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Ma ZH, Gao MH, Cheng HT, Song WW, Lu LJ, Lyu WY. Differences in rice component distribution across layers and their relationship with taste. J Sci Food Agric 2024; 104:1824-1832. [PMID: 37884460 DOI: 10.1002/jsfa.13074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Rice taste is closely associated with endosperm composition, which varies among different rice layers. Although clarifying the relationship between this difference and nutritional taste can guide rice breeding and cultivation practices, research on this topic is limited. RESULTS Here, typical rice varieties having excellent and poor taste characteristics were selected to analyze the distribution characteristics and differences of their components. The varieties with excellent taste exhibited lower apparent amylose content (AAC) and protein content (PC), lesser short-chain (Fa) and long-chain (Fb3 ) amylopectin (AP) and more medium-chain (Fb1+2 ) AP, higher long-to-short chain ratio (Fa:Fb3 ), and higher nitrogen (N), magnesium (Mg) and calcium (Ca) content in layer 1 (L1) than the varieties with poor taste. Layer 2 (L2) played a key role in AAC and PC regulation in the varieties with excellent taste by reducing AAC and appropriately increasing PC, consequently improving rice taste. AP structure in layer 3 (L3) substantially affected the taste of the two types of varieties. The mineral content was the highest in L1, and increased potassium (K), Ca, and Mg content improved taste in all varieties. CONCLUSION AAC in each layer contributes to rice taste. PC and minerals primarily act on L1 and L2, whereas AP acts on L2 and L3. Therefore, the endosperm formation process should be exploited for improving rice taste. Furthermore, key resources and cultivation should be identified and regulated, respectively, to improve rice taste. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Zhao-Hui Ma
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Ming-Hui Gao
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Hai-Tao Cheng
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Wen-Wen Song
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Lian-Ji Lu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Wen-Yan Lyu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
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Shu X, Zhang X, Wang S, Fu T, Ding Z, Yang Y, Wang Z, Zhao S, Xu J, Zhou J, Ju J, Huang J, Yao Y, Wang Y, Dong G. Simplified panicle fertilization is applicable to japonica cultivars, but splits are preferred in indica rice for a higher paddy yield under wheat straw return. Front Plant Sci 2024; 15:1273774. [PMID: 38352646 PMCID: PMC10861670 DOI: 10.3389/fpls.2024.1273774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Introduction The panicle fertilization strategy for japonica and indica rice under wheat straw return (SR) has not been updated, especially on the elaboration of their impacts on spikelet differentiation and degeneration. This study aimed to verify the hypothesis that SR increases spikelet number by reducing spikelet degeneration and to explore the possibility of simplifying panicle fertilization. Methods In three consecutive years, four varieties of japonica and indica rice were field-grown in Yangzhou, Jiangsu Province, China. Six panicle fertilization rates and split treatments were applied to SR and no straw return (NR) conditions. Results The results showed that SR promoted rice yield significantly by 3.77%, and the highest yields were obtained under the T2 (split panicle fertilization at the panicle initiation (PI) and spikelet primordium differentiation (SPD) stages) and T1 (panicle fertilization only at the PI stage) treatments, for indica and japonica rice, respectively. Correlation and path analysis revealed that the number of spikelets per panicle was the most attributable to yield variation. SR significantly increased the concentration of alkali hydrolyzable N in the soil 40 days after rice transplantation, significantly increased the nitrogen accumulation per stem (NA) during the SPD-pollen mother cell meiosis (PMC) stage, and increased the brassinosteroids level in the young panicles at the PMC stage. SR also reduced the degeneration rate of spikelets (DRS) and increased the number of surviving spikelets (NSS). The dry matter accumulation per stem was more important to increasing the NA in japonica rice at the PMC stage, whereas NA was more affected by the N content than the dry matter accumulation in indica rice. In japonica rice, panicle N application once only at the PI stage combined with the N released from SR was enough to improve the plant N content, reduce the DRS, and increase the NSS. For indica rice, split application of N panicle fertilization at both the PI and SPD stages was still necessary to achieve a maximum NSS. Discussion In conclusion, under wheat SR practice, panicle fertilization could be simplified to once in japonica rice with a significant yield increase, whereas equal splits might still be optimal for indica rice.
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Affiliation(s)
- Xiaowei Shu
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, Jiangsu, China
| | - Shushen Wang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tong Fu
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhouyu Ding
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ying Yang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zihan Wang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shiru Zhao
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jiejiao Xu
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Juan Zhou
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jing Ju
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jianye Huang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Youli Yao
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yulong Wang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Guichun Dong
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
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Escolà G, González-Miguel VM, Campo S, Catala-Forner M, Domingo C, Marqués L, San Segundo B. Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety. Plants (Basel) 2023; 12:3536. [PMID: 37896000 PMCID: PMC10667994 DOI: 10.3390/plants12203536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars.
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Affiliation(s)
- Glòria Escolà
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Víctor M. González-Miguel
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
| | - Mar Catala-Forner
- Institute of Agrifood Research and Technology (IRTA), Field Crops, Ctra. Balada km. 1, 43870 Tarragona, Spain;
| | - Concha Domingo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Departamento del Arroz and Centro de Genómica. Ctra Moncada-Náquera km 10.7, 46113 Moncada, Spain;
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, S.C.L. (COPSEMAR) Avda del Mar 1, 46410 Sueca, Spain;
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), C/de la Vall Moronta, CRAG Building, 08193 Barcelona, Spain; (G.E.); (V.M.G.-M.); (S.C.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08193 Barcelona, Spain
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Wang Y, Wang Y, Chen W, Dong Y, Zhang G, Deng H, Liu X, Lu X, Wang F, Chen G, Xiao Y, Tang W. Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar "IR64" and japonica cultivar "Koshihikari" at the seedling stage. Front Genet 2023; 14:1135577. [PMID: 37153001 PMCID: PMC10160441 DOI: 10.3389/fgene.2023.1135577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars.
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Affiliation(s)
- Yingfeng Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yubo Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Wenjuan Chen
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yating Dong
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guilian Zhang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Huabing Deng
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Xiong Liu
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Xuedan Lu
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Feng Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guihua Chen
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yunhua Xiao
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
- *Correspondence: Yunhua Xiao, ; Wenbang Tang,
| | - Wenbang Tang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- *Correspondence: Yunhua Xiao, ; Wenbang Tang,
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Ji H, Shin Y, Lee C, Oh H, Yoon IS, Baek J, Cha YS, Lee GS, Kim SL, Kim KH. Genomic Variation in Korean japonica Rice Varieties. Genes (Basel) 2021; 12:genes12111749. [PMID: 34828355 PMCID: PMC8623644 DOI: 10.3390/genes12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022] Open
Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties.
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Liu C, Peng P, Li W, Ye C, Zhang S, Wang R, Li D, Guan S, Zhang L, Huang X, Guo Z, Guo J, Long Y, Li L, Pan G, Tian B, Xiao J. Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding. Genomics 2021; 113:3083-91. [PMID: 34237377 DOI: 10.1016/j.ygeno.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/23/2022]
Abstract
Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.
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Chen C, Deng X, Kong W, Qaseem MF, Zhao S, Li Y, Wu AM. Rice Straws With Different Cell Wall Components Differ on Abilities of Saccharification. Front Bioeng Biotechnol 2021; 8:624314. [PMID: 33553128 PMCID: PMC7855461 DOI: 10.3389/fbioe.2020.624314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Rice straw has an enormous amount of biomass for energy use, but the complexity of the cell wall component hinders technical processes. Although belonging to rice straws, the straws from different varieties should be with different treatment strategies to obtain best energy efficiency. To confirm this hypothesis, 7 different rice varieties (RPY GENG, RIL269, RIL272, RIL31, RIL57, RIL06, LUOHUI 9) with different cell wall traits from RIL population were evaluated for their response toward different pretreatments. For japonica RPY GENG, 2% of H2SO4 acid was best pre-treatment while high acid (5% of H2SO4) pretreatment caused undue loss. For Indica LUOHUI 9 rice, high acid pretreatment was suitable, while RIL57 had maximum of glucose yield with high alkali (10% NaOH) pretreatment. High-concentration alkali pretreatment is the most convenient and effective pretreatment method for the treatment of unknown varieties of rice straws, because the lignin has been removed and has the lowest negative effects on the glucose yield under the high alkali condition. As the RILs used in this study vary considerably in their wall structure, an understanding of their response to different pre-treatments confirms our hypothesis and help us to understand the influence of different wall compositions on the final output.
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Affiliation(s)
- Chen Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Xiaoxiao Deng
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weilong Kong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mirza Faisal Qaseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yangsheng Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
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Brabham C, Norsworthy JK, González-Torralva F. Presence of the HPPD Inhibitor Sensitive 1 Gene and ALS S653N Mutation in Weedy Oryza sativa Sensitive to Benzobicyclon. Plants (Basel) 2020; 9:E1576. [PMID: 33202609 DOI: 10.3390/plants9111576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/17/2022]
Abstract
Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha−1, SC formulation) at 30 days after treatment (DAT). Thirty-four percent of plants were homozygous for the HIS1 allele and 98% of these plants exhibited field tolerance. However, the his1 genotype did not always correlate with field data. Only 52% of his1 plants were considered sensitive, indicating that the single nucleotide polymorphisms (SNPs) chosen in the KASP assay are not a reliable tool in predicting his1 homozygous plants. In an additional experiment, 86% of the 344 plants with at least one copy of the ALSS653N trait harbored a HIS1 allele, suggesting fields infested with IMI herbicide-resistant weedy rice are unlikely to be controlled with benzobicyclon.
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Seo J, Lee SM, Han JH, Shin NH, Lee YK, Kim B, Chin JH, Koh HJ. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11050562. [PMID: 32443496 PMCID: PMC7290844 DOI: 10.3390/genes11050562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/18/2023] Open
Abstract
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
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Affiliation(s)
- Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - So-Myeong Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Yoon Kyung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
- Correspondence: (J.H.C.); (H.-J.K.)
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Correspondence: (J.H.C.); (H.-J.K.)
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Izzard L, Chung M, Dunning Hotopp J, Vincent G, Paris D, Graves S, Stenos J. Isolation of a divergent strain of Rickettsia japonica from Dew's Australian bat Argasid ticks (Argas (Carios) dewae) in Victoria, Australia. Ticks Tick Borne Dis 2018; 9:1484-8. [PMID: 30025798 DOI: 10.1016/j.ttbdis.2018.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 11/20/2022]
Abstract
A divergent strain of Rickettsia japonica was isolated from a Dew's Australian bat argasid tick, Argas (Carios) dewae, collected in southern Victoria, Australia and a full-genome analysis along with sequencing of 5 core gene fragments was undertaken. This isolate was designated Rickettsia japonica str. argasii (ATCC VR-1665, CSUR R179).
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Takajo I, Sekizuka T, Fujita H, Kawano A, Kawaguchi T, Matsuda M, Kubo K, Miyauchi S, Umekita K, Nagatomo Y, Kuroda M, Takasaki T, Okayama A, Ando S. Possible Case of Novel Spotted Fever Group Rickettsiosis in Traveler Returning to Japan from India. Emerg Infect Dis 2018; 22:1079-82. [PMID: 27192498 PMCID: PMC4880103 DOI: 10.3201/eid2206.151985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A 60-year-old woman experienced fever, headache, rash, and altered vision after
returning to Japan from India. Testing detected elevated antibody titers to spotted
fever group rickettsia; PCR on blood yielded positive results for the rickettsial
outer membrane protein A gene. We isolated a unique rickettsial
agent and performed a full-genome analysis.
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Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, Tian D, Yang S, Wang L. Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars. BMC Genomics 2017; 18:307. [PMID: 28420345 PMCID: PMC5395770 DOI: 10.1186/s12864-017-3702-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 04/08/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Asian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions. RESULTS By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica. CONCLUSIONS This research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.
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Affiliation(s)
- Yang Yuan
- The Applied Plant Genomics Laboratory, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qijun Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shuiyun Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Feng F, Li Y, Qin X, Liao Y, Siddique KHM. Changes in Rice Grain Quality of Indica and Japonica Type Varieties Released in China from 2000 to 2014. Front Plant Sci 2017; 8:1863. [PMID: 29163589 PMCID: PMC5671604 DOI: 10.3389/fpls.2017.01863] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
China is the first country to use heterosis successfully for commercial rice production. This study compared the main quality characteristics (head rice rate, chalky rice rate, chalkiness degree, gel consistency, amylose content, and length-to-width ratio) of 635 rice varieties (not including upland and glutinous rice) released from 2000 to 2014 to establish the quality status and offer suggestions for future rice breeding for grain quality in China. In the past 15 years, grain quality in japonica rice and indica hybrid rice has improved. In japonica rice, inbred varieties have increased head rice rates and decreased chalkiness degree over time, while hybrid rice varieties have decreased chalky rice rates and chalkiness degree. In indica hybrid rice, the chalkiness degree and amylose contents have decreased and gel consistency has increased. Improvements in grain quality in indica inbred rice have been limited, with some increases in head rice rate and decreases in chalky rice rate and amylose content. From 2010 to 2014, the percentage of indica varieties meeting the Grade III national standard of rice quality for different quality traits was low, especially for chalky rice rate and chalkiness degree. Japonica varieties have more superior grain quality than indica rice in terms of higher head rice rates and gel consistency, lower chalky rice rates and chalkiness degree, and lower amylose contents, which may explain why the Chinese prefer japonica rice. The japonica rice varieties, both hybrid and inbred, had similar grain qualities, but this varied in indica rice with the hybrid varieties having higher grain quality than inbred varieties due to significantly better head rice rates and lower chalkiness degree. For better quality rice in future, the chalky rice rate and chalkiness degree should be improved in japonica rice along with most of the quality traits in indica rice.
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Affiliation(s)
- Fan Feng
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Yajun Li
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoliang Qin
- College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Xiaoliang Qin,
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Kubo T. Genetic mechanisms of postzygotic reproductive isolation: An epistatic network in rice. Breed Sci 2013; 63:359-66. [PMID: 24399907 PMCID: PMC3859346 DOI: 10.1270/jsbbs.63.359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/27/2013] [Indexed: 05/10/2023]
Abstract
Products of interspecific crosses often show abnormal phenotypes such as sterility, weakness and inviability. These phenomena play an important role in speciation as mechanisms of postzygotic reproductive isolation (RI). During the past two decades, genetics studies in rice have characterized a number of gene loci responsible for postzygotic RI. I have identified 10 loci including three sets of epistatic networks in a single inter-subspecific cross (Oryza sativa ssp. indica × japonica). These results suggest that RI genes cause developmental dysfunction of vegetative and/or reproductive organs through a variety of molecular pathways. The latest molecular studies demonstrated that hybrid incompatibility is mainly due to deleterious interactions caused by species-specific mutations of two or more genes, mediated by proteins acting within the same molecular pathway. Because genetic interactions provide a perspective on gene function, epistatic networks are a key to the understanding of the molecular basis of postzygotic RI. In this review, I focus on recent progress in postzygotic RI studies in rice and discuss the evolutionary significance as well as implications for improving rice productivity.
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Affiliation(s)
- Takahiko Kubo
- Plant Genetics Laboratory, National Institute of Genetics,
Mishima, Shizuoka 411-8540,
Japan
- Department of Life Science, Graduate University for Advanced Studies (SOKENDAI),
1111 Yata, Mishima, Shizuoka 411-8540,
Japan
- Corresponding author (e-mail: )
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