiota in NDDs, and highlights a vicious cycle of gut dysbiosis, immune-mediated chronic neuroinflammation, impaired autophagy and proteinopathies, which contributes to the development of neurodegeneration in Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis, amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We also discuss novel therapeutic strategies targeting the modulation of gut dysbiosis through prebiotics, probiotics, synbiotics or dietary interventions, and faecal microbial transplantation (FMT) in the management of NDDs.
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Affiliation(s)
- Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, KA, India; Centre for Experimental Pharmacology and Toxicology (CPT), JSS Academy of Higher Education & Research, Mysuru 570015, KA, India.
| | - Musthafa Mohamed Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat 123, Oman; Ageing and Dementia Research Group, Sultan Qaboos University, Muscat 123, Oman; Biomedical Sciences Department, University of Pacific, Sacramento, CA, USA.
| | - A G Rathipriya
- Food and Brain Research Foundation, Chennai 600 094, Tamil Nadu, India
| | - Muhammed Bishir
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, KA, India
| | - Bipul Ray
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, KA, India; Centre for Experimental Pharmacology and Toxicology (CPT), JSS Academy of Higher Education & Research, Mysuru 570015, KA, India
| | - Arehally M Mahalakshmi
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, KA, India
| | - A H Tousif
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, KA, India; Centre for Experimental Pharmacology and Toxicology (CPT), JSS Academy of Higher Education & Research, Mysuru 570015, KA, India
| | - Meena K Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
| | - Rajpal Singh Kashyap
- Research Centre, Dr G. M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Robert P Friedland
- Department of Neurology, University of Louisville, Louisville, KY 40292, USA
| | - Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham NG7 2UH, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK.
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Matsumoto K, Ota Y, Yamakawa T, Ohno T, Seta S, Honda Y, Mizobuchi R, Sato H. Breeding and characterization of the world's first practical rice variety with resistance to brown spot ( Bipolaris oryzae) bred using marker-assisted selection. BREEDING SCIENCE 2021; 71:474-483. [PMID: 34912174 PMCID: PMC8661487 DOI: 10.1270/jsbbs.21023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/23/2021] [Indexed: 06/14/2023]
Abstract
Brown spot (BS) caused by Bipolaris oryzae is a serious disease of rice and decreases grain yield. Breeding for BS resistance is an economical solution but has not hitherto been achieved. To develop a practical BS-resistant variety, we introduced a chromosomal segment including a quantitative trait locus (QTL) for BS resistance, qBSfR11, derived from the BS-resistant local resource 'Tadukan', into the genetic background of the high-yielding but susceptible 'Mienoyume'. Resistance is controlled by a single recessive gene in a 1.3-Mbp region. We named this gene bsr1 (brown spot resistance 1). The near-isogenic line bsr1-NIL had a greater yield with larger grain width than Mienoyume but similar other agronomic traits in fields where BS was mild; it had a significantly lower BS disease score and a 28.8% higher yield in fields where BS was more severe, and it showed resistance to multiple isolates of BS fungus. It showed stable resistance to BS and had excellent agricultural traits in the presence of BS. We developed the bsr1-NIL with resistance to BS and applied it for variety registration to Ministry of Agriculture, Forestry and Fisheries in Japan as 'Mienoyume BSL'. This is the first report for the BS resistant rice variety bred using marker-assisted selection.
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Affiliation(s)
- Kengo Matsumoto
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Yuya Ota
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Tomohiro Yamakawa
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Teppei Ohno
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
- Mie Prefecture Kuwana Agricultural Extension Center, 5-71 Chuo, Kuwana, Mie 511-8567, Japan
| | - Satomi Seta
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Yuto Honda
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Ritsuko Mizobuchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Sato
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Ministry of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
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29
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Ota Y, Matsumoto K, Nakayama Y, Yamakawa T, Ohno T, Mizobuchi R, Sato H. QTL analysis for brown spot resistance in American rice cultivar 'Dawn'. BREEDING SCIENCE 2021; 71:491-495. [PMID: 34912176 PMCID: PMC8661489 DOI: 10.1270/jsbbs.21015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/18/2021] [Indexed: 06/14/2023]
Abstract
Rice brown spot (BS), caused by Bipolaris oryzae, causes yield loss and deterioration of grain quality. Using single-nucleotide polymorphism (SNP) markers, we conducted quantitative trait locus (QTL) analysis of BS resistance in backcross inbred lines (BILs) from a cross between an American rice cultivar, 'Dawn' (resistant), and 'Koshihikari' (susceptible). Four QTLs for BS resistance were detected in a three-year field evaluation, and 'Dawn' contributed the resistance alleles at all QTLs. The QTL with the greatest effect, qBSR6-kd, explained 15.1% to 20.3% of the total phenotypic variation. Although disease score and days to heading (DTH) were negatively correlated in all three years, qBSR6-kd was located near a QTL for DTH at which the 'Dawn' allele promoted heading. Another BS resistance QTL (qBSR3.1-kd) was unlinked to the QTLs for DTH. Therefore, these two QTLs are likely to be useful for breeding BS-resistant varieties without delaying heading. The other two BS resistance QTLs (qBSR3.2-kd and qBSR7-kd) were located near DTH QTLs at which the 'Dawn' alleles delayed heading. The QTLs reported here will be good candidates for developing BS-resistant cultivars.
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Affiliation(s)
- Yuya Ota
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Kengo Matsumoto
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Yukinori Nakayama
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Tomohiro Yamakawa
- Mie Prefecture Agricultural Research Institute, 530 Ureshinokawakita, Matsusaka, Mie 515-2316, Japan
| | - Teppei Ohno
- Kuwana Agricultural Forestry Fisheries Office, Kuwana, Mie 511-8567, Japan
| | - Ritsuko Mizobuchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Sato
- Ministry of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan
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Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons. Sci Rep 2021; 11:15780. [PMID: 34349177 PMCID: PMC8339031 DOI: 10.1038/s41598-021-95268-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.
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31
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Pezzotti G, Zhu W, Chikaguchi H, Marin E, Boschetto F, Masumura T, Sato YI, Nakazaki T. Raman Molecular Fingerprints of Rice Nutritional Quality and the Concept of Raman Barcode. Front Nutr 2021; 8:663569. [PMID: 34249986 PMCID: PMC8260989 DOI: 10.3389/fnut.2021.663569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
The nutritional quality of rice is contingent on a wide spectrum of biochemical characteristics, which essentially depend on rice genome, but are also greatly affected by growing/environmental conditions and aging during storage. The genetic basis and related identification of genes have widely been studied and rationally linked to accumulation of micronutrients in grains. However, genetic classifications cannot catch quality fluctuations arising from interannual, environmental, and storage conditions. Here, we propose a quantitative spectroscopic approach to analyze rice nutritional quality based on Raman spectroscopy, and disclose analytical algorithms for the determination of: (i) amylopectin and amylose concentrations, (ii) aromatic amino acids, (iii) protein content and structure, and (iv) chemical residues. The proposed Raman algorithms directly link to the molecular composition of grains and allow fast/non-destructive determination of key nutritional parameters with minimal sample preparation. Building upon spectroscopic information at the molecular level, we newly propose to represent the nutritional quality of labeled rice products with a barcode specially tailored on the Raman spectrum. The Raman barcode, which can be stored in databases promptly consultable with barcode scanners, could be linked to diet applications (apps) to enable a rapid, factual, and unequivocal product identification based on direct molecular screening.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Orthopedic Surgery, Tokyo Medical University, Tokyo, Japan.,The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan.,Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Haruna Chikaguchi
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, Kyoto, Japan
| | - Yo-Ichiro Sato
- Research Center for Japanese Food Culture, Kyoto Prefectural University, Kyoto, Japan
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
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Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B, Wang Y, Qian Y, Fan S, Li W, Wang J, He M, Yin J, Li T, Jiang N, Chen X, Liang C, Li S. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 2021; 184:3542-3558.e16. [PMID: 34051138 DOI: 10.1016/j.cell.2021.04.046] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2021] [Accepted: 04/24/2021] [Indexed: 12/30/2022]
Abstract
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
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Affiliation(s)
- Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weilan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bingtian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yangwen Qian
- Biogle Genome Editing Center, Changzhou, Jiangsu, China
| | - Shijun Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Kim MS, Yang JY, Yu JK, Lee Y, Park YJ, Kang KK, Cho YG. Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers. PLANTS 2021; 10:plants10040804. [PMID: 33921910 PMCID: PMC8073074 DOI: 10.3390/plants10040804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/03/2022]
Abstract
The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.
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Affiliation(s)
- Me-Sun Kim
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Young Yang
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Kyung Yu
- Syngenta Crop Protection LLC, Seeds Research, 9 Davis Dr. Research Triangle Park, Durham, NC 27709, USA;
| | - Yi Lee
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Yong-Jin Park
- College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea
- Correspondence: (K.-K.K.); (Y.-G.C.)
| | - Yong-Gu Cho
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
- Correspondence: (K.-K.K.); (Y.-G.C.)
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Fujino K, Kawahara Y, Koyanagi KO, Shirasawa K. Translation of continuous artificial selection on phenotype into genotype during rice breeding programs. BREEDING SCIENCE 2021; 71:125-133. [PMID: 34377060 PMCID: PMC8329892 DOI: 10.1270/jsbbs.20089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/25/2020] [Indexed: 06/13/2023]
Abstract
Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Yoshihiro Kawahara
- Institute of Crop Science, National Agricultural Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- Advanced Analysis Center, National Agricultural Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Kanako O. Koyanagi
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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35
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Nakano H, Iwasawa N, Takai T, Arai‐Sanoh Y, Kondo M. Grain weight and the concentrations of phenylpropanoid glycosides and γ‐oryzanol in response to heat stress during ripening in rice. Cereal Chem 2021. [DOI: 10.1002/cche.10428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hiroshi Nakano
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Kyushu Okinawa Agricultural Research Center National Agriculture and Food Research Organization (NARO) Fukuoka Japan
| | - Norio Iwasawa
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
| | - Toshiyuki Takai
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Japan International Research Center for Agricultural Sciences (JIRCAS) Ibaraki Japan
| | - Yumiko Arai‐Sanoh
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
| | - Motohiko Kondo
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Graduate School of Bioagricultural Sciences Nagoya University Furocho Japan
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36
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Pezzotti G, Zhu W, Chikaguchi H, Marin E, Masumura T, Sato YI, Nakazaki T. Raman spectroscopic analysis of polysaccharides in popular Japanese rice cultivars. Food Chem 2021; 354:129434. [PMID: 33756327 DOI: 10.1016/j.foodchem.2021.129434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/14/2020] [Accepted: 02/19/2021] [Indexed: 02/08/2023]
Abstract
Analytical algorithms based on Raman spectroscopy are proposed for the determination of amylopectin and amylose concentrations in polished white rice, and applied to characterize and compare linear and branched polysaccharide structures in nine different types of Japanese rice. A selected algorithm used symmetric bending vibrations of the COC glycosidic linkage from a relatively narrow spectral zone between 830 and 895 cm-1. It specifically compared the intensity of Raman signals from two types of bending common to both starch components (C1-O-C5 and C1-O-C4 at 868 and 855 cm-1, respectively) and that at the branch point peculiar to amylopectin (C1-O-C6 at 844 cm-1). Raman data were confronted with data collected by conventional amylose-iodine colorimetry method. Consistency was found between Raman and colorimetric methods over the entire series of tested rice cultivars, thus validating the newly proposed spectroscopic algorithm. The amylose content of the tested rice species broadly varied between 1.2 and 20.4%. The proposed Raman algorithm allows fast and nondestructive determination of amylose content in rice with minimal sample preparation. These characteristics might be key in the development of portable Raman devices capable to promptly screen polysaccharides in different rice cultivars with respect to their interannual and plantation-related fluctuations.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan; The Center for Advanced Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0854, Japan; Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan.
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Haruna Chikaguchi
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yo-Ichiro Sato
- Research Center for Japanese Food Culture, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa 619-0218, Japan
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Suzuki Y. Achieving Food Authenticity and Traceability Using an Analytical Method Focusing on Stable Isotope Analysis. ANAL SCI 2021; 37:189-199. [PMID: 33229826 DOI: 10.2116/analsci.20sar14] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/13/2020] [Indexed: 11/23/2022]
Abstract
High-value agricultural products are characterized by the geographical conditions of the production areas such as climatic and soil conditions. These products are protected by the geographical indication (GI) protection system, which has been introduced in more than 100 countries. Because GI products are expensive in the market, products are often mislabeled as GI. Thus, there is an urgent need for the development of analytical methods that enable the tracing of geographical origins of food materials. Stable isotope analysis is used to trace the geographical origin of food materials. In this study, we review the applications for tracing the geographical origin of agricultural products (especially rice, beef, and honey) focusing on an analytical method for analyzing stable isotopes (δD, δ13C, δ15N, δ18O, and δ34S).
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Affiliation(s)
- Yaeko Suzuki
- Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
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Hori K, Suzuki K, Ishikawa H, Nonoue Y, Nagata K, Fukuoka S, Tanaka J. Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars. RICE (NEW YORK, N.Y.) 2021; 14:8. [PMID: 33415511 PMCID: PMC7790929 DOI: 10.1186/s12284-020-00447-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/17/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar 'Koshihikari' and an indica rice cultivar 'Takanari'. RESULTS We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of 'Koshihikari' chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1-5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2-4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1-5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the 'Koshihikari' genetic background. CONCLUSION The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.
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Affiliation(s)
- Kiyosumi Hori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Keitaro Suzuki
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Haruka Ishikawa
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazufumi Nagata
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Present address: St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, Kanagawa, 216-8511, Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Junichi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance. Sci Rep 2020; 10:19855. [PMID: 33199753 PMCID: PMC7670413 DOI: 10.1038/s41598-020-76949-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/22/2020] [Indexed: 11/26/2022] Open
Abstract
Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.
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40
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Kabir M, Haruki N, Rajagopalan U, Umehara M, Kadono H. Nanometer accuracy statistical interferometric technique in monitoring the short-term effects of exogenous plant hormones, auxin and gibberellic acid, on rice plants. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:261-271. [PMID: 33088189 PMCID: PMC7557655 DOI: 10.5511/plantbiotechnology.20.0225c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/25/2020] [Indexed: 06/08/2023]
Abstract
Statistical interferometric technique (SIT) is a highly sensitive, high speed non-contact, and non-destructive optical technique developed by our group capable of measuring instantaeoues sub-nanometer displacements. SIT applied to plant leaf elongation revealed nanometric intrinsic fluctuaitons (NIF) that are robust and sensitive to variations in the environment making NIF as a measure of healthiness of the plants. In this study, exogenous plant hormones, auxin (2,4-dichlorophenoxyacetic acid-2,4-D), and gibberellic acid (GA3), along with an auxin transport inhibitor 2,3,5-triiodobenzoic acid-TIBA, that affect plant growth were used to investigate their effects on NIF. Rice (Oriza sativa) seedlings were used, and their roots were exposed to 1, 2, and 4 µM 2,4-D, and the auxin transport inhibitor, TIBA, of 10, and 20 µM for 22 h and GA3 solution of different concentrations of 10, 40, and 100 µM for 5 h. Results showed significant increment in NIF for 1 µM and reduction for 4 µM 2,4-D while applicaiton of both 10, and 20 µM TIBA led to reduction in NIF. On the other hand, significant increment in NIF for 40 µM, and a significant reduction at a higher concentration of 100 µM for 5 hours of GA3 were also observed in comparison to those of control. Our results indicate that NIF as revealed by SIT could show both the positive and negative effects depending on the concentration of exogenous hormones, and transport inhibitors. Results suggest that SIT could be a valuable tool being sensitive enough to speedily assess the effects of plant growth hormones.
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Affiliation(s)
- Mahjabin Kabir
- Graduate School of Science and Engineering, Saitama University, 255 Shimo Okubo, Sakura-ku, Saitama 338-8570, Japan
- Department of Farm Power and Machinery, Faculty of Agricultural Engineering and Technology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Naruke Haruki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo Okubo, Sakura-ku, Saitama 338-8570, Japan
| | | | - Mikihisa Umehara
- Department of Applied Biosciences, Faculty of Life Sciences, Toyo University, , 1-1-1 Izumino, Itakura-machi, Ora-gun, Gumma 374-0193, Japan
| | - Hirofumi Kadono
- Graduate School of Science and Engineering, Saitama University, 255 Shimo Okubo, Sakura-ku, Saitama 338-8570, Japan
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41
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Mo Y, Jeong JM, Ha SK, Kim J, Lee C, Lee GP, Jeung JU. Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines. Genes (Basel) 2020; 11:E957. [PMID: 32825032 PMCID: PMC7565938 DOI: 10.3390/genes11090957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the gene mechanisms controlling days to heading (DH) is important in rice breeding for adaption in the target environment. Using a recombinant inbred line population derived from the cross between two japonica rice cultivars, Koshihikari and Baegilmi, we identified three consistent quantitative trait loci (QTLs) for DH for two years, qDH3, qDH6, and qDH7 on chromosomes 3, 6, and 7, respectively. While Baegilmi contributed the allele for early heading at qDH6 and qDH7 with the additive effect of five days each, Koshihikari contributed the allele for early heading at qDH3 with the additive effect of three days. Notably, pyramiding two or more alleles for early heading at these QTLs accelerated heading effectively. Sequencing of Hd16, Hd1, and Ghd7, the previously known heading date genes underlying qDH3, qDH6, and qDH7, respectively, revealed that Baegilmi and Koshihikari carry different alleles at the three genes. Molecular markers were developed to screen the allelic compositions of the three genes among 295 Korean commercial rice cultivars. The results showed that few cultivars carry alleles for early heading at the three genes, highlighting that DH can be further accelerated and fine-tuned in breeding programs by combining the desirable alleles of Hd16, Hd1, and Ghd7.
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Affiliation(s)
- Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jong-Min Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Su-Kyung Ha
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jinhee Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Changmin Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546, Korea;
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
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Liu H, Zhou X, Li Q, Wang L, Xing Y. CCT domain-containing genes in cereal crops: flowering time and beyond. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1385-1396. [PMID: 32006055 DOI: 10.1007/s00122-020-03554-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/23/2020] [Indexed: 05/04/2023]
Abstract
The review summarizes the functions of the plant special transcription factors CCT family genes in multiple traits and discusses the molecular breeding strategies with CCT family genes in the future. Plants integrate circadian clock and external signals such as temperature and photoperiod to synchronize flowering with seasonal environmental changes. This process makes cereal crops including short-day crops, such as rice and maize, and long-day crops, such as wheat and barley, better adapt to varied growth zones from temperate to tropical regions. CCT family genes involve circadian clock and photoperiodic flowering pathways and help plants set a suitable flowering time to produce offspring. Beyond the flowering time, CCT family genes in cereal crops are associated with biomass and grain yield. Moreover, recent studies showed that they also associate with photosynthesis, nutrition use efficiency and stress tolerance. Here, we systematically review the progress in functional characterization of CCT family genes in flowering, geographical adaptation and grain yield formation, raise the core questions related to their molecular mechanisms and discuss how to practice them in genetic improvement in cereal crops by combining gene diagnosis and top-level design.
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Affiliation(s)
- Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Qiuping Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China.
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43
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Teramoto S, Uga Y. A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:3194308. [PMID: 33313548 PMCID: PMC7706345 DOI: 10.34133/2020/3194308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/02/2020] [Indexed: 05/10/2023]
Abstract
Root distribution in the soil determines plants' nutrient and water uptake capacity. Therefore, root distribution is one of the most important factors in crop production. The trench profile method is used to observe the root distribution underground by making a rectangular hole close to the crop, providing informative images of the root distribution compared to other root phenotyping methods. However, much effort is required to segment the root area for quantification. In this study, we present a promising approach employing a convolutional neural network for root segmentation in trench profile images. We defined two parameters, Depth50 and Width50, representing the vertical and horizontal centroid of root distribution, respectively. Quantified parameters for root distribution in rice (Oryza sativa L.) predicted by the trained model were highly correlated with parameters calculated by manual tracing. These results indicated that this approach is useful for rapid quantification of the root distribution from the trench profile images. Using the trained model, we quantified the root distribution parameters among 60 rice accessions, revealing the phenotypic diversity of root distributions. We conclude that employing the trench profile method and a convolutional neural network is reliable for root phenotyping and it will furthermore facilitate the study of crop roots in the field.
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Affiliation(s)
- S. Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Y. Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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44
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LEE JS, SREENIVASULU N, HAMILTON RS, KOHLI A. Brown Rice, a Diet Rich in Health Promoting Properties. J Nutr Sci Vitaminol (Tokyo) 2019; 65:S26-S28. [DOI: 10.3177/jnsv.65.s26] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jae-Sung LEE
- Strategic Innovations Platform, International Rice Research Institute
| | - Nese SREENIVASULU
- Strategic Innovations Platform, International Rice Research Institute
| | | | - Ajay KOHLI
- Strategic Innovations Platform, International Rice Research Institute
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45
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Late flowering in F 1 hybrid rice brought about by the complementary effect of quantitative trait loci. Genetica 2019; 147:351-358. [PMID: 31432314 DOI: 10.1007/s10709-019-00075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Late flowering sometimes occurs in F1 hybrids between rice varieties (Oryza sativa L.), although the parental varieties show similar days-to-flowering (DTF). The genetic architecture prompting the occurrence of such late flowering is poorly understood. To clarify the genetic architecture of late flowering in F1 hybrids from a cross between rice varieties, 'Koshihikari' and 'IR64', we performed quantitative trait locus (QTL) analysis using an F2 population (selfed progeny of an F1 plant), in which heterozygous genotypes should segregate in a certain proportion in a Mendelian manner. The QTL analysis detected three significant QTLs. At one QTL (putatively Heading date 1), the 'Koshihikari' allele increased DTF, and at the other two QTLs (putatively Heading date 6 and Oryza sativa Pseudo-Response Regulator 37/Heading date 2), the 'IR64' alleles increased DTF. All alleles at these three QTLs showed partial dominance. The combination of the QTLs explained 82.2% of the total phenotypic variance of DTF in the F2 population, with contribution from epistasis between QTLs. There was no difference between DTFs of F1 hybrids and heterozygous genotypes for the three QTLs. Our results demonstrated that the complementary effects accompanied by epistasis of at least three QTLs were responsible for late flowering in F1 hybrids.
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46
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Nonoue Y, Hori K, Ono N, Shibaya T, Ogiso-Tanaka E, Mizobuchi R, Fukuoka S, Yano M. Detection of heading date QTLs in advanced-backcross populations of an elite indica rice cultivar, IR64. BREEDING SCIENCE 2019; 69:352-358. [PMID: 31481845 PMCID: PMC6711732 DOI: 10.1270/jsbbs.18172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 05/24/2023]
Abstract
IR64 is one of the world's most popular rice cultivars. To collect genetic factors involved in controlling its heading date, we developed 70 reciprocal advanced-backcross populations with a total of 6284 individuals at the BC4F2 generation from crosses between Koshihikari and IR64. We detected 29 QTLs associated with heading date on chromosomes 3, 5-8, 10, and 12. Twenty QTLs were located in the same chromosome regions as previously isolated heading date genes (Hd1, Hd6, Hd16, Ghd7, DTH8, Hd17, and Hd18). The rest were located in other chromosome regions. We found more number of QTLs than previous studies using mapping populations of IR64. Fine mapping in additional advanced-backcross populations clearly revealed that QTLs on the long arm of chromosome 7 are overlapping and seem to be a novel genetic factor for heading date because of their different locations from OsPRR37. Our results suggest that the difference in heading date between IR64 and Koshihikari is genetically controlled by many factors, and that a non-functional allele of Hd1 contributes to early heading of IR64 in the genetic background of functional alleles of other heading date QTLs and genes such as Hd6 and Hd16.
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Affiliation(s)
- Yasunori Nonoue
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Nozomi Ono
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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47
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Kimura K, Hori K, Yonezawa K, Nishibori F, Oka D, Iijima K, Saito A, Tsujii Y, Takano K. Effect of Good Eating Quality Gene Loci of Koshihikari on the Composition of Low Molecular Weight Compounds of Polished and Cooked Rice. J JPN SOC FOOD SCI 2019. [DOI: 10.3136/nskkk.66.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Keiichi Kimura
- Department of Agricultural Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture
| | - Kiyosumi Hori
- Institute of Crop Science, National Agriculture and Food Research Organization
| | - Kayo Yonezawa
- Department of Agricultural Chemistry, Faculty of Applied Biosciences, Tokyo University of Agriculture
| | - Fumiya Nishibori
- Food Processing Technology Center, Faculty of Applied Bioscience, Tokyo University of Agriculture
| | - Daiki Oka
- Department of Agricultural Chemistry, Faculty of Applied Biosciences, Tokyo University of Agriculture
| | - Ken Iijima
- Institute of Crop Science, National Agriculture and Food Research Organization
| | - Akihiro Saito
- Department of Agricultural Chemistry, Faculty of Applied Biosciences, Tokyo University of Agriculture
| | - Yoshimasa Tsujii
- Department of Agricultural Chemistry, Faculty of Applied Biosciences, Tokyo University of Agriculture
| | - Katsumi Takano
- Department of Agricultural Chemistry, Faculty of Applied Biosciences, Tokyo University of Agriculture
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48
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Hasegawa T, Sakai H, Tokida T, Usui Y, Nakamura H, Wakatsuki H, Chen CP, Ikawa H, Zhang G, Nakano H, Matsushima MY, Hayashi K. A High-Yielding Rice Cultivar "Takanari" Shows No N Constraints on CO 2 Fertilization. FRONTIERS IN PLANT SCIENCE 2019; 10:361. [PMID: 31024578 PMCID: PMC6460941 DOI: 10.3389/fpls.2019.00361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/08/2019] [Indexed: 05/06/2023]
Abstract
Enhancing crop yield response to elevated CO2 concentrations (E-[CO2]) is an important adaptation measure to climate change. A high-yielding indica rice cultivar "Takanari" has recently been identified as a potential candidate for high productivity in E-[CO2] resulting from its large sink and source capacities. To fully utilize these traits, nitrogen should play a major role, but it is unknown how N levels influence the yield response of Takanari to E-[CO2]. We therefore compared grain yield and quality of Takanari with those of Koshihikari, a standard japonica cultivar, in response to Free-Air CO2 enrichment (FACE, +200 μmol mol-1) under three N levels (0, 8, and 12 g m-2) over three seasons. The biomass of both cultivars increased under E-[CO2] at all N levels; however, the harvest index decreased under E-[CO2] in the N-limited treatment for Koshihikari but not for Takanari. The decreased harvest index of Koshihikari resulted from limited enhancement of spikelet number under N-limitation. In contrast, spikelet number increased in E-[CO2] in Takanari even without N application, resulting in significant yield enhancement, averaging 18% over 3 years, whereas Koshihikari exhibited virtually no increase in yield in E-[CO2] under the N-limited condition. Grain appearance quality of Koshihikari was severely reduced by E-[CO2], most notably in N-limited and hot conditions, by a substantial increase in chalky grain, but chalky grain % did not increase in E-[CO2] even without N fertilizer. These results indicated that Takanari could retain its high yield advantage over Koshihikari with limited increase in chalkiness even under limited N conditions and that it could be a useful genetic resource for improving N use efficiency under E-[CO2].
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Affiliation(s)
- Toshihiro Hasegawa
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Japan
| | - Hidemitsu Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takeshi Tokida
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yasuhiro Usui
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Memuro, Japan
| | | | - Hitomi Wakatsuki
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Charles P. Chen
- Department of Biology and Chemistry, Azusa Pacific University, Azusa, CA, United States
| | - Hiroki Ikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Guoyou Zhang
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Japan
| | - Hiroshi Nakano
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Japan
| | | | - Kentaro Hayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
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Iijima K, Suzuki K, Hori K, Ebana K, Kimura K, Tsujii Y, Takano K. Endosperm enzyme activity is responsible for texture and eating quality of cooked rice grains in Japanese cultivars. Biosci Biotechnol Biochem 2018; 83:502-510. [PMID: 30458671 DOI: 10.1080/09168451.2018.1547624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars.
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Affiliation(s)
- Ken Iijima
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Keitaro Suzuki
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kiyosumi Hori
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kaworu Ebana
- b Genetic Resources Center , NARO , Tsukuba , Japan
| | - Keiichi Kimura
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Yoshimasa Tsujii
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Katsumi Takano
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
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Mackill DJ. Special Issue: Iconic Rice Varieties. RICE (NEW YORK, N.Y.) 2018; 11:16. [PMID: 29629475 PMCID: PMC5890004 DOI: 10.1186/s12284-018-0214-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 05/20/2023]
Affiliation(s)
- David J Mackill
- Mars, Inc., Department of Plant Sciences, University of California, Davis, CA, 95618, USA.
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