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Li M, Liu Z, Jiang N, Laws B, Tiskevich C, Moose SP, Topp CN. Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture. FRONTIERS IN PLANT SCIENCE 2024; 14:1260005. [PMID: 38288407 PMCID: PMC10822944 DOI: 10.3389/fpls.2023.1260005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
A central goal of biology is to understand how genetic variation produces phenotypic variation, which has been described as a genotype to phenotype (G to P) map. The plant form is continuously shaped by intrinsic developmental and extrinsic environmental inputs, and therefore plant phenomes are highly multivariate and require comprehensive approaches to fully quantify. Yet a common assumption in plant phenotyping efforts is that a few pre-selected measurements can adequately describe the relevant phenome space. Our poor understanding of the genetic basis of root system architecture is at least partially a result of this incongruence. Root systems are complex 3D structures that are most often studied as 2D representations measured with relatively simple univariate traits. In prior work, we showed that persistent homology, a topological data analysis method that does not pre-suppose the salient features of the data, could expand the phenotypic trait space and identify new G to P relations from a commonly used 2D root phenotyping platform. Here we extend the work to entire 3D root system architectures of maize seedlings from a mapping population that was designed to understand the genetic basis of maize-nitrogen relations. Using a panel of 84 univariate traits, persistent homology methods developed for 3D branching, and multivariate vectors of the collective trait space, we found that each method captures distinct information about root system variation as evidenced by the majority of non-overlapping QTL, and hence that root phenotypic trait space is not easily exhausted. The work offers a data-driven method for assessing 3D root structure and highlights the importance of non-canonical phenotypes for more accurate representations of the G to P map.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Zhengbin Liu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Ni Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Benjamin Laws
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Christine Tiskevich
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stephen P. Moose
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Gifford ML, Xu G, Dupuy LX, Vissenberg K, Rebetzke G. Root architecture and rhizosphere-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:503-507. [PMID: 38197460 PMCID: PMC10773993 DOI: 10.1093/jxb/erad488] [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: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024]
Abstract
Plant roots fulfil crucial tasks during a plant's life. As roots encounter very diverse conditions while exploring the soil for resources, their growth and development must be responsive to changes in the rhizosphere, resulting in root architectures that are tailor-made for all prevailing circumstances. Using multi-disciplinary approaches, we are gaining more intricate insights into the regulatory mechanisms directing root system architecture. This Special Issue provides insights into our advancement of knowledge on different aspects of root development and identifies opportunities for future research.
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Affiliation(s)
- Miriam L Gifford
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Guohua Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lionel X Dupuy
- Department of Conservation of Natural Resources, Neiker, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Plant Biochemistry and Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Stavromenos PC 71410, Heraklion, Crete, Greece
| | - Greg Rebetzke
- CSIRO Agriculture and Food, PO Box 1700, Canberra ACT 2601, Australia
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Hostetler AN, Morais de Sousa Tinoco S, Sparks EE. Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:553-562. [PMID: 37798135 DOI: 10.1093/jxb/erad390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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Wang H, Wang H, Liu H, Wan T, Li Y, Zhang K, Shabala S, Li X, Chen Y, Yu M. Aluminium stress-induced modulation of root gravitropism in pea (Pisum sativum) via auxin signalling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108315. [PMID: 38157836 DOI: 10.1016/j.plaphy.2023.108315] [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: 09/01/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Aluminium (Al) toxicity stands out as a primary cause of crop failure in acidic soils. The root gravity setpoint angle (GSA), one of the important traits of the root system architecture (RSA), plays a pivotal role in enabling plants to adapt to abiotic stress. This study explored the correlation between GSA and Al stress using hydroponic culture with pea (Pisum sativum) plants. The findings revealed that under Al stress, GSA increased in newly developed lateral roots. Notably, this response remained consistent regardless of the treatment duration, extending for at least 3 days during the experiment. Furthermore, exposure to Al led to a reduction in both the size and quantity of starch granules, pivotal components linked to gravity perception. The accumulation of auxin in root transition zone increased. This variation was mirrored in the expression of genes linked to granule formation and auxin efflux, particularly those in the PIN-formed family. This developmental framework suggested a unique role for the root gravitropic response that hinges on starch granules and auxin transport, acting as mediators in the modulation of GSA under Al stress. Exogenous application of indole-3-acetic acid (IAA) and the auxin efflux inhibitor N-1-naphthylphthalamic acid (NPA) had an impact on the root gravitropic response to Al stress. The outcomes indicate that Al stress inhibited polar auxin transport and starch granule formation, the two processes crucial for gravitropism. This impairment led to an elevation in GSA and a reconfiguration of RSA. This study introduces a novel perspective on how plant roots react to Al toxicity, culminating in RSA modification in the context of acidic soil with elevated Al concentrations.
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Affiliation(s)
- Hui Wang
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China
| | - Huayang Wang
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Houzhou Liu
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China
| | - Tao Wan
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China
| | - Yalin Li
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China
| | - Ketong Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sergey Shabala
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China; School of Biological Sciences, University of Western Australia, Perth, 6009, Australia
| | - Xuewen Li
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China.
| | - Yinglong Chen
- School of Agriculture and Environment & Institute of Agriculture, University of Western Australia, Perth, 6009, Australia.
| | - Min Yu
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China; School of Agriculture and Environment & Institute of Agriculture, University of Western Australia, Perth, 6009, Australia.
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Chang Y, Lv G. Nitraria sibirica adapts to long-term soil water deficit by reducing photosynthesis, stimulating antioxidant systems, and accumulating osmoregulators. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108265. [PMID: 38091936 DOI: 10.1016/j.plaphy.2023.108265] [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: 09/26/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Amid climate change and shifts in precipitation patterns, drought conditions are expanding worldwide. Drought stress severely threatens plant growth in arid and semi-arid regions, wherein shrubs play a crucial role in maintaining ecological stability. Despite its ecological significance, studies are lacking on how Nitraria sibirica adapts to long-term drought stress. Therefore, in this study, to elucidate the mechanism of drought stress adaptation in N. sibirica, we analysed morphological, physiological, and transcriptional characteristics of plants in two soil habitats: riparian (moist) and desert (arid). The results showed that in desert soils, as soil water content decreased, leaf thickness increased, while plant height and leaf area decreased. Physiologically, photosynthesis decreased; soluble sugar, starch, proline, and hydrogen peroxide content increased significantly; while soluble proteins decreased significantly. Additionally, membrane lipid peroxidation products and antioxidant enzyme activities significantly increased under drought stress. Then, Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis identified 313 key genes, which were considered the most significantly enriched in the photosynthesis and photosynthetic antenna protein pathways. Further, we found that the proteins encoding photosystem II (PsbP, PsbQ, PsbR, PsbY, and Psb27), photosystem I (PsaD, PsaF, PsaG, PsaH, PsaK, and PsaO), photosynthetic electron transport (PetF), and light-trapping antenna proteins were significantly downregulated under drought stress. Taken together, these results suggest that N. sibirica adapts to long-term drought conditions by suppressing photosynthesis, activating antioxidant systems, and recruiting osmoregulators. This study provides a basis for elucidating the growth mechanisms of N. sibirica under long-term drought stress conditions.
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Affiliation(s)
- Yaling Chang
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, 830046, PR China; Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, 830046, PR China.
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, 830046, PR China; Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, 830046, PR China.
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Zaman Z, Iqbal R, Jabbar A, Zahra N, Saleem B, Kiran A, Maqbool S, Rasheed A, Naeem MK, Khan MR. Genetic Signature Controlling Root System Architecture in Diverse Spring Wheat Germplasm. PHYSIOLOGIA PLANTARUM 2024; 176:e14183. [PMID: 38343301 DOI: 10.1111/ppl.14183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 02/15/2024]
Abstract
Roots are the main sensing organ, initiating multiple signaling pathways in response to abiotic factors, including nutrients, drought, and salt stress. A focus on improving the root system architecture is a key strategy to mitigate these stresses in wheat crop. In the present study, a diversity panel comprising indigenous landraces and historical cultivars from Pakistan was characterized for the root system architecture (RSA) and important loci were identified using a genome-wide association study (GWAS). RSA of the diversity panel was characterized 30 days after sowing in brunch tubes, and root images were taken. A high-throughput root imaging analysis using Rhizovision software was performed by setting the scale to extract the eight RSA traits and four plant biomass-related traits. GWAS identified 323 association signals for 12 root and biomass traits present on all wheat chromosomes, while the most important and reliable genetic loci (based on pleotropic loci and candidate genes) were identified on chromosomes 2A, 2B, 5A, 5D, 6A, 7B, and 7D for RSA. SNP annotation and transcriptome profiling identified nine candidate genes regulating the RSA and plant biomass traits, including ROOTLESS WITH UNDETECTABLE MERISTEM1, MYB TRANSCRIPTION FACTOR4, BRASSINOSTEROID INSENSITIVE1, SLENDER RICE1, AUXIN-RESPONSIVE FACTOR25, SCARECROW, NARROW LEAF2, PIN-FORMED1 AND PHOSPHATE TRANSCRIPTION FACTOR1. This study provided pre-breeding information for deep-rooting genotypes and associated markers that will accelerate the incorporation of such traits in breeding.
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Affiliation(s)
- Zahra Zaman
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Rubab Iqbal
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- Department of Botany, University of Agriculture, Faisalabad
| | - Abdul Jabbar
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Aysha Kiran
- Department of Botany, University of Agriculture, Faisalabad
| | - Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
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57
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Zou Y, Zhang Y, Cui J, Gao J, Guo L, Zhang Q. Nitrogen fertilization application strategies improve yield of the rice cultivars with different yield types by regulating phytohormones. Sci Rep 2023; 13:21803. [PMID: 38071312 PMCID: PMC10710506 DOI: 10.1038/s41598-023-48491-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Rice (Oryza sativa L.) is the most important food crop worldwide, and its sustainable development is essential to ensure global food security. Panicle morphological and physiological characteristics plays an important role in rice yield formation. However, under different nitrogen (N) fertilization strategies, it is not clear whether the morphological and physiological state of panicles at panicle development stage affects the formation of yield. To understand how the panicle differentiation and development, and grain yield are affected by the N fertilization strategies, and clarify the relationship between related traits and yield in the process of panicle development in different cultivars. In this study consisted of no N fertilizer and four N fertilization strategies, a panicle weight type (PWT) rice cultivar, Dongfu 114 (DF114) and a panicle number type (PNT) rice cultivar, Longdao 11 (LD11) were grown in the field. The results showed that N fertilization strategies could improve the nitrogen use efficiency and yield of rice, but the response of different rice varieties to N fertilizer strategies was different. Different from the DF114, the further increase of panicle N fertilizer ratio could not further improve the yield of LD11, and the highest grain yield of DF114 and LD11 was obtained under N4 and N3 conditions, respectively. In addition, this study found that N fertilizer strategies can affect the content of phytohormones in rice at the panicle differentiation stage, and then regulate the differentiation and development of rice panicles to affect yield. It is of great significance to optimize the application mode of N fertilizer according to the characteristics of varieties to improve rice yield and ensure food security.
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Affiliation(s)
- Yue Zou
- Agronomy College Jilin Agricultural University, Changchun, 130118, China
- Key Laboratory of Germplasm Innovation and Physiological Ecology of Grain Crops in Cold Region, Ministry of Education, Harbin, 150030, China
| | - Yuchen Zhang
- Agronomy College Jilin Agricultural University, Changchun, 130118, China
| | - Jiehao Cui
- Agronomy College Jilin Agricultural University, Changchun, 130118, China
| | - Jiacong Gao
- Agronomy College Jilin Agricultural University, Changchun, 130118, China
| | - Liying Guo
- Agronomy College Jilin Agricultural University, Changchun, 130118, China.
| | - Qiang Zhang
- Agronomy College Jilin Agricultural University, Changchun, 130118, China.
- Key Laboratory of Germplasm Innovation and Physiological Ecology of Grain Crops in Cold Region, Ministry of Education, Harbin, 150030, China.
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58
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Zhang N, Gui S, Wang Y. LAZing around: The intricate dance of amyloplast sedimentation and gravity sensing in plants. MOLECULAR PLANT 2023; 16:1887-1889. [PMID: 37919895 DOI: 10.1016/j.molp.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Ning Zhang
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signaling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Songtao Gui
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yonghong Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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59
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Benitez-Alfonso Y, Soanes BK, Zimba S, Sinanaj B, German L, Sharma V, Bohra A, Kolesnikova A, Dunn JA, Martin AC, Khashi U Rahman M, Saati-Santamaría Z, García-Fraile P, Ferreira EA, Frazão LA, Cowling WA, Siddique KHM, Pandey MK, Farooq M, Varshney RK, Chapman MA, Boesch C, Daszkowska-Golec A, Foyer CH. Enhancing climate change resilience in agricultural crops. Curr Biol 2023; 33:R1246-R1261. [PMID: 38052178 DOI: 10.1016/j.cub.2023.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.
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Affiliation(s)
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sibongile Zimba
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK; Horticulture Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Liam German
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Anastasia Kolesnikova
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Jessica A Dunn
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Azahara C Martin
- Institute for Sustainable Agriculture (IAS-CSIC), Córdoba 14004, Spain
| | - Muhammad Khashi U Rahman
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Zaki Saati-Santamaría
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain; Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Paula García-Fraile
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Evander A Ferreira
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Leidivan A Frazão
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Wallace A Cowling
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Muhammad Farooq
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia; Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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60
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Jacquet S, Li S, Mian R, Kassem MA, Rashad L, Viera S, Reta F, Reta J, Yuan J. Evaluating the Response of Glycine soja Accessions to Fungal Pathogen Macrophomina phaseolina during Seedling Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3807. [PMID: 38005704 PMCID: PMC10675638 DOI: 10.3390/plants12223807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 11/26/2023]
Abstract
Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.
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Affiliation(s)
- Shirley Jacquet
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 141 Experiment Station Road, P.O. Box 345, Stoneville, MS 38776, USA;
| | - Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 3127 Ligon St., Raleigh, NC 27607, USA;
| | - My Abdelmajid Kassem
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Layla Rashad
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Sonia Viera
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Francisco Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Juan Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Jiazheng Yuan
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
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Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky JR, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo VL, Lucas SM, Lazic D, Gailing O, Carlson J, Staton M. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (BETHESDA, MD.) 2023; 13:jkad209. [PMID: 37708394 PMCID: PMC10627279 DOI: 10.1093/g3journal/jkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.
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Affiliation(s)
- Beant Kapoor
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Tatyana Zhebentyayeva
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40506, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Kuelheim
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, MI 49931, USA
| | - Mark Coggeshall
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Chris Heim
- Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Leites
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, USDA-FS, SRS-4160, Department of Ecology & Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Victoria L DeLeo
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Lucas
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Desanka Lazic
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Lower Saxony 37077, Germany
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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Sharma N, Raman H, Wheeler D, Kalenahalli Y, Sharma R. Data-driven approaches to improve water-use efficiency and drought resistance in crop plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111852. [PMID: 37659733 DOI: 10.1016/j.plantsci.2023.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.
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Affiliation(s)
- Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia.
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
| | - Yogendra Kalenahalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India
| | - Rita Sharma
- Department of Biological Sciences, BITS Pilani, Pilani Campus, Rajasthan 333031, India
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Dalal M, Mansi, Mayandi K. Zoom-in to molecular mechanisms underlying root growth and function under heterogeneous soil environment and abiotic stresses. PLANTA 2023; 258:108. [PMID: 37898971 DOI: 10.1007/s00425-023-04262-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023]
Abstract
MAIN CONCLUSION The review describes tissue-specific and non-cell autonomous molecular responses regulating the root system architecture and function in plants. Phenotypic plasticity of roots relies on specific molecular and tissue specific responses towards local and microscale heterogeneity in edaphic factors. Unlike gravitropism, hydrotropism in Arabidopsis is regulated by MIZU KUSSIE1 (MIZ1)-dependent asymmetric distribution of cytokinin and activation of Arabidopsis response regulators, ARR16 and ARR17 on the lower water potential side of the root leading to higher cell division and root bending. The cortex specific role of Abscisic acid (ABA)-activated SNF1-related protein kinase 2.2 (SnRK2.2) and MIZ1 in elongation zone is emerging for hydrotropic curvature. Halotropism involves clathrin-mediated internalization of PIN FORMED 2 (PIN2) proteins at the side facing higher salt concentration in the root tip, and ABA-activated SnRK2.6 mediated phosphorylation of cortical microtubule-associated protein Spiral2-like (SP2L) in the root transition zone, which results in anisotropic cell expansion and root bending away from higher salt. In hydropatterning, Indole-3-acetic acid 3 (IAA3) interacts with SUMOylated-ARF7 (Auxin response factor 7) and prevents expression of Lateral organ boundaries-domain 16 (LBD16) in air-side of the root, while on wet side of the root, IAA3 cannot repress the non-SUMOylated-ARF7 thereby leading to LBD16 expression and lateral root development. In root vasculature, ABA induces expression of microRNA165/microRNA166 in endodermis, which moves into the stele to target class III Homeodomain leucine zipper protein (HD-ZIP III) mRNA in non-cell autonomous manner. The bidirectional gradient of microRNA165/6 and HD-ZIP III mRNA regulates xylem patterning under stress. Understanding the tissue specific molecular mechanisms regulating the root responses under heterogeneous and stress environments will help in designing climate-resilient crops.
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Affiliation(s)
- Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| | - Mansi
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Karthikeyan Mayandi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
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Chen J, Yu R, Li N, Deng Z, Zhang X, Zhao Y, Qu C, Yuan Y, Pan Z, Zhou Y, Li K, Wang J, Chen Z, Wang X, Wang X, He SN, Dong J, Deng XW, Chen H. Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants. Cell 2023; 186:4788-4802.e15. [PMID: 37741279 PMCID: PMC10615846 DOI: 10.1016/j.cell.2023.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/04/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains uncharacterized. The LAZY proteins are known as key regulators of gravitropism, and lazy mutants show striking gravitropic defects. Here, we report that gravistimulation by reorientation triggers mitogen-activated protein kinase (MAPK) signaling-mediated phosphorylation of Arabidopsis LAZY proteins basally polarized in root columella cells. Phosphorylation of LAZY increases its interaction with several translocons at the outer envelope membrane of chloroplasts (TOC) proteins on the surface of amyloplasts, facilitating enrichment of LAZY proteins on amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and root differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle-movement-triggered molecular polarity formation.
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Affiliation(s)
- Jiayue Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Renbo Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Vegetable Research Center, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Na Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zhaoguo Deng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xinxin Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yaran Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chengfu Qu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yanfang Yuan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhexian Pan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yangyang Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kunlun Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiajun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhiren Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaoyi Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolian Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shu-Nan He
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haodong Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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Marti-Jerez K, Català-Forner M, Tomàs N, Murillo G, Ortiz C, Sánchez-Torres MJ, Vitali A, Lopes MS. Agronomic performance and remote sensing assessment of organic and mineral fertilization in rice fields. FRONTIERS IN PLANT SCIENCE 2023; 14:1230012. [PMID: 37860263 PMCID: PMC10582757 DOI: 10.3389/fpls.2023.1230012] [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: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Introduction Rice heavily relies on nitrogen fertilizers, posing environmental, resource, and geopolitical challenges. This study explores sustainable alternatives like animal manure and remote sensing for resource-efficient rice cultivation. It aims to assess the long-term impact of organic fertilization and remote sensing monitoring on agronomic traits, yield, and nutrition. Methods A six-year experiment in rice fields evaluated fertilization strategies, including pig slurry (PS) and chicken manure (CM) with mineral fertilizers (MIN), MIN-only, and zero-fertilization. Traits, yield, spectral responses, and nutrient content were measured. Sentinel-2 remote sensing tracked crop development. Results Cost-effective organic fertilizers (PS and CM) caused a 13% and 15% yield reduction but still doubled zero-fertilization yield. PS reduced nitrogen leaching. Heavy metals in rice grains were present at safe amounts. Organic-fertilized crops showed nitrogen deficiency at the late vegetative stages, affecting yield. Sentinel-2 detected nutrient deficiencies through NDVI. Discussion Organic fertilizers, especially PS, reduce nitrogen loss, benefiting the environment. However, they come with yield trade-offs and nutrient management challenges that can be managed and balanced with reduced additional mineral applications. Sentinel-2 remote sensing helps manage nutrient deficiencies. In summary, this research favors cost-effective organic fertilizers with improved nutrient management for sustainable rice production.
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Affiliation(s)
- Karen Marti-Jerez
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Mar Català-Forner
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Núria Tomàs
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Gemma Murillo
- Ministry of Climate Action, Food and Rural Agenda, Lleida, Spain
| | - Carlos Ortiz
- Ministry of Climate Action, Food and Rural Agenda, Lleida, Spain
| | | | - Andrea Vitali
- Ente Nazionale Risi, Rice Research Centre, Castello d’Agogna, Italy
| | - Marta S. Lopes
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Lleida, Spain
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Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Rahmati Ishka M, Julkowska M. Tapping into the plasticity of plant architecture for increased stress resilience. F1000Res 2023; 12:1257. [PMID: 38434638 PMCID: PMC10905174 DOI: 10.12688/f1000research.140649.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 03/05/2024] Open
Abstract
Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.
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68
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Ramappa S, Joshi MA, Krishna H, Dunna V, Jain N, Sreevathsa R, Devate NB. Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study. Genes (Basel) 2023; 14:1902. [PMID: 37895250 PMCID: PMC10606372 DOI: 10.3390/genes14101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat's capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (-0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance -log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress.
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Affiliation(s)
- S Ramappa
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Monika A. Joshi
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Dunna
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rohini Sreevathsa
- Division of Molecular Biology and Biotechnology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Chandnani R, Qin T, Ye H, Hu H, Panjvani K, Tokizawa M, Macias JM, Medina AA, Bernardino K, Pradier PL, Banik P, Mooney A, V Magalhaes J, T Nguyen H, Kochian LV. Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0097. [PMID: 37780968 PMCID: PMC10538525 DOI: 10.34133/plantphenomics.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.
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Affiliation(s)
- Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- NRGene Canada, 110 Research Dr Suite 101, Saskatoon, SK, Canada
| | - Tongfei Qin
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Heng Ye
- Division of Plant Sciences and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Haifei Hu
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong, China
| | - Karim Panjvani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mutsutomo Tokizawa
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Javier Mora Macias
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alma Armenta Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Pierre-Luc Pradier
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pankaj Banik
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ashlyn Mooney
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Henry T Nguyen
- Division of Plant Sciences and Technology, University of Missouri, Columbia, MO 65211, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Menamo T, Borrell AK, Mace E, Jordan DR, Tao Y, Hunt C, Kassahun B. Genetic dissection of root architecture in Ethiopian sorghum landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:209. [PMID: 37715848 DOI: 10.1007/s00122-023-04457-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 08/28/2023] [Indexed: 09/18/2023]
Abstract
KEY MESSAGE This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.
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Affiliation(s)
- Temesgen Menamo
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Andrew K Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Bantte Kassahun
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia.
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Wani SH. Editorial: Mechanisms of abiotic stress responses and tolerance in plants: physiological, biochemical and molecular interventions, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1272255. [PMID: 37780497 PMCID: PMC10535095 DOI: 10.3389/fpls.2023.1272255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
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Bacher H, Montagu A, Herrmann I, Walia H, Schwartz N, Peleg Z. Stress-induced deeper rooting introgression enhances wheat yield under terminal drought. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4862-4874. [PMID: 36787201 DOI: 10.1093/jxb/erad059] [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: 10/06/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Water scarcity is the primary environmental constraint affecting wheat growth and production and is increasingly exacerbated due to climatic fluctuation, which jeopardizes future food security. Most breeding efforts to improve wheat yields under drought have focused on above-ground traits. Root traits are closely associated with various drought adaptability mechanisms, but the genetic variation underlying these traits remains untapped, even though it holds tremendous potential for improving crop resilience. Here, we examined this potential by re-introducing ancestral alleles from wild emmer wheat (Triticum turgidum ssp. dicoccoides) and studied their impact on root architecture diversity under terminal drought stress. We applied an active sensing electrical resistivity tomography approach to compare a wild emmer introgression line (IL20) and its drought-sensitive recurrent parent (Svevo) under field conditions. IL20 exhibited greater root elongation under drought, which resulted in higher root water uptake from deeper soil layers. This advantage initiated at the pseudo-stem stage and increased during the transition to the reproductive stage. The increased water uptake promoted higher gas exchange rates and enhanced grain yield under drought. Overall, we show that this presumably 'lost' drought-induced mechanism of deeper rooting profile can serve as a breeding target to improve wheat productiveness under changing climate.
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Affiliation(s)
- Harel Bacher
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Aviad Montagu
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ittai Herrmann
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Nimrod Schwartz
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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Chen L, Zhang B, Xia L, Yue D, Han B, Sun W, Wang F, Lindsey K, Zhang X, Yang X. The GhMAP3K62-GhMKK16-GhMPK32 kinase cascade regulates drought tolerance by activating GhEDT1-mediated ABA accumulation in cotton. J Adv Res 2023; 51:13-25. [PMID: 36414168 PMCID: PMC10491974 DOI: 10.1016/j.jare.2022.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Drought is the principal abiotic stress that severely impacts cotton (Gossypium hirsutum) growth and productivity. Upon sensing drought, plants activate stress-related signal transduction pathways, including ABA signal and mitogen-activated protein kinase (MAPK) cascade. However, as the key components with the fewest members in the MAPK cascade, the function and regulation of GhMKKs need to be elucidated. In addition, the relationship between MAPK module and the ABA core signaling pathway remains incompletely understood. OBJECTIVE Here we aim to elucidate the molecular mechanism of cotton response to drought, with a focus on mitogen-activated protein kinase (MAPK) cascades activating ABA signaling. METHODS Biochemical, molecular and genetic analysis were used to study the GhMAP3K62-GhMKK16-GhMPK32-GhEDT1 pathway genes. RESULTS A nucleus- and membrane-localized MAPK cascade pathway GhMAP3K62-GhMKK16-GhMPK32, which targets and phosphorylates the nuclear-localized transcription factor GhEDT1, to activate downstream GhNCED3 to mediate ABA-induced stomatal closure and drought response was characterized in cotton. Overexpression of GhMKK16 promotes ABA accumulation, and enhances drought tolerance via regulating stomatal closure under drought stress. Conversely, RNAi-mediated knockdown of GhMKK16 expression inhibits ABA accumulation, and reduces drought tolerance. Virus-induced gene silencing (VIGS)-mediated knockdown of either GhMAP3K62, GhMPK32 or GhEDT1 expression represses ABA accumulation and reduces drought tolerance through inhibiting stomatal closure. Expression knockdown of GhMPK32 or GhEDT1 in GhMKK16-overexpressing cotton reinstates ABA content and stomatal opening-dependent drought sensitivity to wild type levels. GhEDT1 could bind to the HD boxes in the promoter of GhNCED3 to activate its expression, resulting in ABA accumulation. We propose that the MAPK cascade GhMAP3K62-GhMKK16-GhMPK32 pathway functions on drought response through ABA-dependent stomatal movement in cotton.
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Affiliation(s)
- Lin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Bing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Linjie Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Fengjiao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China; Hubei Hongshan Laboratory, Wuhan, China.
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Shi R, Seiler C, Knoch D, Junker A, Altmann T. Integrated phenotyping of root and shoot growth dynamics in maize reveals specific interaction patterns in inbreds and hybrids and in response to drought. FRONTIERS IN PLANT SCIENCE 2023; 14:1233553. [PMID: 37719228 PMCID: PMC10502302 DOI: 10.3389/fpls.2023.1233553] [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: 06/02/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023]
Abstract
In recent years, various automated methods for plant phenotyping addressing roots or shoots have been developed and corresponding platforms have been established to meet the diverse requirements of plant research and breeding. However, most platforms are only either able to phenotype shoots or roots of plants but not both simultaneously. This substantially limits the opportunities offered by a joint assessment of the growth and development dynamics of both organ systems, which are highly interdependent. In order to overcome these limitations, a root phenotyping installation was integrated into an existing automated non-invasive high-throughput shoot phenotyping platform. Thus, the amended platform is now capable of conducting high-throughput phenotyping at the whole-plant level, and it was used to assess the vegetative root and shoot growth dynamics of five maize inbred lines and four hybrids thereof, as well as the responses of five inbred lines to progressive drought stress. The results showed that hybrid vigour (heterosis) occurred simultaneously in roots and shoots and was detectable as early as 4 days after transplanting (4 DAT; i.e., 8 days after seed imbibition) for estimated plant height (EPH), total root length (TRL), and total root volume (TRV). On the other hand, growth dynamics responses to progressive drought were different in roots and shoots. While TRV was significantly reduced 10 days after the onset of the water deficit treatment, the estimated shoot biovolume was significantly reduced about 6 days later, and EPH showed a significant decrease even 2 days later (8 days later than TRV) compared with the control treatment. In contrast to TRV, TRL initially increased in the water deficit period and decreased much later (not earlier than 16 days after the start of the water deficit treatment) compared with the well-watered plants. This may indicate an initial response of the plants to water deficit by forming longer but thinner roots before growth was inhibited by the overall water deficit. The magnitude and the dynamics of the responses were genotype-dependent, as well as under the influence of the water consumption, which was related to plant size.
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Affiliation(s)
- Rongli Shi
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Christiane Seiler
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Quedlinburg, Germany
| | - Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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Nishimura T, Mori S, Shikata H, Nakamura M, Hashiguchi Y, Abe Y, Hagihara T, Yoshikawa HY, Toyota M, Higaki T, Morita MT. Cell polarity linked to gravity sensing is generated by LZY translocation from statoliths to the plasma membrane. Science 2023; 381:1006-1010. [PMID: 37561884 DOI: 10.1126/science.adh9978] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Organisms have evolved under gravitational force, and many sense the direction of gravity by means of statoliths in specialized cells. In flowering plants, starch-accumulating plastids, known as amyloplasts, act as statoliths to facilitate downstream gravitropism. The gravity-sensing mechanism has long been considered a mechanosensing process by which amyloplasts transmit forces to intracellular structures, but the molecular mechanism underlying this has not been elucidated. We show here that LAZY1-LIKE (LZY) family proteins involved in statocyte gravity signaling associate with amyloplasts and the proximal plasma membrane. This results in polar localization according to the direction of gravity. We propose a gravity-sensing mechanism by which LZY translocation to the plasma membrane signals the direction of gravity by transmitting information on the position of amyloplasts.
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Affiliation(s)
- Takeshi Nishimura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
| | - Shogo Mori
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Hiromasa Shikata
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
| | - Moritaka Nakamura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Yasuko Hashiguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshinori Abe
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
| | - Takuma Hagihara
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
| | | | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Miyo Terao Morita
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
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Solanki M, Shukla LI. Recent advances in auxin biosynthesis and homeostasis. 3 Biotech 2023; 13:290. [PMID: 37547917 PMCID: PMC10400529 DOI: 10.1007/s13205-023-03709-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03709-6.
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Affiliation(s)
- Manish Solanki
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
- Puducherry, India
| | - Lata Israni Shukla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
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Nguyen TT, Pham DT, Nguyen NH, Do PT, To HTM. The Germin-like protein gene OsGER4 is involved in heat stress response in rice root development. Funct Integr Genomics 2023; 23:271. [PMID: 37561192 DOI: 10.1007/s10142-023-01201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important dietary carbohydrate sources for half of the world's population. However, it is not well adapted to environmental stress conditions, necessitating to create new and improved varieties to help ensure sufficient rice production in the face of rising populations and shrinking arable land. Recently, the development of the CRISPR/Cas9 gene editing system has allowed researchers to study functional genomics and engineer new rice varieties with great efficiency compared to conventional methods. In this study, we investigate the involvement of OsGER4, a germin-like protein identified by a genome-wide association study that is associated with rice root development under a stress hormone jasmonic acids treatment. Analysis of the OsGER4 promoter region revealed a series of regulatory elements that connect this gene to ABA signaling and water stress response. Under heat stress, osger4 mutant lines produce a significantly lower crown root than wild-type Kitaake rice. The loss of OsGER4 also led to the reduction of lateral root development. Using the GUS promoter line, OsGER4 expression was detected in the epidermis of the crown root primordial, in the stele of the crown root, and subsequently in the primordial of the lateral root. Taken together, these results illustrated the involvement of OsGER4 in root development under heat stress by regulating auxin transport through plasmodesmata, under control by both ABA and auxin signaling.
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Affiliation(s)
- Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Dan The Pham
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Nhung Hong Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam.
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Fan S, Amombo E, Yin Y, Wang G, Avoga S, Wu N, Li Y. Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115315. [PMID: 37542983 DOI: 10.1016/j.ecoenv.2023.115315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023]
Abstract
Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.
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Affiliation(s)
- Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Erick Amombo
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune 70000, Morocco
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Gunagyang Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Sheila Avoga
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430061, PR China
| | - Nan Wu
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China.
| | - Yating Li
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China.
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79
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Wang J, Li C, Li L, Gao L, Hu G, Zhang Y, Reynolds MP, Zhang X, Jia J, Mao X, Jing R. DIW1 encoding a clade I PP2C phosphatase negatively regulates drought tolerance by de-phosphorylating TaSnRK1.1 in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1918-1936. [PMID: 37158049 DOI: 10.1111/jipb.13504] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
Drought seriously impacts wheat production (Triticum aestivum L.), while the exploitation and utilization of genes for drought tolerance are insufficient. Leaf wilting is a direct reflection of drought tolerance in plants. Clade A PP2Cs are abscisic acid (ABA) co-receptors playing vital roles in the ABA signaling pathway, regulating drought response. However, the roles of other clade PP2Cs in drought tolerance, especially in wheat, remain largely unknown. Here, we identified a gain-of-function drought-induced wilting 1 (DIW1) gene from the wheat Aikang 58 mutant library by map-based cloning, which encodes a clade I protein phosphatase 2C (TaPP2C158) with enhanced protein phosphatase activity. Phenotypic analysis of overexpression and CRISPR/Cas9 mutant lines demonstrated that DIW1/TaPP2C158 is a negative regulator responsible for drought resistance. We found that TaPP2C158 directly interacts with TaSnRK1.1 and de-phosphorylates it, thus inactivating the TaSnRK1.1-TaAREB3 pathway. TaPP2C158 protein phosphatase activity is negatively correlated with ABA signaling. Association analysis suggested that C-terminal variation of TaPP2C158 changing protein phosphatase activity is highly correlated with the canopy temperature, and seedling survival rate under drought stress. Our data suggest that the favorable allele with lower phosphatase activity of TaPP2C158 has been positively selected in Chinese breeding history. This work benefits us in understanding the molecular mechanism of wheat drought tolerance, and provides elite genetic resources and molecular markers for improving wheat drought tolerance.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ge Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Zhao Y, Lu K, Zhang W, Guo W, Chao E, Yang Q, Zhang H. PagDA1a and PagDA1b expression improves salt and drought resistance in transgenic poplar through regulating ion homeostasis and reactive oxygen species scavenging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107898. [PMID: 37482028 DOI: 10.1016/j.plaphy.2023.107898] [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: 04/18/2023] [Revised: 07/02/2023] [Accepted: 07/16/2023] [Indexed: 07/25/2023]
Abstract
DA1/DAR proteins play a crucial role in plant biomass production. However, their functions in woody plants in response to abiotic stress are still unknown. In this study, a total number of six PagDA1/DAR family genes were identified in the poplar genome, and the biological functions of PagDA1a and PagDA1b in the resistance to salt and drought stresses were investigated in transgenic poplar. PagDA1a and PagDA1b were ubiquitously expressed in roots, stems, and leaves, with predominant expression in roots, and were significantly induced by abiotic stress and ABA. Transgenic poplar overexpressing either PagDA1a or PagDA1b showed restrained growth but improved resistance to salt and drought stresses. Further ion content and antioxidant enzyme expression analyses exhibited that transgenic poplar accumulated less sodium (Na+), hydrogen peroxide (H2O2) and malondialdehyde (MDA) in the leaves, accompanied with increased activity of superoxide dismutase (SOD), ascorbate peroxidase (APX) and catalase (CAT), and up-regulated transcription of SOD1, APX1, and CAT2. Our observations demonstrate that PagDA1a and PagDA1b improve salt and drought tolerance through ion homeostasis optimization and ROS scavenging ability enhancement in transgenic poplar, and both can be used for the future genetic breeding of new salt and drought tolerant tree species.
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Affiliation(s)
- Yanqiu Zhao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong, 265400, China
| | - Kaifeng Lu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong, 265400, China
| | - Weilin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, Zhejiang, 311300, China
| | - Wei Guo
- Taishan Academy of Forestry Sciences, Luohanya Road, Taian, Shandong, 27100, China
| | - Erkun Chao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China; College of Life Sciences, Qufu Normal University, 57 Jingxuanxi Road, Qufu, Shandong, 273165, China
| | - Qingshan Yang
- Shandong Academy of Forestry, 42 Wenhua East Road, Jinan, Shandong, 250014, China.
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China; College of Life Sciences, Qufu Normal University, 57 Jingxuanxi Road, Qufu, Shandong, 273165, China; Zhaoyuan Shenghui Agricultural Technology Development Co., Ltd, North of Beiyuanzhuang Village, Fushan County, Zhaoyuan, Shandong, 265400, China.
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81
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Ost C, Cao HX, Nguyen TL, Himmelbach A, Mascher M, Stein N, Humbeck K. Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes. Int J Mol Sci 2023; 24:12065. [PMID: 37569441 PMCID: PMC10418636 DOI: 10.3390/ijms241512065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.
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Affiliation(s)
- Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Thuy Linh Nguyen
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Göttingen, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
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82
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Kocaoglan EG, Radhakrishnan D, Nakayama N. Synthetic developmental biology: molecular tools to re-design plant shoots and roots. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3864-3876. [PMID: 37155965 PMCID: PMC10826796 DOI: 10.1093/jxb/erad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
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Affiliation(s)
- Elif Gediz Kocaoglan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Dhanya Radhakrishnan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Naomi Nakayama
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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83
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Hassan MA, Dahu N, Hongning T, Qian Z, Yueming Y, Yiru L, Shimei W. Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1215371. [PMID: 37534289 PMCID: PMC10391551 DOI: 10.3389/fpls.2023.1215371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.
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Affiliation(s)
- Muhammad A. Hassan
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ni Dahu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tong Hongning
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Qian
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yi Yueming
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Li Yiru
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Wang Shimei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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84
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Bektas H, Hohn CE, Lukaszewski AJ, Waines JG. On the Possible Trade-Off between Shoot and Root Biomass in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2513. [PMID: 37447071 DOI: 10.3390/plants12132513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
Numerous studies have shown that under a limited water supply, a larger root biomass is associated with an increased above-ground biomass. Root biomass, while genetically controlled, is also greatly affected by the environment with varying plasticity levels. In this context, understanding the relationship between the biomass of shoots and roots appears prudent. In this study, we analyze this relationship in a large dataset collected from multiple experiments conducted up to different growth stages in bread wheat (Triticum aestivum L.) and its wild relatives. Four bread wheat mapping populations as well as wild and domesticated members of the Triticeae tribe were evaluated for the root and shoot biomass allocation patterns. In the analyzed dataset the root and shoot biomasses were directly related to each other, and to the heading date, and the correlation values increased in proportion to the length of an experiment. On average, 84.1% of the observed variation was explained by a positive correlation between shoot and root biomass. Scatter plots generated from 6353 data points from numerous experiments with different wheats suggest that at some point, further increases in root biomass negatively impact the shoot biomass. Based on these results, a preliminary study with different water availability scenarios and growth conditions was designed with two cultivars, Pavon 76 and Yecora Rojo. The duration of drought and water level significantly affected the root/shoot biomass allocation patterns. However, the responses of the two cultivars were quite different, suggesting that the point of diminishing returns in increasing root biomass may be different for different wheats, reinforcing the need to breed wheats for specific environmental challenges.
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Affiliation(s)
- Harun Bektas
- Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Christopher E Hohn
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - John Giles Waines
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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85
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Li X, Wasson AP, Zwart AB, Whan A, Ryan PR, Forrest K, Hayden M, Chin S, Richards R, Delhaize E. Physical Mapping of QTLs for Root Traits in a Population of Recombinant Inbred Lines of Hexaploid Wheat. Int J Mol Sci 2023; 24:10492. [PMID: 37445670 DOI: 10.3390/ijms241310492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals.
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Affiliation(s)
- Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Anton P Wasson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | | | - Alex Whan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Peter R Ryan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sabrina Chin
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | | | - Emmanuel Delhaize
- Australian Plant Phenomics Facility, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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86
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Xu K, Lou Q, Wang D, Li T, Chen S, Li T, Luo L, Chen L. Overexpression of a novel small auxin-up RNA gene, OsSAUR11, enhances rice deep rootedness. BMC PLANT BIOLOGY 2023; 23:319. [PMID: 37316787 DOI: 10.1186/s12870-023-04320-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/27/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Deep rooting is an important factor affecting rice drought resistance. However, few genes have been identified to control this trait in rice. Previously, we identified several candidate genes by QTL mapping of the ratio of deep rooting and gene expression analysis in rice. RESULTS In the present work, we cloned one of these candidate genes, OsSAUR11, which encodes a small auxin-up RNA (SAUR) protein. Overexpression of OsSAUR11 significantly enhanced the ratio of deep rooting of transgenic rice, but knockout of this gene did not significantly affect deep rooting. The expression of OsSAUR11 in rice root was induced by auxin and drought, and OsSAUR11-GFP was localized both in the plasma membrane and cell nucleus. Through an electrophoretic mobility shift assay and gene expression analysis in transgenic rice, we found that the transcription factor OsbZIP62 can bind to the promoter of OsSAUR11 and promote its expression. A luciferase complementary test showed that OsSAUR11 interacts with the protein phosphatase OsPP36. Additionally, expression of several auxin synthesis and transport genes (e.g., OsYUC5 and OsPIN2) were down-regulated in OsSAUR11-overexpressing rice plants. CONCLUSIONS This study revealed a novel gene OsSAUR11 positively regulates deep rooting in rice, which provides an empirical basis for future improvement of rice root architecture and drought resistance.
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Affiliation(s)
- Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Di Wang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tiemei Li
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Shoujun Chen
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China.
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China.
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China.
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, China.
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87
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Kuya N, Nishijima R, Kitomi Y, Kawakatsu T, Uga Y. Transcriptome profiles of rice roots under simulated microgravity conditions and following gravistimulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193042. [PMID: 37360733 PMCID: PMC10288856 DOI: 10.3389/fpls.2023.1193042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
Root system architecture affects the efficient uptake of water and nutrients in plants. The root growth angle, which is a critical component in determining root system architecture, is affected by root gravitropism; however, the mechanism of root gravitropism in rice remains largely unknown. In this study, we conducted a time-course transcriptome analysis of rice roots under conditions of simulated microgravity using a three-dimensional clinostat and following gravistimulation to detect candidate genes associated with the gravitropic response. We found that HEAT SHOCK PROTEIN (HSP) genes, which are involved in the regulation of auxin transport, were preferentially up-regulated during simulated microgravity conditions and rapidly down-regulated by gravistimulation. We also found that the transcription factor HEAT STRESS TRANSCRIPTION FACTOR A2s (HSFA2s) and HSFB2s, showed the similar expression patterns with the HSPs. A co-expression network analysis and an in silico motif search within the upstream regions of the co-expressed genes revealed possible transcriptional control of HSPs by HSFs. Because HSFA2s are transcriptional activators, whereas HSFB2s are transcriptional repressors, the results suggest that the gene regulatory networks governed by HSFs modulate the gravitropic response through transcriptional control of HSPs in rice roots.
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Affiliation(s)
- Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yuka Kitomi
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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88
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Li J, Wang Z, Song C, Nie Y, Li H, Kong M, Cong H, Wang S, Yin N, Hu L, Bermudez RS, He W. Identification of LsLAZY1 gene in Leymus secalinus and validation of its function in Arabidopsis thaliana. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:783-790. [PMID: 37520815 PMCID: PMC10382429 DOI: 10.1007/s12298-023-01326-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023]
Abstract
Root systems anchor plants to the substrate in addition to transporting water and nutrients, playing a fundamental role in plant survival. The LAZY1 gene mediates gravity signal transduction and participates in root and shoot development and auxin flow in many plants. In this study, a regulator, LsLAZY1, was identified from Leymus secalinus based on previous transcriptome data. The conserved domain and evolutionary relationship were further analyzed comprehensively. The role of LsLAZY1 in root development was investigated by genetic transformation and associated gravity response and phototropism assay. Subcellular localization showed that LsLAZY1 was localized in the nucleus. LsLAZY1 overexpression in Arabidopsis thaliana (Col-0) increased the length of the primary roots (PRs) and the number of lateral roots (LRs) compared to Col-0. Furthermore, 35S:LsLAZY1 transgenic seedlings affected auxin transport and showed a stronger gravitational and phototropic responses. It also promoted auxin accumulation at the root tips. These results indicated that LsLAZY1 affects root development and auxin transport. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01326-4.
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Affiliation(s)
- Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Zenghui Wang
- Shandong Institute of Pomology, Tai’an, 271000 Shandong China
| | - Chunying Song
- Xilin Gol League Agricultural and Animal Product Quality and Safety Monitoring Center, Xilinhot City, 026000 China
| | - Yanshun Nie
- Fengtang Ecological Agriculture Technology Research and Development Co. LTD, Tai’an, 271000 Shandong China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Mengmeng Kong
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Hanhan Cong
- School of Information Science and Engineering, University of Jinan, Jinan, 250022 China
| | - Siqi Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Ning Yin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Linyue Hu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Ramon Santos Bermudez
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
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89
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Wimalagunasekara SS, Weeraman JWJK, Tirimanne S, Fernando PC. Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa). J Genet Eng Biotechnol 2023; 21:69. [PMID: 37246172 DOI: 10.1186/s43141-023-00515-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/06/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance. RESULTS Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs. CONCLUSIONS These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
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Affiliation(s)
| | - Janith W J K Weeraman
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
| | - Shamala Tirimanne
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Pasan C Fernando
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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90
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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91
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Hu LL, Zheng LW, Zhu XL, Ma SJ, Zhang KY, Hua YP, Huang JY. Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed. BMC PLANT BIOLOGY 2023; 23:248. [PMID: 37170202 PMCID: PMC10173674 DOI: 10.1186/s12870-023-04256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Histone modification is an important epigenetic regulatory mechanism and essential for stress adaptation in plants. However, systematic analysis of histone modification genes (HMs) in Brassicaceae species is lacking, and their roles in response to abiotic stress have not yet been identified. RESULTS In this study, we identified 102 AtHMs, 280 BnaHMs, 251 BcHMs, 251 BjHMs, 144 BnHMs, 155 BoHMs, 137 BrHMs, 122 CrHMs, and 356 CsHMs in nine Brassicaceae species, respectively. Their chromosomal locations, protein/gene structures, phylogenetic trees, and syntenies were determined. Specific domains were identified in several Brassicaceae HMs, indicating an association with diverse functions. Syntenic analysis showed that the expansion of Brassicaceae HMs may be due to segmental and whole-genome duplications. Nine key BnaHMs in allotetraploid rapeseed may be responsible for ammonium, salt, boron, cadmium, nitrate, and potassium stress based on co-expression network analysis. According to weighted gene co-expression network analysis (WGCNA), 12 BnaHMs were associated with stress adaptation. Among the above genes, BnaPRMT11 simultaneously responded to four different stresses based on differential expression analysis, while BnaSDG46, BnaHDT10, and BnaHDA1 participated in five stresses. BnaSDG46 was also involved in four different stresses based on WGCNA, while BnaSDG10 and BnaJMJ58 were differentially expressed in response to six different stresses. In summary, six candidate genes for stress resistance (BnaPRMT11, BnaSDG46, BnaSDG10, BnaJMJ58, BnaHDT10, and BnaHDA1) were identified. CONCLUSIONS Taken together, these findings help clarify the biological roles of Brassicaceae HMs. The identified candidate genes provide an important reference for the potential development of stress-tolerant oilseed plants.
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Affiliation(s)
- Lin-Lin Hu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China
| | - Li-Wei Zheng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China
| | - Xin-Lei Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Sheng-Jie Ma
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China
| | - Kai-Yan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Zhengzhou Key Laboratory of Quality Improvement and Efficient Nutrient Use for Main Economic Crops, Henan, China.
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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92
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Tu M, Du C, Yu B, Wang G, Deng Y, Wang Y, Chen M, Chang J, Yang G, He G, Xiong Z, Li Y. Current advances in the molecular regulation of abiotic stress tolerance in sorghum via transcriptomic, proteomic, and metabolomic approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1147328. [PMID: 37235010 PMCID: PMC10206308 DOI: 10.3389/fpls.2023.1147328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench), a monocot C4 crop, is an important staple crop for many countries in arid and semi-arid regions worldwide. Because sorghum has outstanding tolerance and adaptability to a variety of abiotic stresses, including drought, salt, and alkaline, and heavy metal stressors, it is valuable research material for better understanding the molecular mechanisms of stress tolerance in crops and for mining new genes for their genetic improvement of abiotic stress tolerance. Here, we compile recent progress achieved using physiological, transcriptome, proteome, and metabolome approaches; discuss the similarities and differences in how sorghum responds to differing stresses; and summarize the candidate genes involved in the process of responding to and regulating abiotic stresses. More importantly, we exemplify the differences between combined stresses and a single stress, emphasizing the necessity to strengthen future studies regarding the molecular responses and mechanisms of combined abiotic stresses, which has greater practical significance for food security. Our review lays a foundation for future functional studies of stress-tolerance-related genes and provides new insights into the molecular breeding of stress-tolerant sorghum genotypes, as well as listing a catalog of candidate genes for improving the stress tolerance for other key monocot crops, such as maize, rice, and sugarcane.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Canghao Du
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guoli Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yanbin Deng
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Xiong
- Laboratory of Forage and Endemic Crop Biology (Inner Mongolia University), Ministry of Education, School of Life Sciences, Hohhot, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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93
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Jiménez JDLC, Pedersen O. Mitigation of Greenhouse Gas Emissions from Rice via Manipulation of Key Root Traits. RICE (NEW YORK, N.Y.) 2023; 16:24. [PMID: 37160782 PMCID: PMC10169991 DOI: 10.1186/s12284-023-00638-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
Rice production worldwide represents a major anthropogenic source of greenhouse gas emissions. Nitrogen fertilization and irrigation practices have been fundamental to achieve optimal rice yields, but these agricultural practices together with by-products from plants and microorganisms, facilitate the production, accumulation and venting of vast amounts of CO2, CH4 and N2O. We propose that the development of elite rice varieties should target root traits enabling an effective internal O2 diffusion, via enlarged aerenchyma channels. Moreover, gas tight barriers impeding radial O2 loss in basal parts of the roots will increase O2 diffusion to the root apex where molecular O2 diffuses into the rhizosphere. These developments result in plants with roots penetrating deeper into the flooded anoxic soils, producing higher volumes of oxic conditions in the interface between roots and rhizosphere. Molecular O2 in these zones promotes CH4 oxidation into CO2 by methanotrophs and nitrification (conversion of NH4+ into NO3-), reducing greenhouse gas production and at the same time improving plant nutrition. Moreover, roots with tight barriers to radial O2 loss will have restricted diffusional entry of CH4 produced in the anoxic parts of the rhizosphere and therefore plant-mediated diffusion will be reduced. In this review, we describe how the exploitation of these key root traits in rice can potentially reduce greenhouse gas emissions from paddy fields.
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Affiliation(s)
- Juan de la Cruz Jiménez
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, Copenhagen, 2100, Denmark.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, Copenhagen, 2100, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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94
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Shim Y, Seong G, Choi Y, Lim C, Baek SA, Park YJ, Kim JK, An G, Kang K, Paek NC. Suppression of cuticular wax biosynthesis mediated by rice LOV KELCH REPEAT PROTEIN 2 supports a negative role in drought stress tolerance. PLANT, CELL & ENVIRONMENT 2023; 46:1504-1520. [PMID: 36683564 DOI: 10.1111/pce.14549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Drought tolerance is important for grain crops, including rice (Oryza sativa); for example, rice cultivated under intermittent irrigation produces less methane gas compared to rice grown in anaerobic paddy field conditions, but these plants require greater drought tolerance. Moreover, the roles of rice circadian-clock genes in drought tolerance remain largely unknown. Here, we show that the mutation of LOV KELCH REPEAT PROTEIN 2 (OsLKP2) enhanced drought tolerance by increasing cuticular wax biosynthesis. Among ZEITLUPE family genes, OsLKP2 expression specifically increased under dehydration stress. OsLKP2 knockdown (oslkp2-1) and knockout (oslkp2-2) mutants exhibited enhanced drought tolerance. Cuticular waxes inhibit non-stomatal water loss. Under drought conditions, total wax loads on the leaf surface increased by approximately 10% in oslkp2-1 and oslkp2-2 compared to the wild type, and the transcript levels of cuticular wax biosynthesis genes were upregulated in the oslkp2 mutants. Yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that OsLKP2 interacts with GIGANTEA (OsGI) in the nucleus. The osgi mutants also showed enhanced tolerance to drought stress, with a high density of wax crystals on their leaf surface. These results demonstrate that the OsLKP2-OsGI interaction negatively regulates wax accumulation on leaf surfaces, thereby decreasing rice resilience to drought stress.
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Affiliation(s)
- Yejin Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gayeong Seong
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yumin Choi
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chaemyeong Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seung-A Baek
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Young Jin Park
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Kiyoon Kang
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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95
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Gao J, Zhao Y, Zhao Z, Liu W, Jiang C, Li J, Zhang Z, Zhang H, Zhang Y, Wang X, Sun X, Li Z. RRS1 shapes robust root system to enhance drought resistance in rice. THE NEW PHYTOLOGIST 2023; 238:1146-1162. [PMID: 36862074 DOI: 10.1111/nph.18775] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
A strong root system facilitates the absorption of water and nutrients from the soil, to improve the growth of crops. However, to date, there are still very few root development regulatory genes that can be used in crop breeding for agriculture. In this study, we cloned a negative regulator gene of root development, Robust Root System 1 (RRS1), which encodes an R2R3-type MYB family transcription factor. RRS1 knockout plants showed enhanced root growth, including longer root length, longer lateral root length, and larger lateral root density. RRS1 represses root development by directly activating the expression of OsIAA3 which is involved in the auxin signaling pathway. A natural variation in the coding region of RRS1 changes the transcriptional activity of its protein. RRS1T allele, originating from wild rice, possibly increases root length by means of weakening regulation of OsIAA3. Knockout of RRS1 enhances drought resistance by promoting water absorption and improving water use efficiency. This study provides a new gene resource for improving root systems and cultivating drought-resistant rice varieties with important values in agricultural applications.
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Affiliation(s)
- Jie Gao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhikun Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Liu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Conghui Jiang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jinjie Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yage Zhang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Xiaoning Wang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
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Habuš Jerčić I, Bošnjak Mihovilović A, Matković Stanković A, Lazarević B, Goreta Ban S, Ban D, Major N, Tomaz I, Banjavčić Z, Kereša S. Garlic Ecotypes Utilise Different Morphological, Physiological and Biochemical Mechanisms to Cope with Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091824. [PMID: 37176881 PMCID: PMC10180593 DOI: 10.3390/plants12091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Drought negatively affects plants by altering morphological, physiological and metabolic processes and ultimately reducing yields. Garlic (Allium sativum L.), an important member of the Alliaceae family, is also sensitive to drought and maximizing the yield of garlic bulbs is largely dependent on water availability. The objective of this study was to determine the effects of drought stress on morphological and physiological characteristics, as well as on phenolic, sugar, inulin and free amino acid content and antioxidant activity in two Croatian garlic ecotypes, 'Istarski crveni' (IC) and Istarski bijeli (IB). Drought was induced by using polyethylene glycol 8000 (PEG) solution (-0.6 MPa) starting 21 days after clove planting and lasted for 20 days. Drought reduced plant height, number of leaves and plant weight, but increased root length in both ecotypes compared to the control treatment. Among the physiological parameters, significant differences were observed between the two ecotypes studied in the spectral characteristics of the leaves, namely reflection in red, green and blue, VAL, values of the vegetation indices related to the chlorophyll content (CHI, GI), and the anthocyanin content (ARI). Ecotype IC showed higher antioxidant activity in the control treatment due to higher total phenolic content (TPC), but under drought conditions higher DPPH radical scavenging activity was determined in ecotype IB and higher values of FRAP in IC. Sucrose and glucose generally decreased under drought, while inulin increased in IB but decreased in IC. Total free amino acid content increased under drought in both ecotypes. In conclusion, drought tolerance of IB might be associated with increased accumulation of inulin and higher levels of amino acids, especially those shown to contribute to drought resistance. In IC, drought tolerance is associated with an increase in some amino acid compounds and better root growth in depth, probably due to a more efficient translocation of sucrose to the underground part of the plant.
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Affiliation(s)
- Ivanka Habuš Jerčić
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Anita Bošnjak Mihovilović
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Ana Matković Stanković
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Boris Lazarević
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Smiljana Goreta Ban
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Dean Ban
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Nikola Major
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Ivana Tomaz
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Zrinka Banjavčić
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Snježana Kereša
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
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Yue L, Xie B, Cao X, Chen F, Wang C, Xiao Z, Jiao L, Wang Z. The Mechanism of Manganese Ferrite Nanomaterials Promoting Drought Resistance in Rice. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13091484. [PMID: 37177029 PMCID: PMC10180523 DOI: 10.3390/nano13091484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Strategies to reduce the risk of drought damage are urgently needed as intensified climate change threatens agricultural production. One potential strategy was using nanomaterials (NMs) to enhance plant resistance by regulating various physiological and biochemical processes. In the present study, 10 mg kg-1 manganese ferrite (MnFe2O4) NMs had the optimal enhancement to elevate the levels of biomass, photosynthesis, nutrient elements, and polysaccharide in rice by 10.9-525.0%, respectively, under drought stress. The MnFe2O4 NMs were internalized by rice plants, which provided the possibility for rice to better cope with drought. Furthermore, as compared with drought control and equivalent ion control, the introduction of MnFe2O4 NMs into the roots significantly upregulated the drought-sensing gene CLE25 (29.4%) and the receptor gene NCED3 (59.9%). This activation stimulated downstream abscisic acid, proline, malondialdehyde, and wax biosynthesis by 23.3%, 38.9%, 7.2%, and 26.2%, respectively. In addition, 10 mg·kg-1 MnFe2O4 NMs significantly upregulated the relative expressions of OR1, AUX2, AUX3, PIN1a, and PIN2, and increased IAA content significantly, resulting in an enlarged root angle and a deeper and denser root to help the plant withstand drought stresses. The nutritional quality of rice grains was also improved. Our study provides crucial insight for developing nano-enabled strategies to improve crop productivity and resilience to climate change.
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Affiliation(s)
- Le Yue
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Budiao Xie
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Liya Jiao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
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Xie S, Liu H, Ma T, Shen S, Zheng H, Yang L, Liu L, Wei Z, Xin W, Zou D, Wang J. Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Japonica Rice under Low Nitrogen Stress. Int J Mol Sci 2023; 24:ijms24097699. [PMID: 37175411 PMCID: PMC10178291 DOI: 10.3390/ijms24097699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation under low N conditions to improve NUE. In this study, changes in the rice morphological, physiological, and yield-related traits under low N (13.33 ppm) and control N (40.00 ppm) conditions were performed. These results show that, compared with control N conditions, photosynthesis and growth were inhibited and the carbon (C)/N and photosynthetic nitrogen use efficiency (PNUE) were enhanced under low N conditions. To understand the post-translational modification mechanism underlying the rice response to low N conditions, comparative phosphoproteomic analysis was performed, and differentially modified proteins (DMPs) were further characterized. Compared with control N conditions, a total of 258 DMPs were identified under low N conditions. The modification of proteins involved in chloroplast development, chlorophyll synthesis, photosynthesis, carbon metabolism, phytohormones, and morphology-related proteins were differentially altered, which was an important reason for changes in rice morphological, physiological, and yield-related traits. Additionally, inconsistent changes in level of transcription and protein modification, indicates that the study of phosphoproteomics under low N conditions is also important for us to better understand the adaptation mechanism of rice to low N stress. These results provide insights into global changes in the response of rice to low N stress and may facilitate the development of rice cultivars with high NUE by regulating the phosphorylation level of carbon metabolism and rice morphology-related proteins.
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Affiliation(s)
- Shupeng Xie
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Suihua Branch of Heilongjiang Academy of Agricultural Science, Suihua 152052, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Tianze Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Shen Shen
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Lichao Liu
- Suihua Branch of Heilongjiang Academy of Agricultural Science, Suihua 152052, China
| | - Zhonghua Wei
- Suihua Branch of Heilongjiang Academy of Agricultural Science, Suihua 152052, China
| | - Wei Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
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99
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Alemu A, Batista L, Singh PK, Ceplitis A, Chawade A. Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:92. [PMID: 37009920 PMCID: PMC10068637 DOI: 10.1007/s00122-023-04352-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Linkage disequilibrium (LD)-based haplotyping with subsequent SNP tagging improved the genomic prediction accuracy up to 0.07 and 0.092 for Fusarium head blight resistance and spike width, respectively, across six different models. Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Pawan K Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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100
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Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, Khurana P, Khurana JP. Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1207-1231. [PMID: 36404527 DOI: 10.1111/pce.14496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Susmita M Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Martin Kieffer
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Global Food and Environment Institute, University of Leeds, Leeds, UK
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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