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Verma PK, Verma S, Pandey N. Root system architecture in rice: impacts of genes, phytohormones and root microbiota. 3 Biotech 2022; 12:239. [PMID: 36016841 PMCID: PMC9395555 DOI: 10.1007/s13205-022-03299-9] [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: 03/14/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.
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Affiliation(s)
- Pankaj Kumar Verma
- Department of Botany, University of Lucknow, Lucknow, India
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shikha Verma
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, India
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Hanzawa E, Sasaki K, Nagai S, Obara M, Fukuta Y, Uga Y, Miyao A, Hirochika H, Higashitani A, Maekawa M, Sato T. Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2013; 6:30. [PMID: 24280269 PMCID: PMC3874653 DOI: 10.1186/1939-8433-6-30] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/15/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. RESULTS The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. CONCLUSION These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.
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Affiliation(s)
- Eiko Hanzawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kazuhiro Sasaki
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Present address: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Shinsei Nagai
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Mitsuhiro Obara
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Akio Miyao
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hirohiko Hirochika
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Atsushi Higashitani
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Tadashi Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- RIKEN Innovation Center, Ion Beam Breeding Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Jung JKH, McCouch S. Getting to the roots of it: Genetic and hormonal control of root architecture. FRONTIERS IN PLANT SCIENCE 2013; 4:186. [PMID: 23785372 PMCID: PMC3685011 DOI: 10.3389/fpls.2013.00186] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 05/22/2013] [Indexed: 05/17/2023]
Abstract
Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.
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Affiliation(s)
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell UniversityIthaca, NY, USA
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Rigas S, Ditengou FA, Ljung K, Daras G, Tietz O, Palme K, Hatzopoulos P. Root gravitropism and root hair development constitute coupled developmental responses regulated by auxin homeostasis in the Arabidopsis root apex. THE NEW PHYTOLOGIST 2013; 197:1130-1141. [PMID: 23252740 DOI: 10.1111/nph.12092] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/10/2012] [Indexed: 05/17/2023]
Abstract
Active polar transport establishes directional auxin flow and the generation of local auxin gradients implicated in plant responses and development. Auxin modulates gravitropism at the root tip and root hair morphogenesis at the differentiation zone. Genetic and biochemical analyses provide evidence for defective basipetal auxin transport in trh1 roots. The trh1, pin2, axr2 and aux1 mutants, and transgenic plants overexpressing PIN1, all showing impaired gravity response and root hair development, revealed ectopic PIN1 localization. The auxin antagonist hypaphorine blocked root hair elongation and caused moderate agravitropic root growth, also leading to PIN1 mislocalization. These results suggest that auxin imbalance leads to proximal and distal developmental defects in Arabidopsis root apex, associated with agravitropic root growth and root hair phenotype, respectively, providing evidence that these two auxin-regulated processes are coupled. Cell-specific subcellular localization of TRH1-YFP in stele and epidermis supports TRH1 engagement in auxin transport, and hence impaired function in trh1 causes dual defects of auxin imbalance. The interplay between intrinsic cues determining root epidermal cell fate through the TTG/GL2 pathway and environmental cues including abiotic stresses modulates root hair morphogenesis. As a consequence of auxin imbalance in Arabidopsis root apex, ectopic PIN1 mislocalization could be a risk aversion mechanism to trigger root developmental responses ensuring root growth plasticity.
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Affiliation(s)
- Stamatis Rigas
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens, 118 55, Greece
| | - Franck Anicet Ditengou
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Gerasimos Daras
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens, 118 55, Greece
| | - Olaf Tietz
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Klaus Palme
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- Centre of Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, Habsburgerstr. 49, D-79104, Freiburg, Germany
- Freiburg Institute of Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104, Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104, Freiburg, Germany
| | - Polydefkis Hatzopoulos
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens, 118 55, Greece
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Jung JKH, McCouch S. Getting to the roots of it: Genetic and hormonal control of root architecture. FRONTIERS IN PLANT SCIENCE 2013. [PMID: 23785372 DOI: 10.3389/fpls.2013.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.
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Affiliation(s)
- Janelle K H Jung
- Department of Plant Breeding and Genetics, Cornell University Ithaca, NY, USA
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Jung JKH, McCouch S. Getting to the roots of it: Genetic and hormonal control of root architecture. FRONTIERS IN PLANT SCIENCE 2013. [PMID: 23785372 DOI: 10.3389/fpls.2013.00186/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.
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Affiliation(s)
- Janelle K H Jung
- Department of Plant Breeding and Genetics, Cornell University Ithaca, NY, USA
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Ali B, Hasnain S. Efficacy of bacterial auxin on in vitro growth of Brassica oleracea L. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9297-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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