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Sun Z, Mei T, Tan X, Feng T, Li R, Duan S, Zhao H, Ye Y, Liu B, Zhou A, Ai H, Huang X. The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:759. [PMID: 38592751 PMCID: PMC10975181 DOI: 10.3390/plants13060759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.
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Affiliation(s)
- Zhanglun Sun
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Tianrun Mei
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Xuan Tan
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Tingting Feng
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Ruining Li
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Sumei Duan
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Yafeng Ye
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230001, China; (Y.Y.); (B.L.)
| | - Binmei Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230001, China; (Y.Y.); (B.L.)
| | - Aifeng Zhou
- Anhui Xin Fu Xiang Tian Ecological Agriculture Co., Ltd., Maanshan 238200, China;
| | - Hao Ai
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
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Naqvi RZ, Mahmood MA, Mansoor S, Amin I, Asif M. Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops. FRONTIERS IN PLANT SCIENCE 2024; 14:1273859. [PMID: 38259913 PMCID: PMC10800452 DOI: 10.3389/fpls.2023.1273859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
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Pérez J, Hernández-Soto A, Abdelnour-Esquivel A, Vargas-Segura W, Watson-Guido W, Gatica-Arias A. In Vitro Gamma Mutagenesis Techniques in Rice (Oryza sativa L. var. Lazarroz FL). Methods Mol Biol 2024; 2788:243-255. [PMID: 38656518 DOI: 10.1007/978-1-0716-3782-1_14] [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] [Indexed: 04/26/2024]
Abstract
Gamma radiation (60Co)-induced mutagenesis offers an alternative to develop rice lines by accelerating the spontaneous mutation process and increasing the pool of allelic variants available for breeding. Ionizing radiation works by direct or indirect damage to DNA and subsequent mutations. The technique can take advantage of in vitro protocols to optimize resources and accelerate the development of traits. This is achieved by exposing mutants to a selection agent of interest in controlled conditions and evaluating large numbers of plants in reduced areas. This chapter describes the protocol for establishing gamma radiation dosimetry and in vitro protocols for optimization at the laboratory level using seeds as the starting material, followed by embryogenic cell cultures, somatic embryogenesis, and regeneration. The final product of the protocol is a genetically homogeneous population of Oryza sativa that can be evaluated for breeding against abiotic and biotic stresses.
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Affiliation(s)
- Jason Pérez
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Costa Rica, Cartago, Costa Rica.
| | - Alejandro Hernández-Soto
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Costa Rica, Cartago, Costa Rica
| | - Ana Abdelnour-Esquivel
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Costa Rica, Cartago, Costa Rica
| | - Walter Vargas-Segura
- Gamma Irradiation Laboratory, School of Physics, Costa Rica Institute of Technology, Costa Rica, Cartago, Costa Rica
| | - William Watson-Guido
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Costa Rica, Cartago, Costa Rica
| | - Andrés Gatica-Arias
- Laboratorio Biotecnología de Plantas, Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
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Yamazaki K, Sotta N, Fujiwara T. M 2 plants derived from different tillers of a chemically mutagenized rice M 1 plant carry independent sets of mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:597-603. [PMID: 37433661 DOI: 10.1111/tpj.16390] [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: 04/28/2023] [Revised: 07/01/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Generation of mutant populations with high genetic diversity is key for mutant screening and crop breeding. For this purpose, the single-seed descent method, in which one mutant line is established from a single mutagenized seed, is commonly used. This method ensures the independence of the mutant lines, but the size of the mutant population is limited because it is no greater than the number of fertile M1 plants. The rice mutant population size can be increased if a single mutagenized plant produces genetically independent siblings. Here, we used whole-genome resequencing to examine the inheritance of mutations from a single ethyl methanesulfonate (EMS)-mutagenized seed (M1 ) of Oryza sativa in its progeny (M2 ). We selected five tillers from each of three M1 plants. A single M2 seed was selected from each tiller, and the distributions of mutations induced by EMS were compared. Surprisingly, in most pairwise combinations of M2 siblings from the same parent, ≥85.2-97.9% of all mutations detected were not shared between the siblings. This high percentage suggests that the M2 siblings were derived from different cells of the M1 embryo and indicates that several genetically independent lines can be obtained from a single M1 plant. This approach should allow a large reduction in the number of M0 seeds needed to obtain a mutant population of a certain size in rice. Our study also suggests that multiple tillers of a rice plant originate from different cells of the embryo.
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Affiliation(s)
- Kiyoshi Yamazaki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naoyuki Sotta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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Mangena P, Mushadu PN. Colchicine-Induced Polyploidy in Leguminous Crops Enhances Morpho-Physiological Characteristics for Drought Stress Tolerance. Life (Basel) 2023; 13:1966. [PMID: 37895348 PMCID: PMC10607973 DOI: 10.3390/life13101966] [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: 07/30/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Legumes play a significant role in the alleviation of food insecurity, maintaining soil fertility, and achieving sustainable crop production under adverse environmental conditions. The increased demand in legume production contemplates that attention on the genetic improvement of these crops through various means such as genetic engineering and mutation breeding should take a centre stage in global agriculture. Therefore, this paper provides a succinct analysis of the currently available literature on morphological and physiological traits in polyploidised leguminous plants to counter the adverse effects of drought stress. The effects of colchicine on various morphological and physiological traits of polyploidised legumes compared to their diploid counterparts were examined. Numerous reports revealed variations in these traits, such as improved root and shoot growth, plant biomass, chloroplastidic content, protein, RNA, and DNA. The differences observed were also associated with the strong relationship between plant ploidy induction and colchicine application. Furthermore, the analysis indicated that polyploidisation remains dose-dependent and may be achievable within a shorter space of time as this antimitotic chemical interferes with chromosome separations in somatic plant cells. The efficiency of this process also depends on the advancement of treatment conditions (in vitro, in vivo, or ex vitro) and the successful regeneration of polyploidised plants for adaptation under drought stress conditions. As such, the improvement in metabolite profile and other essential growth characteristics serves as a clear indication that induced polyploidy needs to be further explored to confer resilience to environmental stress and improve crop yield under drought stress conditions in leguminous plants.
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Affiliation(s)
- Phetole Mangena
- Department of Biodiversity, Faculty of Science and Agriculture, School of Molecular and Life Sciences, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa;
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Shamshad A, Rashid M, Jankuloski L, Ashraf K, Sultan K, Alamri S, Siddiqui MH, Munir T, Zaman QU. Effect of ethyl methanesulfonate mediated mutation for enhancing morpho-physio-biochemical and yield contributing traits of fragrant rice. PeerJ 2023; 11:e15821. [PMID: 37780391 PMCID: PMC10540773 DOI: 10.7717/peerj.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/10/2023] [Indexed: 10/03/2023] Open
Abstract
Background Chemical mutagenesis has been successfully used for increasing genetic diversity in crop plants. More than 800 novel mutant types of rice (Oryza sativa L.) have been developed through the successful application of numerous mutagenic agents. Among a wide variety of chemical mutagens, ethyl-methane-sulfonate (EMS) is the alkylating agent that is most commonly employed in crop plants because it frequently induces nucleotide substitutions as detected in numerous genomes. Methods In this study, seeds of the widely consumed Basmati rice variety (Super Basmati, Oryza sativa L.) were treated with EMS at concentrations of 0.25%, 0.50%, 0.75%, 1.0%, and 1.25% to broaden its narrow genetic base. Results Sensitivity to a chemical mutagen such as ethyl methanesulfonate (EMS) was determined in the M1 generation. Results in M1 generation revealed that as the levels of applied EMS increased, there was a significant reduction in the germination percent, root length, shoot length, plant height, productive tillers, panicle length, sterile spikelet, total spikelet, and fertility percent as compared to the control under field conditions. All the aforementioned parameters decreased but there was an increase in EMS mutagens in an approximately linear fashion. Furthermore, there was no germination at 1.25% of EMS treatment for seed germination. A 50% germination was recorded between 0.50% and 0.75% EMS treatments. After germination, the subsequent parameters, viz. root length and shoot length had LD50 between 05.0% and 0.75% EMS dose levels. Significant variation was noticed in the photosynthetic and water related attributes of fragrant rice. The linear increase in the enzymatic attributes was noticed by the EMS mediated treatments. After the establishment of the plants in the M1 generation in the field, it was observed that LD50 for fertility percentage was at EMS 1.0% level, for the rice variety. Conclusion Hence, it is concluded that for creating genetic variability in the rice variety (Super Basmati), EMS doses from 0.5% to 0.75% are the most efficient, and effective.
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Affiliation(s)
- Areeqa Shamshad
- Nuclear Institute for Agriculture and Biology College (NIAB-C), PIEAS, Islamabad, Pakistan
| | - Muhammad Rashid
- Nuclear Institute for Agriculture and Biology College (NIAB-C), PIEAS, Islamabad, Pakistan
| | - Ljupcho Jankuloski
- International Atomic Energy Agency, Joint FAO/IAEA Centre, Plant Breeding and Genetics Section, Vienna, Austria
| | - Kamran Ashraf
- Department of Bioengineering and Biotechnology, School of Biotechnology, Kunming University of Science and Technology, Shanghai, China
- Department of Food Sciences, Government College University Faisalabad, Sahiwal Campus, Faisalabad, Pakistan
| | - Khawar Sultan
- Department of Environmental Sciences, The University of Lahore, Lahore, Pakistan
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Tehzeem Munir
- Department of Environmental Sciences, The University of Lahore, Lahore, Pakistan
| | - Qamar uz Zaman
- Department of Environmental Sciences, The University of Lahore, Lahore, Pakistan
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Ali M, Abdelkawy AM, Darwish DBE, Alatawi HA, Alshehri D, Al-Amrah H, Soudy FA. Changes in Metabolite Profiling and Expression Levels of Key Genes Involved in the Terpenoid Biosynthesis Pathway in Garden Sage ( Salvia officinalis) under the Effect of Hydrazine Hydrate. Metabolites 2023; 13:807. [PMID: 37512514 PMCID: PMC10385164 DOI: 10.3390/metabo13070807] [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: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Mutagenesis is a highly efficient tool for establishing genetic variation and is widely used for genetic enhancement in various plants. The key benefit of mutation breeding is the prospect of enhancing one or several characteristics of a variety without altering the genetic background. In this study, we exposed the seeds of Salvia officinalis to four concentrations of hydrazine hydrate (HZ), i.e., (0%, 0.1%, 0.2%, and 0.3%) for 6 h. The contents of terpenoid compounds in the S. officinalis plantlets driven from the HZ-treated seeds were determined by GC-MS, which resulted in the identification of a total of 340 phytochemical compounds; 163 (87.48%), 145 (84.49%), 65 (97.45%), and 62 (98.32%), from the four concentrations of HZ (0%, 0.1%, 0.2%, and 0.3%), respectively. Furthermore, we used the qRT-PCR system to disclose the "transcriptional control" for twelve TPS genes related to terpenoid and terpene biosynthesis, namely, SoGPS, SoMYRS, SoNEOD, SoCINS, SoSABS, SoLINS, SoFPPS, SoHUMS, SoTPS6, SoSQUS, SoGGPS, and SoGA2. Altogether, results are likely to ensure some positive relationship between the concentrations of the chemical mutagen HZ used for treating the seeds, the type and amount of the produced terpenes, and the expression of their corresponding genes.
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Affiliation(s)
- Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo 11753, Egypt
| | - Aisha M Abdelkawy
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University (Girls Branch), Cairo 11751, Egypt
| | - Doaa Bahaa Eldin Darwish
- Biology Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
| | - Hanan Ali Alatawi
- Department of Biological Sciences, University Collage of Haqel, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Dikhnah Alshehri
- Biology Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Hadba Al-Amrah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fathia A Soudy
- Genetics and Genetic Engineering Department, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
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Zou M, Tong S, Zou T, Wang X, Wu L, Wang J, Guo T, Xiao W, Wang H, Huang M. A new method for mutation inducing in rice by using DC electrophoresis bath and its mutagenic effects. Sci Rep 2023; 13:6707. [PMID: 37185291 PMCID: PMC10126576 DOI: 10.1038/s41598-023-33742-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Mutation breeding is a significant means of increasing breeding efficiency and accelerating breeding process. In present study, we explored a new method for mutations inducing in rice (Oryza sativa L.) by using direct current electrophoresis bath (DCEB). The results showed that 20 mM NaCl solution is the optimal buffer, and the mortality of rice seeds followed an upward trend with increasing voltage and processing time of DCEB. By exploring the mutagenic effects of γ-irradiation and DCEB on seed vigor and physiological damages, we found that the physiological damages induced by DCEB on seed vigor were significant compared with that by γ-irradiation. We screened two mutants with low filled grain percentage and one mutant with abnormal hull from the M2 generations. These three mutants were confirmed to be authentic mutants based on 48 SSR markers followed by the protocol NY/T 1433-2014. Whole-genome resequencing detected a total of 503 and 537 polymorphisms in the two mutants, respectively, and the DCEB mutagenesis induced mainly InDel variants, while the exon region of mutant genes occupied a large proportion, especially the SNP variants, which occupied about 20% of the mutation sites in the exon region.
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Affiliation(s)
- Minmin Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Sun Tong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ting Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xinyi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Linxuan Wu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jiafeng Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Tao Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Wuming Xiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Hui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ming Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Taura S, Ichitani K. Chromosomal Location of xa19, a Broad-Spectrum Rice Bacterial Blight Resistant Gene from XM5, a Mutant Line from IR24. PLANTS (BASEL, SWITZERLAND) 2023; 12:602. [PMID: 36771686 PMCID: PMC9919685 DOI: 10.3390/plants12030602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Bacterial blight is an important rice disease caused by bacteria named Xanthomonas oryzae pv. oryzae (Xoo). XM5 is an Xoo resistant mutant line with the genetic background of IR24, an Indica Xoo susceptible cultivar, induced by a chemical mutagen N-methyl-N-nitrosourea (MNU). XM5 carries a recessive Xoo resistant gene, xa19. Trisomic analysis was conducted using the cross between XM5 and the trisomic series under the genetic background of IR24, showing that xa19 was located on chromosome 7. The approximate chromosomal location was found using 37 surely resistant plants in the F2 population from XM5 × Kinmaze, which was susceptible to most Japanese Xoo races. The IAS44 line carries a Japonica cultivar Asominori chromosomal segment covering the xa19 locus under the IR24 genetic background. Linkage analysis using the F2 population from the cross between XM5 and IAS44 revealed that xa19 was located within the 0.8 cM region between RM8262 and RM6728. xa19 is not allelic to the known Xoo resistant genes. However, its location suggests that it might be allelic to a lesion-mimic mutant gene spl5, some alleles of which are resistant to several Xoo races. Together with xa20 and xa42, three Xoo resistant genes were induced from IR24 by MNU. The significance of chemical mutagen as a source of Xoo resistance was discussed.
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Affiliation(s)
- Satoru Taura
- Institute of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Katsuyuki Ichitani
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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Roy A, Sahu PK, Das C, Bhattacharyya S, Raina A, Mondal S. Conventional and new-breeding technologies for improving disease resistance in lentil ( Lens culinaris Medik). FRONTIERS IN PLANT SCIENCE 2023; 13:1001682. [PMID: 36743558 PMCID: PMC9896981 DOI: 10.3389/fpls.2022.1001682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/02/2022] [Indexed: 06/02/2023]
Abstract
Lentil, an important cool season food legume, is a rich source of easily digestible protein, folic acid, bio-available iron, and zinc nutrients. Lentil grows mainly as a sole crop in the winter after harvesting rice in South Asia. However, the annual productivity is low due to its slow growth during the early phase, competitive weed infestation, and disease outbreaks during the crop growth period. Disease resistance breeding has been practiced for a long time to enhance resistance to various diseases. Often the sources of resistance are available in wild crop relatives. Thus, wide hybridization and the ovule rescue technique have helped to introgress the resistance trait into cultivated lentils. Besides hybridization, induced mutagenesis contributed immensely in creating variability for disease tolerance, and several disease-resistant mutant lines have been developed. However, to overcome the limitations of traditional breeding approaches, advancement in molecular marker technologies, and genomics has helped to develop disease-resistant and climate-resilient lentil varieties with more precision and efficiency. This review describes types of diseases, disease screening methods, the role of conventional and new breeding technologies in alleviating disease-incurred damage and progress toward making lentil varieties more resilient to disease outbreaks under the shadow of climate change.
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Affiliation(s)
- Anirban Roy
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
- Department of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational & Research Institute (RKMVERI), Ramkrishna Mission Ashrama, Kolkata, India
| | - Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, College of Agriculture, Indira Gandhi Krishi Viswavidyalaya, Raipur, Chhattisgarh, India
| | - Camellia Das
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
| | - Somnath Bhattacharyya
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
| | - Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- Botany Section, Women’s College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
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11
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Sao R, Sahu PK, Patel RS, Das BK, Jankuloski L, Sharma D. Genetic Improvement in Plant Architecture, Maturity Duration and Agronomic Traits of Three Traditional Rice Landraces through Gamma Ray-Based Induced Mutagenesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:3448. [PMID: 36559562 PMCID: PMC9781505 DOI: 10.3390/plants11243448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Mutation breeding offers a simple, fast and efficient way to rectify major defects without altering their original identity. The present study deployed radiation (gamma rays @ 300Gy)-induced mutation breeding for the improvement and revival of three traditional rice landraces, viz., Samundchini, Vishnubhog and Jhilli. Among the various putative mutants identified in the M2 generation, only three, ten and five rice mutants of Samundchini, Vishnubhog and Jhilli, respectively, were advanced to the M4, M5 and M6 generations, along with their parents and three checks for evaluations based on 13 agro-morphological and 16 grain quality traits. Interestingly, all the mutants of the three landraces showed a reduction in days to 50% flowering and plant height as compared to their parents in all the three generations. The reduction in days to 50% flowering ranges from 4.94% (Vishnubhog Mutant V-67) to 21.40% (Jhilli Mutant J-2-13), whereas the reduction in plant height varies from 11.28% (Vishnubhog Mutant V-45-2, Vishnubhog Mutant V-67) to 37.65% (Jhilli Mutant J-15-1). Furthermore, two, six and three mutants of Samundchini, Vishnubhog and Jhilli have increased their yield potential over their corresponding parents, respectively. Interestingly, Samundchini Mutant S-18-1 (22.45%), Vishnubhog Mutant V-74-6 (36.87%) and Jhilli Mutant J-13-5 (25.96%) showed the highest yield advantages over their parents. Further, a pooled analysis of variance based on a randomized complete block design revealed ample variations among the genotypes for the studied traits. In addition, all the traits consistently showed high to moderate PCV and GCV and a slight difference between them in all three generations indicated the negligible effect of the environment. Moreover, in the association analysis, the traits, viz., fertile spikelets/panicle, panicle length, total tillers/plant, spikelet fertility percent and 100-seed weight showed the usual grain yield/plant, whereas the traits hulling (%) and milling (%) with HRR (%) consistently showed high direct effects and significant positive correlations. The SSR marker-based genome similarity in rice mutants and corresponding parents ranged from 95.60% to 71.70% (Vishnubhog); 95.62% to 89.10% (Samundchini) and 95.62% to 80.40% (Jhilli), indicating the trueness of the mutants. Moreover, the UPGMA algorithm and Gower distance-based dendrogram, neighbour joining tree and PCA scatter diagram assured that mutants were grouped with their respective parents and fell into separate clusters showing high similarity between mutants and parents and dissimilarity among the 24 genotypes. Overall, the information and materials generated from the current study will be very useful and informative for students, researchers and plant breeders. Additionally, our results also showed that irradiation could generate a considerable amount of genetic variability and provide new avenues for crop improvement and diversification.
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Affiliation(s)
- Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Raviraj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai 400085, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
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12
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Mistry V, Tiwari P, Patel P, Vishwakarma GS, Lee GJ, Sharma A. Ethyl Methane Sulfonate and Sodium Azide-Mediated Chemical and X-ray-Mediated Physical Mutagenesis Positively Regulate Peroxidase 1 Gene Activity and Biosynthesis of Antineoplastic Vinblastine in Catharanthus roseus. PLANTS (BASEL, SWITZERLAND) 2022; 11:2885. [PMID: 36365340 PMCID: PMC9656251 DOI: 10.3390/plants11212885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Catharanthus roseus synthesizes bioactive therapeutic metabolites, known as monoterpenoid indole alkaloids (MIAs), including antineoplastic vinblastine and vincristine, which have high global demand, and antihypertensive ajmalicine, a serpentine. However, the in planta biosynthesis and accumulation of these phytopharmaceuticals are very low, attributed to their high cytotoxicity in the plant. Considering the low in planta concentration and over-harvesting of plant resources, biotechnological interventions have been undertaken to enhance the production of MIAs in plant systems. The present study was carried out to mutation through chemical and physical mutagenesis with sodium azide, ethyl methane sulfonate and X-rays, respectively, on C. roseus to determine their possible effects on the transcriptional modulation of MIA biosynthetic pathways in planta. The chemical mutagenesis resulted in delayed seed pod development in mutated C. roseus plants, with distinct leaf morphology and flower color. However, X-ray mutagenesis resulted in pollen-less sterile flowers. An HPLC analysis confirmed the higher catharanthine, vindoline and vinblastine content in sodium azide and X-ray mutants, and was further supported by higher PRX1 transcript levels estimated through real-time PCR analysis. The transcription factors WRKY1 and ORCA2 were found negatively regulated along with major MIA pathway genes in chemical mutants and their M1 generation, but showed positive regulation in X-ray M0 mutants. The induced mutagenesis of C. roseus provides a prospective strategy to modulate plant transcriptomes and enhance the biosynthesis of pharmaceutically important antineoplastic vinblastine in the plant.
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Affiliation(s)
- Vyoma Mistry
- C. G. Bhakta Institute of Biotechnology, Maliba Campus, Uka Tarsadia University, Surat 394350, India
| | - Pragya Tiwari
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Paresh Patel
- Tarsadia Institute of Chemical Science, Uka Tarsadia University, Bardoli 394350, India
| | - Gajendra Singh Vishwakarma
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 392426, India
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
| | - Abhishek Sharma
- C. G. Bhakta Institute of Biotechnology, Maliba Campus, Uka Tarsadia University, Surat 394350, India
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Koba Institutional Area, Gandhinagar 392426, India
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13
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Ramlal A, Nautiyal A, Baweja P, Kumar Mahto R, Mehta S, Pujari Mallikarunja B, Vijayan R, Saluja S, Kumar V, Kumar Dhiman S, Lal SK, Raju D, Rajendran A. Harnessing heterosis and male sterility in soybean [ Glycine max (L.) Merrill]: A critical revisit. FRONTIERS IN PLANT SCIENCE 2022; 13:981768. [PMID: 36299790 PMCID: PMC9589222 DOI: 10.3389/fpls.2022.981768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Soybean is a predominantly self-pollinated crop. It is also one of the important oilseed legumes. Soybean is an excellent crop having industrial, traditional, culinary, feeding, and cultural roles. Genetic diversity in breeding programs is of prime importance as it ensures the success of any breeding by enhancing the outcomes and results of the plants. The phenomenon wherein the progeny exhibits greater biomass (yield) and a faster rate of development and fertility than its parents is referred to as heterosis. As of now, heterosis is mainly limited to the trait of seed yield and is considered the basis for the development of better (superior) varieties. Male sterility (MS) is extensively used for the production of seeds and the improvement of crops coupled with the traditional breeding programs and molecular technology. Therefore, deployment of MS and heterosis in breeding soybean could yield better outcomes. This review aims to focus on two aspects, namely, MS and heterosis in soybean with its scope for crop improvement.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
- DBC i4 Center, Deshbandhu College, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Sahil Mehta
- School of Agricultural Sciences, K. R. Mangalam University, Gurugram, Haryana, India
| | - Bingi Pujari Mallikarunja
- Division of Genetics, Regional Research Centre, ICAR-Indian Agricultural Research Institute (IARI), Dharwad, Karnataka, India
| | - Roshni Vijayan
- Regional Agricultural Research Station, Kerala Agricultural University, Pattambi, Kerala, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Vijay Kumar
- Department of Botany, Shivaji College, University of Delhi, New Delhi, India
| | - Sunil Kumar Dhiman
- Department of Botany, Kirori Mal College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Dhandapani Raju
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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14
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Sahu PK, Sao R, Choudhary DK, Thada A, Kumar V, Mondal S, Das BK, Jankuloski L, Sharma D. Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease. PLANTS 2022; 11:plants11182386. [PMID: 36145787 PMCID: PMC9504543 DOI: 10.3390/plants11182386] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 01/02/2023]
Abstract
Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | | | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
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15
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Türkoğlu A, Tosun M, Haliloğlu K. Mutagenic effects of sodium azide on in vitro mutagenesis, polymorphism and genomic instability in wheat (Triticum aestivum L.). Mol Biol Rep 2022; 49:10165-10174. [PMID: 36029431 DOI: 10.1007/s11033-022-07896-y] [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: 05/31/2022] [Accepted: 08/22/2022] [Indexed: 10/15/2022]
Abstract
INTRODUCTION Breeding studies are commonly conducted to develop new cultivars with high yield levels and improved quality traits. Chemically-induced mutations are used to create genetic variations in wheat genomes. Various physical and chemical mutagens are used to increase frequency of mutations and facilitate the selection processes. Sodium azide (SA) is largely employed to induce mutations of the genes regulating essential traits. Such mutations may also elucidate gene functions of the mutant phenotypes. Present experiments were conducted to investigate potential use of conventional chemical mutagenesis technique through SA for mature embryo culture in wheat. METHODS AND RESULTS Sodium azide mutagenesis was experimented with 4 treatment durations (1, 2, 3 and 4 h) and 5 treatment concentrations (0, 1, 2, 3 and 4 mM). Mature embryos were subjected to experimental treatments to detect optimum doses of mutagenesis and to estimate polymorphism and genomic instability. Primarily, 50% reduction in number of regenerated plants as compared to the control (LD50) was adopted as the optimum dose. Based on LD50 criterion, the optimum value was achieved at 1 h duration of 4 mM SA concentration. Afterwards, inter-primer binding site markers were applied to investigate polymorphism and genomic instability in the regenerated plants. CONCLUSIONS Present findings revealed that efficiency of chemical mutagenesis could be improved through the use of molecular technology and such mutations may assist plant breeders in developing high-yield cultivars.
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Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya, Türkiye.
| | - Metin Tosun
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye.,Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankırı, Türkiye
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16
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Kubo T, Yamagata Y, Matsusaka H, Toyoda A, Sato Y, Kumamaru T. Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells. RICE (NEW YORK, N.Y.) 2022; 15:38. [PMID: 35841399 PMCID: PMC9288566 DOI: 10.1186/s12284-022-00585-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effective genetic tools that can be grown without regard for biosafety issues. Whole-genome sequencing of mutant individuals reduces the effort required for mutant screening, thereby increasing their utility. In this study, we sequenced members of a mutant library of Oryza sativa cv. Nipponbare derived from treating single fertilized egg cells with N-methyl-N-nitrosourea (MNU). By whole-genome sequencing 266 M1 plants in this mutant library, we identified a total of 0.66 million induced point mutations. This result represented one mutation in every 146-kb of genome sequence in the 373 Mb assembled rice genome. These point mutations were uniformly distributed throughout the rice genome, and over 70,000 point mutations were located within coding sequences. Although this mutant library was a small population, nonsynonymous mutations were found in nearly 61% of all annotated rice genes, and 8.6% (3248 genes) had point mutations with large effects on gene function, such as gaining a stop codon or losing a start codon. WGS showed MNU-mutagenesis using rice fertilized egg cells induces mutations efficiently and is suitable for constructing mutant libraries for an in silico mutant screening system. Expanding this mutant library and its database will provide a useful in silico screening tool that facilitates functional genomics studies with a special emphasis on rice.
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Affiliation(s)
- Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Sato
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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17
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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18
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Kenzhebayeva S, Atabayeva S, Sarsu F, Abekova A, Shoinbekova S, Omirbekova N, Doktyrbay G, Beisenova A, Shavrukov Y. Organ-specific expression of genes involved in iron homeostasis in wheat mutant lines with increased grain iron and zinc content. PeerJ 2022; 10:e13515. [PMID: 35707120 PMCID: PMC9190668 DOI: 10.7717/peerj.13515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/09/2022] [Indexed: 01/17/2023] Open
Abstract
Background Iron deficiency is a well-known nutritional disorder, and the imbalance of trace-elements, specifically iron, is the most common nutrient deficiency of foods across the world, including in Kazakhstan. Wheat has significant nutritional relevance, especially in the provision of iron, however many bread wheat varieties have low iron despite the need for human nourishment. In this study, the expression profiles of wheat homologous genes related to iron homeostasis were investigated. The work resulted in the development of two new M5 mutant lines of spring bread wheat through gamma-irradiation (200 Gy) with higher grain iron and zinc content, lower phytic acid content, and enhanced iron bioavailability compared to the parent variety. Mutant lines were also characterized by higher means of yield associated traits such as grain number per main spike, grain weight per main spike, grain weight per plant, and thousand-grain weight. Methods The homologous genes of bread wheat from several groups were selected for gene expression studies exploring the tight control of iron uptake, translocation rate and accumulation in leaves and roots, and comprised the following: (1) S-adenosylmethionine synthase (SAMS), nicotianamine synthase (NAS1), nicotianamine aminotransferase (NAAT), deoxymugineic acid synthetase (DMAS), involved in the synthesis and release of phytosiderophores; (2) transcription factor basic helix-loop-helix (bHLH); (3) transporters of mugineic acid (TOM), involved in long-distance iron transport; (4) yellow stripe-like (YSlA), and the vacuolar transporter (VIT2), involved in intracellular iron transport and storage; and lastly (5) natural resistance-associated macrophage protein (NRAMP) and ferritin (Fer1A). Results The wheat homologous genes TaSAMS, TaNAS1, and TaDMAS, were significantly up-regulated in the roots of both mutant lines by 2.1-4.7-fold compared to the parent variety. The combined over-expression of TaYSlA and TaVIT2 was also revealed in the roots of mutant lines by 1.3-2.7-fold. In one of the mutant lines, genes encoding intracellular iron transport and storage genes TaNRAMP and TaFer1A-D showed significant up-regulation in roots and leaves (by 1.4- and 3.5-fold, respectively). The highest expression was recorded in the transcription factor TabHLH, which was expressed 13.1- and 30.2-fold in the roots of mutant lines. Our research revealed that genotype-dependent and organ-specific gene expression profiles can provide new insights into iron uptake, translocation rate, storage, and regulation in wheat which aid the prioritization of gene targets for iron biofortification and bioavailability.
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Affiliation(s)
- Saule Kenzhebayeva
- Department of Biotechnology/Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Saule Atabayeva
- Department of Biotechnology/Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Fatma Sarsu
- Plant Breeding and Genetics Section, General Directorate of Agricultural Research and Policies, Ankara, Turkey
| | - Alfiya Abekova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty Region, Kazakhstan
| | - Sabina Shoinbekova
- Department of Biotechnology/Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Nargul Omirbekova
- Department of Biotechnology/Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Gulina Doktyrbay
- Department of Biotechnology/Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aizhan Beisenova
- Department of Molecular Biology, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University of South Australia, Adelaide, Australia
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19
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A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms. PLANTS 2022; 11:plants11111430. [PMID: 35684203 PMCID: PMC9182744 DOI: 10.3390/plants11111430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/04/2023]
Abstract
Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.
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20
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Liu P, He L, Mei L, Zhai W, Chen X, Ma B. Rapid and Directional Improvement of Elite Rice Variety via Combination of Genomics and Multiplex Genome Editing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6156-6167. [PMID: 35575308 DOI: 10.1021/acs.jafc.1c08028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High yield and superior quality are the main goals pursued by breeders for crop improvement. However, both of them are complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombination is time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysis based multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Application of this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, the rare excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created by multiplex genome editing and successfully improved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a method for rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.
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Affiliation(s)
- Pengcheng Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Lumei He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Le Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World. PLANTS 2022; 11:plants11101297. [PMID: 35631721 PMCID: PMC9146367 DOI: 10.3390/plants11101297] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022]
Abstract
Technological applications in agriculture have evolved substantially to increase crop yields and quality to meet global food demand. Conventional techniques, such as seed saving, selective breeding, and mutation breeding (variation breeding), have dramatically increased crop production, especially during the ‘Green Revolution’ in the 1990s. However, newer issues, such as limited arable lands, climate change, and ever-increasing food demand, pose challenges to agricultural production and threaten food security. In the following ‘Gene Revolution’ era, rapid innovations in the biotechnology field provide alternative strategies to further improve crop yield, quality, and resilience towards biotic and abiotic stresses. These innovations include the introduction of DNA recombinant technology and applications of genome editing techniques, such as transcription activator-like effector (TALEN), zinc-finger nucleases (ZFN), and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas) systems. However, the acceptance and future of these modern tools rely on the regulatory frameworks governing their development and production in various countries. Herein, we examine the evolution of technological applications in agriculture, focusing on the motivations for their introduction, technical challenges, possible benefits and concerns, and regulatory frameworks governing genetically engineered product development and production.
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Hernández-Soto A, Pérez J, Fait-Zúñiga R, Rojas-Vásquez R, Gatica-Arias A, Vargas-Segura W, Abdelnour-Esquivel A. A Temporary Immersion System Improves Regeneration of In Vitro Irradiated Recalcitrant Indica Rice ( Oryza sativa L.) Embryogenic Calli. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030375. [PMID: 35161356 PMCID: PMC8838084 DOI: 10.3390/plants11030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 05/17/2023]
Abstract
The development of gamma ray-mutated rice lines is a solution for introducing genetic variability in indica rice varieties already being used by farmers. In vitro gamma ray (60Co) mutagenesis reduces chimeras and allows for a faster selection of desirable traits but requires the optimization of the laboratory procedure. The objectives of the present work were sequencing of matK and rbcL, the in vitro establishment of recalcitrant rice embryogenic calli, the determination of their sensitivity to gamma radiation, and optimization of the generation procedure. All sequenced genes matched perfectly with previously reported matK and rbcL O. sativa genes. Embryogenic calli induction improved using MS medium containing 2 mg L-1 2,4-D, and regeneration was achieved with MS medium with 3 mg L-1 BA and 0.5 mg L-1 NAA. The optimized radiation condition was 60 Gy, (LD20 = 64 Gy) with 83% regeneration. An immersion system (RITA®, Saint-Mathieu-de-Tréviers, France) of either 60 or 120 s every 8 h allowed systematic and homogeneous total regeneration of the recalcitrant line. Other well-known recalcitrant cultivars, CR1821 and CR1113, also had improved regeneration in the immersion system. To our knowledge, this is the first study reporting the use of an immersion system to allow for the regeneration of gamma-ray mutants from recalcitrant indica rice materials.
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Affiliation(s)
- Alejandro Hernández-Soto
- Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Cartago P.O. Box 159-7050, Costa Rica
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Cartago P.O. Box 159-7050, Costa Rica; (J.P.); (R.F.-Z.); (A.A.-E.)
- Correspondence:
| | - Jason Pérez
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Cartago P.O. Box 159-7050, Costa Rica; (J.P.); (R.F.-Z.); (A.A.-E.)
| | - Rebeca Fait-Zúñiga
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Cartago P.O. Box 159-7050, Costa Rica; (J.P.); (R.F.-Z.); (A.A.-E.)
| | - Randall Rojas-Vásquez
- Plant Biotechnology Laboratory, School of Biology, University of Costa Rica, San José P.O. Box 2060, Costa Rica; (R.R.-V.); (A.G.-A.)
- Programa de Posgrado en Ciencias Agrícolas y Recursos Naturales (PPCARN), School of Agronomy, University of Costa Rica, San José P.O. Box 2060, Costa Rica
- Vitroflora Labs S.A., Alajuela 20701, Costa Rica
| | - Andrés Gatica-Arias
- Plant Biotechnology Laboratory, School of Biology, University of Costa Rica, San José P.O. Box 2060, Costa Rica; (R.R.-V.); (A.G.-A.)
- Programa de Posgrado en Biología (PPB), School of Biology, University of Costa Rica, San José P.O. Box 2060, Costa Rica
| | - Walter Vargas-Segura
- Gamma Irradiation Laboratory, School of Physics, Costa Rica Institute of Technology, Cartago P.O. Box 159-7050, Costa Rica;
| | - Ana Abdelnour-Esquivel
- Biotechnology Research Center, Biology School, Costa Rica Institute of Technology, Cartago P.O. Box 159-7050, Costa Rica; (J.P.); (R.F.-Z.); (A.A.-E.)
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18:0 Lyso PC Derived by Bioactivity-Based Molecular Networking from Lentil Mutant Lines and Its Effects on High-Fat Diet-Induced Obese Mice. Molecules 2021; 26:molecules26247547. [PMID: 34946633 PMCID: PMC8707596 DOI: 10.3390/molecules26247547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Lentil (Lens culinaris; Fabaceae), one of the major pulse crops in the world, is an important source of proteins, prebiotics, lipids, and essential minerals as well as functional components such as flavonoids, polyphenols, and phenolic acids. To improve crop nutritional and medicinal traits, hybridization and mutation are widely used in plant breeding research. In this study, mutant lentil populations were generated by γ-irradiation for the development of new cultivars by inducing genetic diversity. Molecular networking via Global Natural Product Social Molecular Networking web platform and dipeptidyl peptide-IV inhibitor screening assay were utilized as tools for structure-based discovery of active components in active mutant lines selected among the lentil population. The bioactivity-based molecular networking analysis resulted in the annotation of the molecular class of phosphatidylcholine (PC) from the most active mutant line. Among PCs, 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (18:0 Lyso PC) was selected for further in vivo study of anti-obesity effect in a high-fat diet (HFD)-induced obese mouse model. The administration of 18:0 Lyso PC not only prevented body weight gain and decreased relative gonadal adipose tissue weight, but also attenuated the levels of total cholesterol, triglycerides, low-density lipoprotein cholesterol, and leptin in the sera of HFD-induced obese mice. Additionally, 18:0 Lyso PC treatment inhibited the increase of adipocyte area and crown-like structures in adipose tissue. Therefore, these results suggest that 18:0 Lyso PC is a potential compound to have protective effects against obesity, improving obese phenotype induced by HFD.
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Mullins E, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Naegeli H, Nogué F, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Casacuberta J, Lenzi P, Munoz Guajardo I, Raffaello T, Rostoks N. In vivo and in vitro random mutagenesis techniques in plants. EFSA J 2021; 19:e06611. [PMID: 34804231 PMCID: PMC8585642 DOI: 10.2903/j.efsa.2021.6611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Mutations are changes in the genetic material that may be transmitted to subsequent generations. Mutations appear spontaneously in nature and are one of the underlying driving forces of evolution. In plants, in vivo and in vitro random mutagenesis relies on the application of physical and chemical mutagens to increase the frequency of mutations thus accelerating the selection of varieties with important agronomic traits. The European Commission has requested EFSA to provide a more detailed description of in vivo and in vitro random mutagenesis techniques and the types of mutations and mechanisms involved, to be able to conclude on whether in vivo and in vitro random mutagenesis techniques are to be considered different techniques. To address the European Commission request, a literature search was conducted to collect information on the random mutagenesis techniques used in plants both in vivo and in vitro, on the type of mutations generated by such techniques and on the molecular mechanisms underlying formation of those mutations. The GMO Panel concludes that most physical and chemical mutagenesis techniques have been applied both in vivo and in vitro; the mutation process and the repair mechanisms act at cellular level and thus there is no difference between application of the mutagen in vivo or in vitro; and the type of mutations induced by a specific mutagen are expected to be the same, regardless of whether such mutagen is applied in vivo or in vitro. Indeed, the same mutation and the derived trait in a given plant species can be potentially obtained using both in vivo and in vitro random mutagenesis and the resulting mutants would be indistinguishable. Therefore, the GMO Panel concludes that the distinction between plants obtained by in vitro or in vivo approaches is not justified.
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25
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Potupureddi G, Balija V, Ballichatla S, C. G. G, Awalellu K, Lekkala S, Jallipalli K, M. G. G, Mohammad E, M M, Arutla S, Burka R, Gouri Shankar L, Ayyangari Phani P, Lella Venkata S, Raman Meenakshi S, B. C. V, Vemuri RB, Brahma K, Madnala R, Patel HK, Sonti RV, Madhav MS. Mutation resource of Samba Mahsuri revealed the presence of high extent of variations among key traits for rice improvement. PLoS One 2021; 16:e0258816. [PMID: 34669755 PMCID: PMC8528289 DOI: 10.1371/journal.pone.0258816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
To create novel variants for morphological, physiological, and biotic stress tolerance traits, induced mutations were created using Ethyl Methane Sulphonate (EMS) in the background of Samba Mahsuri (BPT 5204), a popular and mega rice variety of India. A population derived from 10, 500 M1 plants and their descendants were phenotyped for a wide range of traits leading to the identification of 124 mutants having variations in key agro-morphological traits, and 106 mutants exhibiting variation for physiological traits. Higher yield is the ultimate goal of crop improvement and we identified 574 mutants having higher yield compared to wild type by having better yield attributing traits. Further, a total of 50 mutants showed better panicle exertion phenotypes as compared to Samba Mahsuri leading to enhancement of yield. Upon rigorous screening for three major biotic stresses, 8 mutants showed enhanced tolerance for yellow stem borer (YSB), and 13 different mutants each showed enhanced tolerance for sheath blight (ShB) and bacterial leaf blight (BLB), respectively. In addition, screening at multiple locations that have diverse field isolates identified 3, 3, and 5 lines for tolerance to ShB, YSB and BLB, respectively. On the whole, 1231 desired mutant lines identified at M2 were forwarded to an advanced generation (M5). PCR based allele mining indicated that the BLB tolerant mutants have a different allele than the reported alleles for well-known genes affecting bacterial blight resistance. Whole genome re-sequencing revealed substantial variation in comparison to Samba Mahsuri. The lines showing enhanced tolerance to important biotic stresses (YSB, ShB and BLB) as well as several economically important traits are unique genetic resources which can be utilized for the identification of novel genes/alleles for different traits. The lines which have better agronomic features can be used as pre-breeding lines. The entire mutant population is maintained as a national resource for genetic improvement of the rice crop.
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Affiliation(s)
- Gopi Potupureddi
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Vishalakshi Balija
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Suneel Ballichatla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gokulan C. G.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Komal Awalellu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Swathi Lekkala
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Karteek Jallipalli
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gayathri M. G.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Ershad Mohammad
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Milton M
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Srikanth Arutla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Rajender Burka
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Laha Gouri Shankar
- Crop Protection, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | | | | | - Viraktamath B. C.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | - Kranthi Brahma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Raju Madnala
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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Gautam V, Swaminathan M, Akilan M, Gurusamy A, Suresh M, Kaithamalai B, Joel AJ. Early flowering, good grain quality mutants through gamma rays and EMS for enhancing per day productivity in rice ( Oryza sativa L.). Int J Radiat Biol 2021; 97:1716-1730. [PMID: 34597257 DOI: 10.1080/09553002.2021.1987563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE Rice is the prominent crop of world and it frames the important component of food chain. But, long duration of highly preferred rice varieties requires more water and are prone to biotic and abiotic stresses. Short duration rice varieties serve as a promising alternative in such cases. Hence, the present study was taken up to induce early flowering mutants in popular rice variety Bapatla 2231 (BPT 2231), a long duration medium slender rice variety using gamma rays and Ethyl Methane Sulfonate (EMS) treatment combinations. MATERIALS AND METHODS Five hundred well filled and viable grains of optimum moisture content (12%) were subjected to irradiation with 8 doses comprising 100 Gy, 200 Gy, 300 Gy, 350 Gy, 400 Gy, 450 Gy, 500 Gy and 600 Gy treatments. For combination treatments, the irradiated seeds of gamma rays were further treated with 30 mM concentrations of Ethyl Methane sulfonate (EMS). The irradiated population were raised up to M3 generation for the identification of early maturing mutants. The isolated early maturing mutants in M3 generation were characterized for phenotypic, biochemical and grain qualities. RESULTS The frequency of desirable early maturing mutants was observed more in combination treatments than the individual treatments of gamma rays. A total of 34 early maturing mutants (M) with variation for grain quality and biochemical traits were obtained. The mutants M-1, M-3, M-5, M-32, and M-34 were high yielding with fine grain type. The mutants M-4, M-17, M-18, M-19, M-20, and M-26 were high yielding with bold grain type. The mutants M-22, M-23, M-24, M-27, and M-28 were high in nutrient content. The early mutants matured 40-50 days earlier than control. CONCLUSION In this variety, the combination treatments showed higher mutation frequency, mutagenic effectiveness and efficiency than the gamma rays in induction of both chlorophyll and viable mutants. This study revealed that the combination treatments were more effective in inducing early mutants than the gamma ray treatments alone. The early maturing mutants can be released as variety after evaluation under different yield trials and the mutants with increased nutrient content and varied grain quality can be utilized in hybridization/heterosis breeding programs for rice crop improvement.
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Affiliation(s)
| | | | | | - Anand Gurusamy
- Department of Genetics and Plant Breeding, AC&RI, TNAU, Madurai, India
| | | | | | - A John Joel
- Department of Plant Biotechnology, CPMB, TNAU, Coimbatore, India
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Kim B, Piao R, Lee G, Koh E, Lee Y, Woo S, Jiang W, Septiningsih EM, Thomson MJ, Koh HJ. OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2587-2601. [PMID: 33950284 PMCID: PMC8277627 DOI: 10.1007/s00122-021-03844-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/22/2021] [Indexed: 06/07/2023]
Abstract
Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
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Affiliation(s)
- Backki Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Rihua Piao
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100 China
| | - Gileung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Eunbyeol Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826 Republic of Korea
| | - Wenzhu Jiang
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062 China
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - 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, 08826 Republic of Korea
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Dutta S, Hazra P, Saha S, Acharya B, Bhattacharjee T, Maurya PK, Banerjee S, Chakraborty I, Chattopadhyay A. Applied mutagenesis could improve economically important traits in bitter gourd (Momordica charantia L.). J Genet 2021. [DOI: 10.1007/s12041-021-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abbas A, Yu P, Sun L, Yang Z, Chen D, Cheng S, Cao L. Exploiting Genic Male Sterility in Rice: From Molecular Dissection to Breeding Applications. FRONTIERS IN PLANT SCIENCE 2021; 12:629314. [PMID: 33763090 PMCID: PMC7982899 DOI: 10.3389/fpls.2021.629314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Rice (Oryza sativa L.) occupies a very salient and indispensable status among cereal crops, as its vast production is used to feed nearly half of the world's population. Male sterile plants are the fundamental breeding materials needed for specific propagation in order to meet the elevated current food demands. The development of the rice varieties with desired traits has become the ultimate need of the time. Genic male sterility is a predominant system that is vastly deployed and exploited for crop improvement. Hence, the identification of new genetic elements and the cognizance of the underlying regulatory networks affecting male sterility in rice are crucial to harness heterosis and ensure global food security. Over the years, a variety of genomics studies have uncovered numerous mechanisms regulating male sterility in rice, which provided a deeper and wider understanding on the complex molecular basis of anther and pollen development. The recent advances in genomics and the emergence of multiple biotechnological methods have revolutionized the field of rice breeding. In this review, we have briefly documented the recent evolution, exploration, and exploitation of genic male sterility to the improvement of rice crop production. Furthermore, this review describes future perspectives with focus on state-of-the-art developments in the engineering of male sterility to overcome issues associated with male sterility-mediated rice breeding to address the current challenges. Finally, we provide our perspectives on diversified studies regarding the identification and characterization of genic male sterility genes, the development of new biotechnology-based male sterility systems, and their integrated applications for hybrid rice breeding.
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Affiliation(s)
- Adil Abbas
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Daibo Chen
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Northern Center of China National Rice Research Institute, Shuangyashan, China
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Nkhoma N, Shimelis H, Laing MD, Shayanowako A, Mathew I. Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers. BMC Genet 2020; 21:110. [PMID: 32948123 PMCID: PMC7501654 DOI: 10.1186/s12863-020-00914-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1–8–1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1–8–1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.
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Affiliation(s)
- Nelia Nkhoma
- African Centre for Crop Improvement, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.,Seed Control and Certification Institute, P. O. Box 350199, Chilanga, Lusaka, Zambia
| | - Hussein Shimelis
- African Centre for Crop Improvement, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Mark D Laing
- African Centre for Crop Improvement, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Admire Shayanowako
- African Centre for Crop Improvement, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Isack Mathew
- African Centre for Crop Improvement, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
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Lee SI, Park JW, Kwon SJ, Jo YD, Hong MJ, Kim JB, Choi HI. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. PLANTS 2020; 9:plants9091088. [PMID: 32847097 PMCID: PMC7570246 DOI: 10.3390/plants9091088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.
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