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Li X, Cui X, Ran R, Chen G, Zhao P. Genomic variation induced by a low concentration of ethyl methanesulfonate (EMS) in quinoa 'Longli-4' variety. BOTANICAL STUDIES 2024; 65:15. [PMID: 38967711 PMCID: PMC11226418 DOI: 10.1186/s40529-024-00427-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
Quinoa (Chenopodium quinoa, 2n = 4x = 36), a super pseudocereal crop, has been introduced into China nearly 60 years. Many excellent varieties have been developed through massive selection; however, few are developed through mutagenesis breeding. In this study, the 'Longli-4' variety, locally cultivated in Gansu province, Northwest China, was selected for experimentation. The grains of 'Longli-4' were treated with ethyl methanesulfonate (EMS) at a concentration of 0.8% for 8 h. Nine plants from independent M2 families were randomly selected to investigate the mutagenesis effect of EMS on the quinoa genome. The results indicated that the single nucleotide polymorphisms (SNPs) induced by EMS were unevenly distributed across all 18 chromosomes, with an average mutation frequency of 91.2 SNPs/Mb, ranging from 4.5 to 203.5 SNPs/Mb. A significant positive correlation between the number of SNPs and chromosome length was identified through linear model analysis. Transitions from G/C to A/T were the most predominated in all variant categories, accounting for 34.4-67.2% of the mutations, and SNPs were significantly enriched in intergenic regions, representing 69.2-75.1% of the total mutations. This study provides empirical support for the application of low concentration EMS treatment in quinoa breeding.
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Affiliation(s)
- Xiaofeng Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, P. R. China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiaoyun Cui
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, P. R. China
| | - Ruilan Ran
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guoxiong Chen
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, P. R. China
| | - Pengshan Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, P. R. China.
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, P. R. China.
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Sang S, Wang Y, Yao G, Ma T, Sun X, Zhang Y, Su N, Tan X, Abbas HMK, Ji S, Zaman QU. A Critical Review of Conventional and Modern Approaches to Develop Herbicide-Resistance in Rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14254. [PMID: 38499939 DOI: 10.1111/ppl.14254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/04/2024] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
Together with rice, weeds strive for nutrients and space in farmland, resulting in reduced rice yield and quality. Planting herbicide-resistant rice varieties is one of the effective ways to control weeds. In recent years, a series of breakthroughs have been made to generate herbicide-resistant germplasm, especially the emergence of biotechnological tools such as gene editing, which provides an inherent advantage for the knock-out or knock-in of the desired genes. In order to develop herbicide-resistant rice germplasm resources, gene manipulation has been conducted to enhance the herbicide tolerance of rice varieties through the utilization of techniques such as physical and chemical mutagenesis, as well as genome editing. Based on the current research and persisting problems in rice paddy fields, research on the generation of herbicide-resistant rice still needs to explore genetic mechanisms, stacking multiple resistant genes in a single genotype, and transgene-free genome editing using the CRISPR system. Current rapidly developing gene editing technologies can be used to mutate herbicide target genes, enabling targeted genes to maintain their biological functions, and reducing the binding ability of target gene encoded proteins to corresponding herbicides, ultimately resulting in herbicide-resistant crops. In this review article, we have summarized the utilization of conventional and modern approaches to develop herbicide-resistant cultivars in rice as an effective strategy for weed control in paddy fields, and discussed the technology and research directions for creating herbicide-resistant rice in the future.
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Affiliation(s)
- Shifei Sang
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Yanan Wang
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Guoqin Yao
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Tengyun Ma
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Xiaohan Sun
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Yijing Zhang
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Nan Su
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Xiaoyu Tan
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agricultural and Forestry, Jiangsu Province, P. R. China
| | | | - Shengdong Ji
- Department of Biotechnology, College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, P. R. China
| | - Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou Bay Seed Laboratory, Hainan University, Sanya, China
- College of Tropical Crops and Forestry, Hainan University, Haikou, China
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Hong Y, Sun Y, Zhang X, Zhang L, Yuan X, Ma Z, Wu M, Chen S. Screening and Identification of Garlic Leaf Blight ( Pleospora herbarum)-Resistant Mutants Induced by Ethyl Methane Sulphonate. Int J Mol Sci 2023; 24:11819. [PMID: 37511578 PMCID: PMC10380478 DOI: 10.3390/ijms241411819] [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: 05/31/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Garlic (Allium sativum L.) is a popular condiment used as both medicine and food. Garlic production in China is severely affected by continuous cropping and is especially affected by leaf blight disease. Garlic is sterile, so it is very important to develop specialized genotypes, such as those for disease resistance, nutritional quality, and plant architecture, through genetic modification and innovation. In this experiment, we applied the induction method using EMS to mutate garlic cloves of cultivar G024. From the mutations, 5000 M0 mutants were generated and planted in the field. Then, 199 M1 mutant lines were screened according to growth potential and resistance to leaf blight. From M2 to M3, 169 generational lines were selected that grew well and were resistant to leaf blight in the field. Thereafter, their resistance to leaf blight was further analyzed in the lab; 21 lines resistant to leaf blight that had good growth potential were identified, among which 3 mutants were significantly different, and these were further screened. Also, transcriptome analysis of two mutants infected with Pleospora herbarum, A150 and G024, was performed, and the results revealed 2026 and 4678 differentially expressed genes (DEGs), respectively. These DEGs were highly enriched in hormone signaling pathway, plant-pathogen interaction, and MAPK signaling pathway. Therefore, the results provide a theoretical and technical basis for the creation of garlic germplasm resistant to leaf blight.
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Affiliation(s)
- Yuanyuan Hong
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yinhui Sun
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xuan Zhang
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lingling Zhang
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xin Yuan
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhaoyang Ma
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Meiqian Wu
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Shuxia Chen
- Shaanxi Engineering Research Center for Vegetables, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
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Zafar K, Khan MZ, Amin I, Mukhtar Z, Zafar M, Mansoor S. Employing template-directed CRISPR-based editing of the OsALS gene to create herbicide tolerance in Basmati rice. AOB PLANTS 2023; 15:plac059. [PMID: 36873055 PMCID: PMC9977225 DOI: 10.1093/aobpla/plac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa) is one of the primary food crops which contributes major portion of daily calorie intake. It is used as model crop for various genome editing studies. Basmati rice was also explored for establishing non-homologous end joining-based genome editing. But it was not clear whether homology-directed repair (HDR)-based genome editing can be done in Basmati rice. The current study was designed to establish HDR-based genome editing in Basmati rice to develop herbicide tolerance. There is severe weed spread when rice is grown via direct planted rice method in various countries to save labour and water resources. Therefore, the use of herbicides is necessary to control weeds. These herbicides can also affect cultivated rice which creates the need to develop herbicide-tolerant rice. In current study, we introduced a point mutation in Acetolactate Synthase gene to convert tryptophan to leucine at position 548. For this purpose, different constructs for HDR were tested with different RNA scaffold and orientation of repair templates. Out of four different architectures, the one having repair template identical to the target DNA strand precisely edited the target site. We successfully established template-directed CRISPR-Cas9 system in Super Basmati rice by detecting desired substitutions at the target site in Acetolactate Synthase locus. Moreover, this editing of Acetolactate Synthase gene resulted in the production of herbicide tolerance in Super Basmati rice. This study suggests that such type of HDR system can be used to precisely edit other genes for crop improvement.
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Affiliation(s)
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
| | - Mehak Zafar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad 37000, Pakistan
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Pandian BA, Sexton-Bowser S, Prasad PV, Jugulam M. Current status and prospects of herbicide-resistant grain sorghum (Sorghum bicolor). PEST MANAGEMENT SCIENCE 2022; 78:409-415. [PMID: 34532972 DOI: 10.1002/ps.6644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Grain sorghum is a versatile crop, which can thrive under limited water and other inputs. However, crop loss from weed infestation continues to be a major constraint in grain sorghum production. Particularly, post-emergence grass weed control is a great challenge in grain sorghum due to the lack of herbicide options. Unlike in other major crops, such as maize or soybean, herbicide-resistant sorghum technology that can facilitate weed control throughout crop growing season is not available to growers yet. The development of herbicide-resistant sorghum can have potential to improve weed management, including post-emergence grass weed control. One of the major concerns in the development of such technology in sorghum is escape of resistance traits into weedy relatives of sorghum (e.g. shattercane and johnsongrass). This review focuses on sources of herbicide resistance in sorghum, the status of the development of herbicide-resistant sorghum technologies, overview of breeding methods, and limitations in the development of such sorghum technology as well as economic benefits for sorghum growers. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Balaji A Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Pv Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
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Galili S, Hershenhorn J, Edelman M, Sobolev V, Smirnov E, Amir-Segev O, Bellalou A, Dor E. Novel Mutation in the Acetohydroxyacid Synthase (AHAS), Gene Confers Imidazolinone Resistance in Chickpea Cicer arietinum L. Plants. PLANTS 2021; 10:plants10122791. [PMID: 34961262 PMCID: PMC8704328 DOI: 10.3390/plants10122791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022]
Abstract
Chickpea (Cicer arietinum L.) is an important crop in crop-rotation management in Israel. Imidazolinone herbicides have a wide spectrum of weed control, but chickpea plants are sensitive to acetohydroxyacid synthase (AHAS; also known as acetolactate synthase [ALS]) inhibitors. Using the chemical mutagen ethyl methanesulfonate (EMS), we developed a chickpea line (M2033) that is resistant to imidazolinone herbicides. A point mutation was detected in one of the two genes encoding the AHAS catalytic subunit of M2033. The transition of threonine to isoleucine at position 192 (203 according to Arabidopsis) conferred resistance of M2033 to imidazolinones, but not to other groups of AHAS inhibitors. The role of this substitution in the resistance of line M2033 was proven by genetic transformation of tobacco plants. This resistance showed a single-gene semidominant inheritance pattern. Conclusion: A novel mutation, T192I (T203I according to Arabidopsis), providing resistance to IMI herbicides but not to other groups of AHAS inhibitors, is described in the AHAS1 protein of EMS-mutagenized chickpea line M2033.
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Affiliation(s)
- Shmuel Galili
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion 7528809, Israel; (O.A.-S.); (A.B.)
- Correspondence: (S.G.); (E.D.)
| | - Joseph Hershenhorn
- Newe Ya’ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 3009503, Israel; (J.H.); (E.S.)
| | - Marvin Edelman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; (M.E.); (V.S.)
| | - Vladimir Sobolev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; (M.E.); (V.S.)
| | - Evgeny Smirnov
- Newe Ya’ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 3009503, Israel; (J.H.); (E.S.)
| | - Orit Amir-Segev
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion 7528809, Israel; (O.A.-S.); (A.B.)
| | - Aharon Bellalou
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion 7528809, Israel; (O.A.-S.); (A.B.)
| | - Evgenia Dor
- Newe Ya’ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 3009503, Israel; (J.H.); (E.S.)
- Correspondence: (S.G.); (E.D.)
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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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9
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Yan W, Deng XW, Yang C, Tang X. The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:579675. [PMID: 33841451 PMCID: PMC8025102 DOI: 10.3389/fpls.2021.579675] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Ethyl methanesulfonate (EMS) is a chemical mutagen believed to mainly induce G/C to A/T transitions randomly in plant genomes. However, mutant screening for phenotypes often gets multiple alleles for one gene but no mutant for other genes. We investigated the potential EMS mutagenesis bias and the possible correlations with sequence context and chromatin structure using the whole genome resequencing data collected from 52 rice EMS mutants. We defined the EMS-induced single nucleotide polymorphic sites (SNPs) and explored the genomic factors associated with EMS mutagenesis bias. Compared with natural SNPs presented in the Rice3K project, EMS showed a preference on G/C sites with flanking sequences also higher in GC contents. The composition of local dinucleotides and trinucleotides was also associated with the efficiency of EMS mutagenesis. The biased distribution of EMS-induced SNPs was positively correlated with CpG numbers, transposable element contents, and repressive epigenetic markers but negatively with gene expression, the euchromatin marker DNase I hypersensitive sites, and active epigenetic markers, suggesting that sequence context and chromatin structure might correlate with the efficiency of EMS mutagenesis. Exploring the genome-wide features of EMS mutagenesis and correlations with epigenetic modifications will help in the understanding of DNA repair mechanism.
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Affiliation(s)
- Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
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10
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Lv Q, Zhang X, Yuan D, Huang Z, Peng R, Peng J, Li Z, Tang L, Liu D, Zhou X, Wang L, Pan L, Shao Y, Mao B, Xin Y, Zhu L, Zhao B, Bai L. Exploring Natural Allelic Variations of the β-Triketone Herbicide Resistance Gene HIS1 for Application in indica Rice and Particularly in Two-Line Hybrid Rice. RICE (NEW YORK, N.Y.) 2021; 14:7. [PMID: 33415497 PMCID: PMC7790941 DOI: 10.1186/s12284-020-00448-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas. RESULTS By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice. CONCLUSIONS Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.
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Affiliation(s)
- Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Xiuli Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Zhiyuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Rui Peng
- Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jiming Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Zuren Li
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Ducai Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiaomao Zhou
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Lifeng Wang
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Lang Pan
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Yeyun Xin
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- Longping Branch of Graduate School, Hunan University, Changsha, China
| | - Lihuang Zhu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China.
- Longping Branch of Graduate School, Hunan University, Changsha, China.
| | - Lianyang Bai
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China.
- Longping Branch of Graduate School, Hunan University, Changsha, China.
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China.
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11
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Sagare DB, Abbai R, Jain A, Jayadevappa PK, Dixit S, Singh AK, Challa V, Alam S, Singh UM, Yadav S, Sandhu N, Kabade PG, Singh VK, Kumar A. More and more of less and less: Is genomics-based breeding of dry direct-seeded rice (DDSR) varieties the need of hour? PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2173-2186. [PMID: 32725933 PMCID: PMC7589319 DOI: 10.1111/pbi.13454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/07/2020] [Accepted: 07/13/2020] [Indexed: 06/02/2023]
Abstract
Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotype-based breeding.
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Affiliation(s)
- Deepti B. Sagare
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Abhinav Jain
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shilpi Dixit
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Arun Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shamshad Alam
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Shailesh Yadav
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | | | - Pramod G. Kabade
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Arvind Kumar
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
- International Rice Research Institute (IRRI)South‐Asia Regional Centre (SARC)VaranasiIndia
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12
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Grover N, Kumar A, Yadav AK, Gopala Krishnan S, Ellur RK, Bhowmick PK, Vinod KK, Bollinedi H, Nagarajan M, Viswanathan C, Sevanthi AMV, Singh NK, Mohapatra T, Singh AK. Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, "Pusa Basmati 1121". RICE (NEW YORK, N.Y.) 2020; 13:68. [PMID: 32930909 PMCID: PMC7492307 DOI: 10.1186/s12284-020-00423-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/20/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. RESULTS We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) "Robin" into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. CONCLUSION Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.
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Affiliation(s)
- Nitasha Grover
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Aruna Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Ashutosh Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, 612101, India
| | - C Viswanathan
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | | | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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13
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Inheritance and Molecular Characterization of a Novel Mutated AHAS Gene Responsible for the Resistance of AHAS-Inhibiting Herbicides in Rapeseed ( Brassica napus L.). Int J Mol Sci 2020; 21:ijms21041345. [PMID: 32079260 PMCID: PMC7072869 DOI: 10.3390/ijms21041345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/04/2020] [Accepted: 02/14/2020] [Indexed: 11/25/2022] Open
Abstract
The use of herbicides is an effective and economic way to control weeds, but their availability for rapeseed is limited due to the shortage of herbicide-resistant cultivars in China. The single-point mutation in the acetohydroxyacidsynthase (AHAS) gene can lead to AHAS-inhibiting herbicide resistance. In this study, the inheritance and molecular characterization of the tribenuron-methyl (TBM)-resistant rapeseed (Brassica napus L.) mutant, K5, are performed. Results indicated that TBM-resistance of K5 was controlled by one dominant allele at a single nuclear gene locus. The novel substitution of cytosine with thymine at position 544 in BnAHAS1 was identified in K5, leading to the alteration of proline with serine at position 182 in BnAHAS1. The TBM-resistance of K5 was approximately 100 times that of its wild-type ZS9, and K5 also showed cross-resistance to bensufuron-methyl and monosulfuron-ester sodium. The BnAHAS1544T transgenic Arabidopsis exhibited higher TBM-resistance than that of its wild-type, which confirmed that BnAHAS1544T was responsible for the herbicide resistance of K5. Simultaneously, an allele-specific marker was developed to quickly distinguish the heterozygous and homozygous mutated alleles BnAHAS1544T. In addition, a method for the fast screening of TBM-resistant plants at the cotyledon stage was developed. Our research identified and molecularly characterized one novel mutative AHAS allele in B. napus and laid a foundation for developing herbicide-resistant rapeseed cultivars.
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14
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Buffon G, Lamb TI, Lopes MCB, Sperotto RA, Timmers LFSM. Push It to the Limit: Identification of Novel Amino Acid Changes on the Acetolactate Synthase Enzyme of Rice That Putatively Confer High Level of Tolerance to Different Imidazolinones. Front Bioeng Biotechnol 2020; 8:73. [PMID: 32117948 PMCID: PMC7033567 DOI: 10.3389/fbioe.2020.00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/28/2020] [Indexed: 11/24/2022] Open
Abstract
Advancements in genetically modified herbicide tolerance technology opened a new way to manage weed populations in crop fields. Since then, many important genetically modified crops that are tolerant to various herbicides have been developed and commercialized. Herbicides primarily act by disrupting key enzymes involved in essential metabolic or physiological processes associated with growth and development of plants. Most of the herbicide tolerant plants have been developed by introducing point mutations (non-GM approach) in the target site of herbicide action, due to the advantage of easier registration/release for commercial cultivation as well as wider public acceptance. Of the various herbicides, Imidazolinones are probably the most widely targeted ones for developing herbicide tolerant crops through non-GM approach. In rice, different mutant lines presenting amino acids changes in acetolactate synthase (ALS) have the ability to tolerate different Imidazolinones, including point mutations of Glycine to Glutamate in position 628, Serine to Asparagine in position 627, and a double mutation Tryptophan to Leucine in position 548/Serine to Isoleucine in position 627. The use of specific herbicides in combination of these mutant lines provides a reliable approach to eliminate weeds in the fields. However, the continuous overuse of a single herbicide multiple times in a growing season increases the potential risk of evolution of resistant weeds, which has become a major concern in agriculture worldwide. For this reason, the development of novel mutations in ALS (Os02g30630) to generate rice plants more tolerant to Imidazolinones than the available mutant rice lines is still a hot topic in plant-herbicide interaction field. Keeping that in mind, we carried out molecular docking experiments of Imidazolinone herbicides imazapic, imazapyr, imazaquin, and imazethapyr to evaluate the interaction of these molecules in the binding cavity of ALS from rice, being able to identify the most important amino acids responsible for the stability of these four herbicides. After introducing point mutations in these specific positions (one at a time) using Alanine scanning mutagenesis method and recalculating the effect in the affinity of herbicide-ALS interaction, we were able to propose novel amino acid residues (mainly Lysine in position 230 and Arginine in position 351) on the structure of ALS presenting a highest impact in the binding of Imidazolinones to ALS when compared to the already known amino acid mutations. This rational approach allows the researcher/farmer to choose the number of point mutations to be inserted in a rice cultivar, which will be dependent on the type of Imidazolinone used. To obtain a rice cultivar capable to tolerate the four Imidazolinone tested at the same time, we suggest six amino acid mutations at positions Val170, Phe180, Lys230, Arg351, Trp548, and Ser627 in the OsALS1.
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Affiliation(s)
- Giseli Buffon
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
| | - Thainá Inês Lamb
- Biological Sciences and Health Center, University of Taquari Valley – Univates, Lajeado, Brazil
| | | | - Raul Antonio Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Biological Sciences and Health Center, University of Taquari Valley – Univates, Lajeado, Brazil
| | - Luís Fernando Saraiva Macedo Timmers
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Biological Sciences and Health Center, University of Taquari Valley – Univates, Lajeado, Brazil
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15
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Poli Y, Nallamothu V, Balakrishnan D, Ramesh P, Desiraju S, Mangrauthia SK, Voleti SR, Neelamraju S. Increased Catalase Activity and Maintenance of Photosystem II Distinguishes High-Yield Mutants From Low-Yield Mutants of Rice var. Nagina22 Under Low-Phosphorus Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:1543. [PMID: 30510556 PMCID: PMC6252357 DOI: 10.3389/fpls.2018.01543] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/02/2018] [Indexed: 05/28/2023]
Abstract
An upland rice variety, Nagina22 (N22) and its 137 ethyl methanesulfonate (EMS)-induced mutants, along with a sensitive variety, Jaya, was screened both in low phosphorus (P) field (Olsen P 1.8) and in normal field (Olsen P 24) during dry season. Based on the grain yield (YLD) of plants in normal field and plants in low P field, 27 gain of function (high-YLD represented as hy) and 9 loss of function (low-YLD represented as ly) mutants were selected and compared with N22 for physiological and genotyping studies. In low P field, hy mutants showed higher P concentration in roots, leaves, grains, and in the whole plant than in ly mutants at harvest. In low P conditions, F v/F m and qN were 24% higher in hy mutants than in ly mutants. In comparison with ly mutants, the superoxide dismutase (SOD) activity in the roots and leaves of hy mutants in low P fields was 9% and 41% higher at the vegetative stage, respectively, but 51% and 14% lower in the roots and leaves at the reproductive stage, respectively. However, in comparison with ly mutants, the catalase (CAT) activity in the roots and leaves of hy mutants in low P fields was 35% higher at the vegetative stage and 15% and 17% higher at the reproductive stage, respectively. Similarly, hy mutants in low P field showed 20% and 80% higher peroxidase (POD) activity in the roots and leaves at the vegetative stage, respectively, but showed 14% and 16% lower POD activity at the reproductive stage in the roots and leaves, respectively. Marker trait association analysis using 48 simple sequence repeat (SSR) markers and 10 Pup1 gene markers showed that RM3648 and RM451 in chromosome 4 were significantly associated with grain YLD, tiller number (TN), SOD, and POD activities in both the roots and leaves in low P conditions only. Similarly, RM3334 and RM6300 in chromosome 5 were associated with CAT activity in leaves in low P conditions. Notably, grain YLD was positively and significantly correlated with CAT activity in the roots and shoots, F v/F m and qN in low P conditions, and the shoots' P concentration and qN in normal conditions. Furthermore, CAT activity in shoots was positively and significantly correlated with TN in both low P and normal conditions. Thus, chromosomal regions and physiological traits that have a role in imparting tolerance to low P in the field were identified.
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Affiliation(s)
- Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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16
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Yugandhar P, Sun Y, Liu L, Negi M, Nallamothu V, Sun S, Neelamraju S, Rai V, Jain A. Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:1-13. [PMID: 29957570 DOI: 10.1016/j.plaphy.2018.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/09/2023]
Abstract
In earlier studies at IIRR, Hyderabad, screening of ∼2000 EMS mutants of the rice variety Nagina22 (N22) resulted in the identification of 11 loss-of-function mutants with zero grain yield in Pi-deprived soil under field condition. Among these mutants, NH101 was selected for comparative analyses with N22 for various morphophysiological and/or molecular traits during growth in a hydroponic system (7 d) and in a pot soil (50% flowering) under different Pi regime. The total length of the seminal and adventitious roots, agronomic traits (panicle length and unfilled spikelet/panicle), activities of the antioxidant enzymes (SOD, POD, and APX), and the relative expression levels of the genes involved in the maintenance of Pi homeostasis (MPH) i.e., OsPHR2, SPX1/2 OsPT4, 6, and 8 showed significant increase in the Pi-deprived mutant compared with N22. Whereas, some of the traits showed significant reduction in NH101 than N22 such as number of tillers and filled spikelets/panicle, yield, contents of Pi and externally secreted APase, activity of CAT, and the relative expression levels of MPH genes i.e., OsmiR399a, OsPHO1;2, OsIPS1, OsPAP10a, OsPT2, 9, and 10. The study highlighted wide spectrum differential effects of the mutation in NH101 on various traits that play important roles governing the maintenance of Pi homeostasis. This mutant thus provides a rich repository of genetic material amenable for the identification of the genes that are pivotal for Pi use efficiency.
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Affiliation(s)
- Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lu Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Manisha Negi
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | | | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sarla Neelamraju
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
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17
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Fartyal D, Agarwal A, James D, Borphukan B, Ram B, Sheri V, Agrawal PK, Achary VMM, Reddy MK. Developing dual herbicide tolerant transgenic rice plants for sustainable weed management. Sci Rep 2018; 8:11598. [PMID: 30072810 PMCID: PMC6072789 DOI: 10.1038/s41598-018-29554-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/14/2018] [Indexed: 11/25/2022] Open
Abstract
Herbicides are important constituents of modern integrated weed management system. However, the continuous use of a single herbicide leads to the frequent evolution of resistant weeds which further challenges their management. To overcome this situation, alternating use of multiple herbicides along with conventional weed-management practices is suitable and recommended. The development of multiple herbicide-tolerant crops is still in its infancy, and only a few crops with herbicide tolerance traits have been reported and commercialized. In this study, we developed transgenic rice plants that were tolerant to both bensulfuron methyl (BM) and glufosinate herbicides. The herbicide tolerant mutant variant of rice AHAS (Acetohydroxyacid synthase) was overexpressed along with codon optimized bacterial bar gene. The developed transgenic lines showed significant tolerance to both herbicides at various stages of plant development. The selected transgenic lines displayed an increased tolerance against 100 μM BM and 30 mg/L phosphinothricin during seed germination stage. Foliar applications further confirmed the dual tolerance to 300 μM BM and 2% basta herbicides without any significant growth and yield penalties. The development of dual-herbicide-tolerant transgenic plants adds further information to the knowledge of crop herbicide tolerance for sustainable weed management in modern agricultural system.
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Affiliation(s)
- Dhirendra Fartyal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Uttarakhand Technical University, Dehradun, Uttarakhand, India
| | - Aakrati Agarwal
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Plant Molecular Biology Lab, Department of Botany, University of Delhi, New Delhi, India
| | - Donald James
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhabesh Borphukan
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Babu Ram
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Uttarakhand Technical University, Dehradun, Uttarakhand, India
| | - Vijay Sheri
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pawan K Agrawal
- National Agricultural Science Fund, Indian Council of Agricultural Research, New Delhi, India
| | - V Mohan Murali Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - M K Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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18
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Sevanthi AMV, Kandwal P, Kale PB, Prakash C, Ramkumar MK, Yadav N, Mahato AK, Sureshkumar V, Behera M, Deshmukh RK, Jeyaparakash P, Kar MK, Manonmani S, Muthurajan R, Gopala KS, Neelamraju S, Sheshshayee MS, Swain P, Singh AK, Singh NK, Mohapatra T, Sharma RP. Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type. FRONTIERS IN PLANT SCIENCE 2018; 9:1179. [PMID: 0 PMCID: PMC6132179 DOI: 10.3389/fpls.2018.01179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/24/2018] [Indexed: 05/07/2023]
Abstract
The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).
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Affiliation(s)
- Amitha M. V. Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- *Correspondence: Amitha M. V. Sevanthi,
| | - Prashant Kandwal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Prashant B. Kale
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - M. K. Ramkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Neera Yadav
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ajay K. Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - V. Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | | | - Meera K. Kar
- ICAR-National Rice Research Institute, Cuttack, India
| | - S. Manonmani
- Tamil Nadu Agricultural University, Coimbatore, India
| | | | - K. S. Gopala
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - P. Swain
- ICAR-National Rice Research Institute, Cuttack, India
| | - Ashok K. Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - N. K. Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - R. P. Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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