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Kirschner GK, Hochholdinger F, Salvi S, Bennett MJ, Huang G, Bhosale RA. Genetic regulation of the root angle in cereals. TRENDS IN PLANT SCIENCE 2024; 29:814-822. [PMID: 38402016 DOI: 10.1016/j.tplants.2024.01.008] [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: 11/12/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
The root angle plays a critical role in efficiently capturing nutrients and water from different soil layers. Steeper root angles enable access to mobile water and nitrogen from deeper soil layers, whereas shallow root angles facilitate the capture of immobile phosphorus from the topsoil. Thus, understanding the genetic regulation of the root angle is crucial for breeding crop varieties that can efficiently capture resources and enhance yield. Moreover, this understanding can contribute to developing varieties that effectively sequester carbon in deeper soil layers, supporting global carbon mitigation efforts. Here we review and consolidate significant recent discoveries regarding the molecular components controlling root angle in cereal crop species and outline the remaining research gaps in this field.
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Affiliation(s)
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, LE12 5RD Nottingham, UK
| | - Guoqiang Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Rahul A Bhosale
- School of Biosciences, University of Nottingham, LE12 5RD Nottingham, UK; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
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Liu S, Zheng Y, Zhao L, Gulam M, Ullah A, Xie G. CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling. PLANT PHYSIOLOGY 2024; 195:1660-1680. [PMID: 38445796 DOI: 10.1093/plphys/kiae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 03/07/2024]
Abstract
Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.
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Affiliation(s)
- Shuang Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuying Zheng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyan Zhao
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mihray Gulam
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aman Ullah
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guosheng Xie
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Chen JC, Lin HY, Novák O, Strnad M, Lee YI, Fang SC. Diverse geotropic responses in the orchid family. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38809156 DOI: 10.1111/pce.14975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
In epiphytes, aerial roots are important to combat water-deficient, nutrient-poor, and high-irradiance microhabitats. However, whether aerial roots can respond to gravity and whether auxin plays a role in regulating aerial root development remain open-ended questions. Here, we investigated the gravitropic response of the epiphytic orchid Phalaenopsis aphrodite. Our data showed that aerial roots of P. aphrodite failed to respond to gravity, and this was correlated with a lack of starch granules/statolith sedimentation in the roots and the absence of the auxin efflux carrier PIN2 gene. Using an established auxin reporter, we discovered that auxin maximum was absent in the quiescent center of aerial roots of P. aphrodite. Also, gravity failed to trigger auxin redistribution in the root caps. Hence, loss of gravity sensing and gravity-dependent auxin redistribution may be the genetic factors contributing to aerial root development. Moreover, the architectural and functional innovations that achieve fast gravitropism in the flowering plants appear to be lost in both terrestrial and epiphytic orchids, but are present in the early diverged orchid subfamilies. Taken together, our findings provide physiological and molecular evidence to support the notion that epiphytic orchids lack gravitropism and suggest diverse geotropic responses in the orchid family.
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Affiliation(s)
- Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Science, Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Yung-I Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Bonfiglioli L, Urbanavičiūtė I, Pagnotta MA. Durum wheat ( Triticum turgidum L. var. durum) root system response to drought and salt stresses and genetic characterization for root-related traits. FRONTIERS IN PLANT SCIENCE 2024; 15:1362917. [PMID: 38584946 PMCID: PMC10995220 DOI: 10.3389/fpls.2024.1362917] [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: 12/29/2023] [Accepted: 02/26/2024] [Indexed: 04/09/2024]
Abstract
Abiotic stresses such as drought and salt are significant threats to crop productivity. The root system adaptation and tolerance to abiotic stresses are regulated by many biochemical reactions, which create a complex and multigenic response. The present study aims to evaluate the diversity of root responses to cyclic abiotic stress in three modern durum wheat varieties and one hydric stress-tolerant landrace in a pot experiment from seedling to more advanced plant development stages. The genotypes responded to abiotic stress during the whole experiment very differently, and at the end of the experiment, nine out of the 13 traits for the landrace J. Khetifa were significantly higher than other genotypes. Moreover, single sequence repeat (SSR) genetic analysis revealed high polymorphism among the genotypes screened and interesting private alleles associated with root system architecture traits. We propose that the markers used in this study could be a resource as material for durum wheat breeding programs based on marker-assisted selection to increase the vegetal material with high drought and salt stress tolerance and to identify candidates with strong early vigor and efficient root systems. This study provides appropriate genetic materials for marker-assisted breeding programs as well as a basic study for the genetic diversity of root traits of durum wheat crops.
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Affiliation(s)
| | | | - Mario A. Pagnotta
- Department of Agricultural and Forest Sciences, Tuscia University, Viterbo, Italy
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Hao B, Zhang R, Zhang C, Wen N, Xia Y, Zhao Y, Li Q, Qiao L, Li W. Characterization of OsPIN2 Mutants Reveal Novel Roles for Reactive Oxygen Species in Modulating Not Only Root Gravitropism but Also Hypoxia Tolerance in Rice Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:476. [PMID: 38498461 PMCID: PMC10892736 DOI: 10.3390/plants13040476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Tolerance to submergence-induced hypoxia is an important agronomic trait especially for crops in lowland and flooding-affected areas. Although rice (Oryza sativa) is considered a flood-tolerant crop, only limited cultivars display strong tolerance to prolonged submergence and/or hypoxic stress. Therefore, characterization of hypoxic resistant genes and/or germplasms have important theoretical and practical significance for rice breeding and sustained improvements. Previous investigations have demonstrated that loss-of-function of OsPIN2, a gene encoding an auxin efflux transporter, results in the loss of root gravitropism due to disrupted auxin transport in the root tip. In this study, we revealed a novel connection between OsPIN2 and reactive oxygen species (ROS) in modulating root gravitropism and hypoxia tolerance in rice. It is shown that the OsPIN2 mutant had decreased accumulation of ROS in root tip, due to the downregulation of glycolate oxidase encoding gene OsGOX6, one of the main H2O2 sources. The morphological defects of root including waved rooting and agravitropism in OsPIN2 mutant may be rescued partly by exogenous application of H2O2. The OsPIN2 mutant exhibited increased resistance to ROS toxicity in roots due to treatment with H2O2. Furthermore, it is shown that the OsPIN2 mutant had increased tolerance to hypoxic stress accompanied by lower ROS accumulation in roots, because the hypoxia stress led to over production of ROS in the roots of the wild type but not in that of OsPIN2 mutant. Accordingly, the anoxic resistance-related gene SUB1B showed differential expression in the root of the WT and OsPIN2 mutant in response to hypoxic conditions. Notably, compared with the wild type, the OsPIN2 mutant displayed a different pattern of auxin distribution in the root under hypoxia stress. It was shown that hypoxia stress caused a significant increase in auxin distribution in the root tip of the WT but not in that of the war1 mutant. In summary, these results suggested that OsPIN2 may play a role in regulating ROS accumulation probably via mediating auxin transport and distribution in the root tip, affecting root gravitropism and hypoxic tolerance in rice seedlings. These findings may contribute to the genetic improvement and identification of potential hypoxic tolerant lines in rice.
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Affiliation(s)
- Bowen Hao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Ruihan Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Chengwei Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Na Wen
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Yu Xia
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Yang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Qinying Li
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Lei Qiao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
| | - Wenqiang Li
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (B.H.); (R.Z.); (C.Z.); (N.W.); (Y.X.); (Y.Z.); (Q.L.); (L.Q.)
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling 712100, China
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Nasr Esfahani M, Sonnewald U. Unlocking dynamic root phenotypes for simultaneous enhancement of water and phosphorus uptake. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108386. [PMID: 38280257 DOI: 10.1016/j.plaphy.2024.108386] [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: 10/03/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
Phosphorus (P) and water are crucial for plant growth, but their availability is challenged by climate change, leading to reduced crop production and global food security. In many agricultural soils, crop productivity is confronted by both water and P limitations. The diminished soil moisture decreases available P due to reduced P diffusion, and inadequate P availability diminishes tissue water status through modifications in stomatal conductance and a decrease in root hydraulic conductance. P and water display contrasting distributions in the soil, with P being concentrated in the topsoil and water in the subsoil. Plants adapt to water- and P-limited environments by efficiently exploring localized resource hotspots of P and water through the adaptation of their root system. Thus, developing cultivars with improved root architecture is crucial for accessing and utilizing P and water from arid and P-deficient soils. To meet this goal, breeding towards multiple advantageous root traits can lead to better cultivars for water- and P-limited environments. This review discusses the interplay of P and water availability and highlights specific root traits that enhance the exploration and exploitation of optimal resource-rich soil strata while reducing metabolic costs. We propose root ideotype models, including 'topsoil foraging', 'subsoil foraging', and 'topsoil/subsoil foraging' for maize (monocot) and common bean (dicot). These models integrate beneficial root traits and guide the development of water- and P-efficient cultivars for challenging environments.
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Affiliation(s)
- Maryam Nasr Esfahani
- Department of Biology, Chair of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany.
| | - Uwe Sonnewald
- Department of Biology, Chair of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany.
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Bian J, Cui Y, Li J, Guan Y, Tian S, Liu X. Genome-wide analysis of PIN genes in cultivated peanuts (Arachis hypogaea L.): identification, subcellular localization, evolution, and expression patterns. BMC Genomics 2023; 24:629. [PMID: 37865765 PMCID: PMC10590530 DOI: 10.1186/s12864-023-09723-5] [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: 07/03/2023] [Accepted: 10/08/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Auxin is an important hormone in plants and the PIN-FORMED (PIN) genes are essential to auxin distribution in growth and developmental processes of plants. Peanut is an influential cash crop, but research into PIN genes in peanuts remains limited. RESULTS In this study, 16 PIN genes were identified in the genome of cultivated peanut, resolving into four subfamilies. All PIN genes were predicted to be located in the plasma membrane and a subcellular location experiment confirmed this prediction for eight of them. The gene structure, cis-elements in the promoter, and evolutionary relationships were elucidated, facilitating our understanding of peanut PINs and their evolution. In addition, the expression patterns of these PINs in various tissues were analyzed according to a previously published transcriptome dataset and qRT-PCR, which gave us a clear understanding of the temporal and spatial expression of PIN genes in different growth stages and different tissues. The expression trend of homologous genes was similar. AhPIN2A and AhPIN2B exhibited predominant expression in roots. AhPIN1A-1 and AhPIN1B-1 displayed significant upregulation following peg penetration, suggesting a potential close association with peanut pod development. Furthermore, we presented the gene network and gene ontology enrichment of these PINs. Notably, AhABCB19 exhibited a co-expression relationship with AhPIN1A and AhPIN1B-1, with all three genes displaying higher expression levels in peanut pegs and pods. These findings reinforce their potential role in peanut pod development. CONCLUSIONS This study details a comprehensive analysis of PIN genes in cultivated peanuts and lays the foundation for subsequent studies of peanut gene function and phenotype.
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Affiliation(s)
- Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Yuanyuan Cui
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Jihua Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Yu Guan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shuhua Tian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China.
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Ouyang Q, Zhang Y, Yang X, Yang C, Hou D, Liu H, Xu H. Overexpression of OsPIN9 Impairs Chilling Tolerance via Disturbing ROS Homeostasis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2809. [PMID: 37570963 PMCID: PMC10421329 DOI: 10.3390/plants12152809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
The auxin efflux transporter PIN-FORMED (PIN) family is one of the major protein families that facilitates polar auxin transport in plants. Here, we report that overexpression of OsPIN9 leads to altered plant architecture and chilling tolerance in rice. The expression profile analysis indicated that OsPIN9 was gradually suppressed by chilling stress. The shoot height and adventitious root number of OsPIN9-overexpressing (OE) plants were significantly reduced at the seedling stage. The roots of OE plants were more tolerant to N-1-naphthylphthalamic acid (NPA) treatment than WT plants, indicating the disturbance of auxin homeostasis in OE lines. The chilling tolerance assay showed that the survival rate of OE plants was markedly lower than that of wild-type (WT) plants. Consistently, more dead cells, increased electrolyte leakage, and increased malondialdehyde (MDA) content were observed in OE plants compared to those in WT plants under chilling conditions. Notably, OE plants accumulated more hydrogen peroxide (H2O2) and less superoxide anion radicals (O2-) than WT plants under chilling conditions. In contrast, catalase (CAT) and superoxide dismutase (SOD) activities in OE lines decreased significantly compared to those in WT plants at the early chilling stage, implying that the impaired chilling tolerance of transgenic plants is probably attributed to the sharp induction of H2O2 and the delayed induction of antioxidant enzyme activities at this stage. In addition, several OsRboh genes, which play a crucial role in ROS production under abiotic stress, showed an obvious increase after chilling stress in OE plants compared to that in WT plants, which probably at least in part contributes to the production of ROS under chilling stress in OE plants. Together, our results reveal that OsPIN9 plays a vital role in regulating plant architecture and, more importantly, is involved in regulating rice chilling tolerance by influencing auxin and ROS homeostasis.
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Affiliation(s)
| | | | | | | | | | | | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China; (Q.O.); (Y.Z.); (X.Y.); (C.Y.); (D.H.); (H.L.)
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Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:155-174. [PMID: 37025008 DOI: 10.1111/tpj.16218] [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: 06/03/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components.
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Affiliation(s)
- Lihui Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Baolin Yao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Xiaoyan Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yiting Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
- Shanxi Agricultural University/Shanxi Academy of Agricultural Sciences, The Industrial Crop Institute, Fenyang, 032200, China
| | - Yuxin Cao
- Key Lab of Agricultural Biotechnology of Yunnan Province, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China
| | - Ruomeng Zhu
- Key Lab of Agricultural Biotechnology of Yunnan Province, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China
| | - Xinqi Lu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Wuying Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Jianping Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Shuanglu Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Han
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan Zhou
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Chongyu Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Haiyan Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiahong He
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Zhongkai Zhang
- Key Lab of Agricultural Biotechnology of Yunnan Province, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
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10
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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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11
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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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12
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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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13
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Wang S, Han S, Zhou X, Zhao C, Guo L, Zhang J, Liu F, Huo Q, Zhao W, Guo Z, Chen X. Phosphorylation and ubiquitination of OsWRKY31 are integral to OsMKK10-2-mediated defense responses in rice. THE PLANT CELL 2023; 35:2391-2412. [PMID: 36869655 DOI: 10.1093/plcell/koad064] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 05/30/2023]
Abstract
Mitogen-activated protein kinase (MPK) cascades play vital roles in plant innate immunity, growth, and development. Here, we report that the rice (Oryza sativa) transcription factor gene OsWRKY31 is a key component in a MPK signaling pathway involved in plant disease resistance in rice. We found that the activation of OsMKK10-2 enhances resistance against the rice blast pathogen Magnaporthe oryzae and suppresses growth through an increase in jasmonic acid and salicylic acid accumulation and a decrease of indole-3-acetic acid levels. Knockout of OsWRKY31 compromises the defense responses mediated by OsMKK10-2. OsMKK10-2 and OsWRKY31 physically interact, and OsWRKY31 is phosphorylated by OsMPK3, OsMPK4, and OsMPK6. Phosphomimetic OsWRKY31 has elevated DNA-binding activity and confers enhanced resistance to M. oryzae. In addition, OsWRKY31 stability is regulated by phosphorylation and ubiquitination via RING-finger E3 ubiquitin ligases interacting with WRKY 1 (OsREIW1). Taken together, our findings indicate that modification of OsWRKY31 by phosphorylation and ubiquitination functions in the OsMKK10-2-mediated defense signaling pathway.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Shuying Han
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xiangui Zhou
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Changjiang Zhao
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Lina Guo
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Junqi Zhang
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Fei Liu
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Qixin Huo
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zejian Guo
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xujun Chen
- Key Laboratory of Pest Monitoring and Green Management, MOA, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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14
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Wang J, Li C, Mao X, Wang J, Li L, Li J, Fan Z, Zhu Z, He L, Jing R. The wheat basic helix-loop-helix gene TabHLH123 positively modulates the formation of crown roots and is associated with plant height and 1000-grain weight under various conditions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2542-2555. [PMID: 36749713 DOI: 10.1093/jxb/erad051] [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: 11/01/2022] [Accepted: 02/03/2023] [Indexed: 06/06/2023]
Abstract
Crown roots are the main components of the fibrous root system in cereal crops and play critical roles in plant adaptation; however, the molecular mechanisms underlying their formation in wheat (Triticum aestivum) have not been fully elucidated. In this study, we identified a wheat basic helix-loop-helix (bHLH) protein, TabHLH123, that interacts with the essential regulator of crown root initiation, MORE ROOT in wheat (TaMOR). TabHLH123 is expressed highly in shoot bases and roots. Ectopic expression of TabHLH123 in rice resulted in more roots compared with the wild type. TabHLH123 regulates the expression of genes controlling crown-root development and auxin metabolism, responses, and transport. In addition, we analysed the nucleotide sequence polymorphisms of TabHLH123s in the wheat genome and identified a superior haplotype, TabHLH123-6B, that is associated with high root dry weight and 1000-grain weight, and short plant height. Our study reveals the role of TabHLH123 in controlling the formation of crown roots and provides beneficial insights for molecular marker-assisted breeding in wheat.
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Affiliation(s)
- Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Shanxi Agricultural University, Taigu 030031, 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
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyi Wang
- 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
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhi Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liheng He
- College of Agronomy, Shanxi Agricultural University, Taigu 030031, 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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15
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Zheng Z, Wang B, Zhuo C, Xie Y, Zhang X, Liu Y, Zhang G, Ding H, Zhao B, Tian M, Xu M, Kong D, Shen R, Liu Q, Wu G, Huang J, Wang H. Local auxin biosynthesis regulates brace root angle and lodging resistance in maize. THE NEW PHYTOLOGIST 2023; 238:142-154. [PMID: 36636793 DOI: 10.1111/nph.18733] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/18/2022] [Indexed: 05/12/2023]
Abstract
Root lodging poses a major threat to maize production, resulting in reduced grain yield and quality, and increased harvest costs. Here, we combined expressional, genetic, and cytological studies to demonstrate a role of ZmYUC2 and ZmYUC4 in regulating gravitropic response of the brace root and lodging resistance in maize. We show that both ZmYUC2 and ZmYUC4 are preferentially expressed in root tips with partially overlapping expression patterns, and the protein products of ZmYUC2 and ZmYUC4 are localized in the cytoplasm and endoplasmic reticulum, respectively. The Zmyuc4 single mutant and Zmyuc2/4 double mutant exhibit enlarged brace root angle compared with the wild-type plants, with larger brace root angle being observed in the Zmyuc2/4 double mutant. Consistently, the brace root tips of the Zmyuc4 single mutant and Zmyuc2/4 double mutant accumulate less auxin and are defective in proper reallocation of auxin in response to gravi-stimuli. Furthermore, we show that the Zmyuc4 single mutant and the Zmyuc2/4 double mutant display obviously enhanced root lodging resistance. Our combined results demonstrate that ZmYUC2- and ZmYUC4-mediated local auxin biosynthesis is required for normal gravity response of the brace roots and provide effective targets for breeding root lodging resistant maize cultivars.
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Affiliation(s)
- Zhigang Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Chuyun Zhuo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Xiaoming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanjun Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Guisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Manqing Tian
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, 00790, Finland
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Guangxia Wu
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Junfei Huang
- Shimadzu (China) Co. Ltd Shenzhen Branch, 518042, Shenzhen, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
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16
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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17
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Hu S, Liu X, Xuan W, Mei H, Li J, Chen X, Zhao Z, Zhao Y, Jeyaraj A, Periakaruppan R, Li XH. Genome-wide identification and characterization of PIN-FORMED (PIN) and PIN-LIKES (PILS) gene family reveals their role in adventitious root development in tea nodal cutting (Camellia Sinensis). Int J Biol Macromol 2023; 229:791-802. [PMID: 36572081 DOI: 10.1016/j.ijbiomac.2022.12.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/28/2022] [Accepted: 12/04/2022] [Indexed: 12/25/2022]
Abstract
Auxin affects all aspects of plant growth and development, including morphogenesis and adaptive responses. Auxin transmembrane transport is promoted by PIN formation (PIN) and a structurally similar PIN-like (PILS) gene family, which jointly controls the directional transport of the auxin between plant cells, and the accumulation of intracellular auxin. At present, there is no study investigating the roles of CslPIN and CslPILS gene family in root development in the tea plant (Camellia sinensis). In this study, 8 CslPIN and 10 CslPILS genes were identified in the tea plant, and their evolutionary relationships, physical and chemical properties, conserved motifs, cis-acting elements, chromosome location, collinearity, and expression characteristics were analyzed. The mechanism of CslPIN and CslPILS in the formation of tea adventitious roots (ARs) was studied by the AR induction system. Through functional verification, the regulation of CslPIN3 gene on root growth and development of tea plant was studied by over-expression of CslPIN3 in Arabidopsis thaliana and in situ hybridization in Camellia sinensis. The results confirmed CslPIN3 was involved in the regulation of root growth and development as well as auxin accumulation. This study provides a better insight into the regulatory mechanism of CslPIN and CslPILS gene family on the formation of AR in tea plant.
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Affiliation(s)
- Shunkai Hu
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xinqiu Liu
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Wei Xuan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Huiling Mei
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jianjie Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xuan Chen
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Zhen Zhao
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yuxin Zhao
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Anburaj Jeyaraj
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Rajiv Periakaruppan
- Department of Biotechnology, PSG College of Arts & Science, Coimbatore 14, Tamilnadu, India
| | - Xing-Hui Li
- International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
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18
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Li Y, Wu L, Ren M, Zhu J, Xu J, Hu H, Quan X, Huang C, Mao C. Functional redundancy of OsPIN1 paralogous genes in regulating plant growth and development in rice. PLANT SIGNALING & BEHAVIOR 2022; 17:2065432. [PMID: 35442849 PMCID: PMC9037464 DOI: 10.1080/15592324.2022.2065432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
The OsPIN1 paralogous genes (OsPIN1a-1d) are important for root and panicle development in rice (Oryza sativa L.). However, the specific role of OsPIN1 paralogous genes is still not clear. To understand the specific roles of PIN1 paralogs in rice, we generated pin1 triple and quadruple mutants by crossing the pin1a pin1b and pin1c pin1d double mutants which we previously created. Compared with the 7-day-old wild type, the pin1a pin1c pin1d and pin1b pin1c pin1d triple mutants showed no obvious phenotype variation except that the pin1a pin1c pin1d triple mutant had shorter primary root and shoot. The pin1a pin1b pin1c and pin1a pin1b pin1d triple mutants exhibited a series of developmental abnormalities, including shorter primary roots, longer root hairs, fewer crown roots and lateral roots, shorter and curved shoots. Furthermore, the pin1a pin1b pin1c pin1d quadruple mutant displayed more severe phenotypic defects which was lethal. In addition, the expression levels of some hormone signal transduction and crown root development related genes, such as OsIAAs, OsARFs, OsRRs, and OsCRLs, were significantly altered in the stem base of all examined pin1 multiple mutants. Taken together, our results demonstrated that the four OsPIN1 paralogous genes function redundantly in regulating rice growth and development.
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Affiliation(s)
- Yong Li
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lingling Wu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meiyan Ren
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianshu Zhu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiming Xu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Han Hu
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaokang Quan
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Chongping Huang
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Chuanzao Mao
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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19
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Wu X, Xie X, Yang S, Yin Q, Cao H, Dong X, Hui J, Liu Z, Jia Z, Mao C, Yuan L. OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1309-1320. [PMID: 35861152 DOI: 10.1093/pcp/pcac104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Optimal plant growth and development rely on morphological and physiological adaptions of the root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of NH4+ transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate the expression of OsPIN2, and the OsPIN2 mutant (lra1) exhibited a strong reduction in NH4+-triggered LR branching, suggesting that the auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.
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Affiliation(s)
- Xiangyu Wu
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Xie
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Shan Yang
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Qianyu Yin
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Huairong Cao
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiaonan Dong
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Jing Hui
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Zhi Liu
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Zhongtao Jia
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province 310058, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
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20
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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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21
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Wang H, Ouyang Q, Yang C, Zhang Z, Hou D, Liu H, Xu H. Mutation of OsPIN1b by CRISPR/Cas9 Reveals a Role for Auxin Transport in Modulating Rice Architecture and Root Gravitropism. Int J Mol Sci 2022; 23:ijms23168965. [PMID: 36012245 PMCID: PMC9409181 DOI: 10.3390/ijms23168965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022] Open
Abstract
The distribution and content of auxin within plant tissues affect a variety of important growth and developmental processes. Polar auxin transport (PAT), mainly mediated by auxin influx and efflux transporters, plays a vital role in determining auxin maxima and gradients in plants. The auxin efflux carrier PIN-FORMED (PIN) family is one of the major protein families involved in PAT. Rice (Oryza sativa L.) genome possesses 12 OsPIN genes. However, the detailed functions of OsPIN genes involved in regulating the rice architecture and gravity response are less well understood. In the present study, OsPIN1b was disrupted by CRISPR/Cas9 technology, and its roles in modulating rice architecture and root gravitropism were investigated. Tissue-specific analysis showed that OsPIN1b was mainly expressed in roots, stems and sheaths at the seedling stage, and the transcript abundance was progressively decreased during the seedling stages. Expression of OsPIN1b could be quickly and greatly induced by NAA, indicating that OsPIN1b played a vital role in PAT. IAA homeostasis was disturbed in ospin1b mutants, as evidenced by the changed sensitivity of shoot and root to NAA and NPA treatment, respectively. Mutation of OsPIN1b resulted in pleiotropic phenotypes, including decreased growth of shoots and primary roots, reduced adventitious root number in rice seedlings, as well as shorter and narrower leaves, increased leaf angle, more tiller number and decreased plant height and panicle length at the late developmental stage. Moreover, ospin1b mutants displayed a curly root phenotype cultured with tap water regardless of lighting conditions, while nutrient solution culture could partially rescue the curly root phenotype in light and almost completely abolish this phenotype in darkness, indicating the involvement of the integration of light and nutrient signals in root gravitropism regulation. Additionally, amyloplast sedimentation was impaired in the peripheral tiers of the ospin1b root cap columella cell, while it was not the main contributor to the abnormal root gravitropism. These data suggest that OsPIN1b not only plays a vital role in regulating rice architecture but also functions in regulating root gravitropism by the integration of light and nutrient signals.
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Affiliation(s)
- Huihui Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Qiqi Ouyang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Chong Yang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Zhuoyan Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Dianyun Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Hao Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
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22
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Ghate T, Soneji K, Barvkar V, Ramakrishnan P, Prusty D, Islam SR, Manna SK, Srivastava AK. Thiourea mediated ROS-metabolites reprogramming restores root system architecture under arsenic stress in rice. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129020. [PMID: 35650738 DOI: 10.1016/j.jhazmat.2022.129020] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/18/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
Arsenic (As) is a ubiquitous carcinogenic metalloid that enters into human food chain, through rice consumption. To unravel the conundrum of oxidative vs. reductive stress, the differential root-system architecture (RSA) was studied under As (a ROS producer) and thiourea (TU; a ROS scavenger) alone treatments, which indicated 0.80- and 0.74-fold reduction in the number of lateral roots (NLR), respectively compared with those of control. In case of As+TU treatment, NLR was increased by 4.35-fold compared with those of As-stress, which coincided with partial restoration of redox-status and auxin transport towards the root-tip. The expression levels of 16 ROS related genes, including RBOHC, UPB-1 C, SHR1, PUCHI, were quantified which provided the molecular fingerprint, in accordance with endogenous ROS signature. LC-MS based untargeted and targeted metabolomics data revealed that As-induced oxidative stress was metabolically more challenging than TU alone-induced reductive stress. Cis/trans-ferruloyl putrescine and γ-glutamyl leucine were identified as novel As-responsive metabolites whose levels were decreased and increased, respectively under As+TU than As-treated roots. In addition, the overall amino acid accumulation was increased in As+TU than As-treated roots, indicating the improved nutritional availability. Thus, the study revealed dynamic interplay between "ROS-metabolites-RSA", to the broader context of TU-mediated amelioration of As-stress in rice.
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Affiliation(s)
- Tejashree Ghate
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India; School of Biological sciencesUM-DAE Center for Excellence in Basic Sciences, University of Mumbai, Vidyanagari 400098, Mumbai
| | - Kanchan Soneji
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India; Division of crop production, ICAR- Indian Institute of Soybean Research, Khandwa Road, Indore 452001, (M.P), India
| | - Vitthal Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India
| | - Padma Ramakrishnan
- Centre for Cellular and Molecular Platforms, GKVK Post, Bengaluru 560065, India
| | - Debasish Prusty
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Sk Ramiz Islam
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Soumen Kanti Manna
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
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23
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Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism. Proc Natl Acad Sci U S A 2022; 119:e2201350119. [PMID: 35881796 PMCID: PMC9351459 DOI: 10.1073/pnas.2201350119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The growth angle roots adopt are critical for capturing soil resources, such as nutrients and water. Despite its agronomic importance, few regulatory genes have been identified in crops. Here we identify the root angle regulatory gene ENHANCED GRAVITROPISM 1 (EGT1) in barley. Strikingly, mutants lacking EGT1 exhibit a steeper angle in every root class. EGT1 appears to function as a component of an antigravitropic offset mechanism that regulates tissue stiffness, which impacts final root growth angle. EGT1 is a hot spot for selection as natural allelic variation within a conserved Tubby domain that is linked with steeper root angle. Analogous EGT1-dependent regulation of root angle in wheat demonstrates broad significance of EGT1 for trait improvement in cereal crops. Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.
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24
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Maqbool S, Hassan MA, Xia X, York LM, Rasheed A, He Z. Root system architecture in cereals: progress, challenges and perspective. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:23-42. [PMID: 35020968 DOI: 10.1111/tpj.15669] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this 'hidden half' provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.
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Affiliation(s)
- Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Adeel Hassan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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25
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Tissue specificity and responses to abiotic stresses and hormones of PIN genes in rice. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01031-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Xu F, Liao H, Zhang Y, Yao M, Liu J, Sun L, Zhang X, Yang J, Wang K, Wang X, Ding Y, Liu C, Rensing C, Zhang J, Yeh K, Xu W. Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying. THE ISME JOURNAL 2022; 16:801-811. [PMID: 34621017 PMCID: PMC8857228 DOI: 10.1038/s41396-021-01133-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022]
Abstract
Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.
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Affiliation(s)
- Feiyun Xu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hanpeng Liao
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yingjiao Zhang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Minjie Yao
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Liu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Leyun Sun
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xue Zhang
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinyong Yang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ke Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoyun Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yexin Ding
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chen Liu
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Christopher Rensing
- grid.256111.00000 0004 1760 2876Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianhua Zhang
- grid.221309.b0000 0004 1764 5980Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kaiwun Yeh
- grid.19188.390000 0004 0546 0241Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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27
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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28
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York LM, Griffiths M, Maaz TM. Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency. Curr Opin Biotechnol 2022; 75:102682. [PMID: 35104719 DOI: 10.1016/j.copbio.2022.102682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023]
Abstract
Nutrient use efficiency (NUE) is typically measured as the ratio of yield to soil nutrient availability but ignores contributions of underlying plant traits. Relevant plant traits can be grouped as root acquisition efficiency, shoot radiation use efficiency, and plant metabolic efficiency. The intentional integration of these traits will lead to synergistic improvements of NUE. Recent progress in trait-focused research includes phenotyping root nutrient uptake rates and respiration, engineering reduced photorespiration, and identification of nutrient assimilation pathways. Traits need to be conceptualized in agricultural systems contexts to improve synchrony of plant demand and soil supply of nutrients, including consideration of crop mixtures. Use of simulation modeling and multi-objective optimization will allow accelerating NUE gains beyond selection for a single ratio.
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Affiliation(s)
- Larry M York
- Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | | | - Tai McClellan Maaz
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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29
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021. [PMID: 34608637 DOI: 10.1111/nph.17572.hal-03379708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T Freschet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
| | - Loïc Pagès
- UR 1115 PSH, Centre PACA, site Agroparc, INRAE, 84914, Avignon cedex 9, France
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Louise H Comas
- USDA-ARS Water Management Research Unit, 2150 Centre Avenue, Bldg D, Suite 320, Fort Collins, CO, 80526, USA
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Catherine Roumet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany CAS, Dukelska 135, 37901, Trebon, Czech Republic
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johannes A Postma
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Thomas S Adams
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - A Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee,, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee,, DD1 4HN, UK
| | - Elison B Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Johannes H C Cornelissen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eric Garnier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Arthur Gessler
- Forest Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Ina C Meier
- Functional Forest Ecology, University of Hamburg, Haidkrugsweg 1, 22885, Barsbütel, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | | | - Laura Rose
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Peter Ryser
- Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, 2300 RA, the Netherlands
| | - Alexia Stokes
- INRAE, AMAP, CIRAD, IRD, CNRS, University of Montpellier, Montpellier, 34000, France
| | - Tao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, Leipzig, 04103, Germany
| | - Nina Wurzburger
- Odum School of Ecology, University of Georgia, 140 E. Green Street, Athens, GA, 30602, USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds, LS2 9JT, UK
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Moemy Gomes de Moraes
- Department of Botany, Institute of Biological Sciences, Federal University of Goiás, 19, 74690-900, Goiânia, Goiás, Brazil
| | - Štěpán Janeček
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Crawley (Perth), WA, Australia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - M Luke McCormack
- Center for Tree Science, Morton Arboretum, 4100 Illinois Rt. 53, Lisle, IL, 60532, USA
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Li C, Li L, Reynolds MP, Wang J, Chang X, Mao X, Jing R. Recognizing the hidden half in wheat: root system attributes associated with drought tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5117-5133. [PMID: 33783492 DOI: 10.1093/jxb/erab124] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/09/2023]
Abstract
Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.
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Affiliation(s)
- 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
| | | | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Chang
- 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, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. PLANT, CELL & ENVIRONMENT 2021; 44:1846-1857. [PMID: 33576018 DOI: 10.1111/pce.14029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin-responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with a high and auxin-mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin-responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1-mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis-based insertion of the INDITTO2 transposon into the DRO1 promoter of the non-adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.
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Affiliation(s)
- Yiting Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
- Shanxi Agricultural University/Shanxi Academy of Agricultural Sciences. The Industrial Crop Institute, Fenyang, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Dong Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Baolin Yao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Si Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Li Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Jie Qian
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xuan Zhou
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Li Han
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Shuanglu Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Canrong Ma
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yanfang Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Chongyu Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qian Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Saijie Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Lina Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xi Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Youchun Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Hao Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Jing Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qiong Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Lichi Li
- International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Sheng Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Zhili Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Lei Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chengyun Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
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Reynolds M, Atkin OK, Bennett M, Cooper M, Dodd IC, Foulkes MJ, Frohberg C, Hammer G, Henderson IR, Huang B, Korzun V, McCouch SR, Messina CD, Pogson BJ, Slafer GA, Taylor NL, Wittich PE. Addressing Research Bottlenecks to Crop Productivity. TRENDS IN PLANT SCIENCE 2021; 26:607-630. [PMID: 33893046 DOI: 10.1016/j.tplants.2021.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/22/2023]
Abstract
Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in 'precompetitive' space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source-sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.
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Affiliation(s)
- Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico, El Batan, Texcoco, Mexico.
| | - Owen K Atkin
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia.
| | - Malcolm Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK.
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian C Dodd
- The Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - M John Foulkes
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Claus Frohberg
- BASF BBC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA.
| | | | - Susan R McCouch
- Plant Breeding & Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Carlos D Messina
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50310, USA.
| | - Barry J Pogson
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia
| | - Gustavo A Slafer
- Department of Crop and Forest Sciences, University of Lleida, AGROTECNIO, CERCA Center, Av. R. Roure 191, 25198 Lleida, Spain; ICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain.
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Peter E Wittich
- Syngenta Seeds B.V., Westeinde 62, 1601 BK, Enkhuizen, The Netherlands.
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1101/2020.12.11.421685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 05/26/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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35
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1111/tpj.15226] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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Rao S, Armstrong R, Silva-Perez V, Tefera AT, Rosewarne GM. Pulse Root Ideotype for Water Stress in Temperate Cropping System. PLANTS 2021; 10:plants10040692. [PMID: 33916833 PMCID: PMC8067327 DOI: 10.3390/plants10040692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022]
Abstract
Pulses are a key component of crop production systems in Southern Australia due to their rotational benefits and potential profit margins. However, cultivation in temperate cropping systems such as that of Southern Australia is limited by low soil water availability and subsoil constraints. This limitation of soil water is compounded by the irregular rainfall, resulting in the absence of plant available water at depth. An increase in the productivity of key pulses and expansion into environments and soil types traditionally considered marginal for their growth will require improved use of the limited soil water and adaptation to sub soil constrains. Roots serve as the interface between soil constraints and the whole plant. Changes in root system architecture (RSA) can be utilised as an adaptive strategy in achieving yield potential under limited rainfall, heterogenous distribution of resources and other soil-based constraints. The existing literature has identified a “‘Steep, Deep and Cheap” root ideotype as a preferred RSA. However, this idiotype is not efficient in a temperate system where plant available water is limited at depth. In addition, this root ideotype and other root architectural studies have focused on cereal crops, which have different structures and growth patterns to pulses due to their monocotyledonous nature and determinant growth habit. The paucity of pulse-specific root architectural studies warrants further investigations into pulse RSA, which should be combined with an examination of the existing variability of known genetic traits so as to develop strategies to alleviate production constraints through either tolerance or avoidance mechanisms. This review proposes a new model of root system architecture of “Wide, Shallow and Fine” roots based on pulse roots in temperate cropping systems. The proposed ideotype has, in addition to other root traits, a root density concentrated in the upper soil layers to capture in-season rainfall before it is lost due to evaporation. The review highlights the potential to achieve this in key pulse crops including chickpea, lentil, faba bean, field pea and lupin. Where possible, comparisons to determinate crops such as cereals have also been made. The review identifies the key root traits that have shown a degree of adaptation via tolerance or avoidance to water stress and documents the current known variability that exists in and amongst pulse crops setting priorities for future research.
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Zhao J, Yang B, Li W, Sun S, Peng L, Feng D, Li L, Di H, He Y, Wang Z. A genome-wide association study reveals that the glucosyltransferase OsIAGLU regulates root growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1119-1134. [PMID: 33130882 DOI: 10.1093/jxb/eraa512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 05/18/2023]
Abstract
Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3, qRL6, qRL7, and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11, namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement.
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Affiliation(s)
- Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Bin Yang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Defeng Feng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Li Li
- Huzhou Agricultural Science and Technology Development Center, Huzhou, People's Republic of China
| | - Hong Di
- Northeast Agricultural University, Harbin, People's Republic of China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
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Yoshida Y, Arita T, Otani J, Sawa S. Visualization of Toyoura sand-grown plant roots by X-ray computer tomography. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:481-484. [PMID: 33850438 PMCID: PMC8034682 DOI: 10.5511/plantbiotechnology.20.0819a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants establish their root system as a three-dimensional structure, which is then used to explore the soil to absorb resources and provide mechanical anchorage. Simplified two-dimensional growth systems, such as agar plates, have been used to study various aspects of plant root biology. However, it remains challenging to study the more realistic three-dimensional structure and function of roots hidden in opaque soil. Here, we optimized X-ray computer tomography (CT)-based visualization of an intact root system by using Toyoura sand, a standard silica sand used in geotechnology research, as a growth substrate. Distinct X-ray attenuation densities of root tissue and Toyoura sand enabled clear image segmentation of the CT data. Sorghum grew especially vigorously in Toyoura sand and it could be used as a model for analyzing root structure optimization in response to mechanical obstacles. The use of Toyoura sand has the potential to link plant root biology and geotechnology applications.
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Affiliation(s)
- Yuki Yoshida
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Tetsuya Arita
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Jun Otani
- 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
| | - Shinichiro Sawa
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- E-mail: Tel & Fax: +81-96-342-3439
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Mounier T, Navarro-Sanz S, Bureau C, Antoine L, Varoquaux F, Durandet F, Périn C. A fast, efficient and high-throughput procedure involving laser microdissection and RT droplet digital PCR for tissue-specific expression profiling of rice roots. BMC Mol Cell Biol 2020; 21:92. [PMID: 33302866 PMCID: PMC7727186 DOI: 10.1186/s12860-020-00312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/10/2020] [Indexed: 11/22/2022] Open
Abstract
Background In rice, the cortex and outer tissues play a key role in submergence tolerance. The cortex differentiates into aerenchyma, which are air-containing cavities that allow the flow of oxygen from shoots to roots, whereas exodermis suberification and sclerenchyma lignification limit oxygen loss from the mature parts of roots by forming a barrier to root oxygen loss (ROL). The genes and their networks involved in the cellular identity and differentiation of these tissues remain poorly understood. Identification and characterization of key regulators of aerenchyma and ROL barrier formation require determination of the specific expression profiles of these tissues. Results We optimized an approach combining laser microdissection (LM) and droplet digital RT-PCR (ddRT-PCR) for high-throughput identification of tissue-specific expression profiles. The developed protocol enables rapid (within 3 days) extraction of high-quality RNA from root tissues with a low contamination rate. We also demonstrated the possibility of extracting RNAs from paraffin blocks stored at 4 °C without any loss of quality. We included a detailed troubleshooting guide that should allow future users to adapt the proposed protocol to other tissues and/or species. We demonstrated that our protocol, which combines LM with ddRT-PCR, can be used as a complementary tool to in situ hybridization for tissue-specific characterization of gene expression even with a low RNA concentration input. We illustrated the efficiency of the proposed approach by validating three of four potential tissue-specific candidate genes detailed in the RiceXpro database. Conclusion The detailed protocol and the critical steps required to optimize its use for other species will democratize tissue-specific transcriptome approaches combining LM with ddRT-PCR for analyses of plants.
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Affiliation(s)
- Thibault Mounier
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Sergi Navarro-Sanz
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Charlotte Bureau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Lefeuvre Antoine
- IAGE Company, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Fabrice Varoquaux
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Franz Durandet
- IAGE Company, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Christophe Périn
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France.
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Yoon J, Cho LH, Yang W, Pasriga R, Wu Y, Hong WJ, Bureau C, Wi SJ, Zhang T, Wang R, Zhang D, Jung KH, Park KY, Périn C, Zhao Y, An G. Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5348-5364. [PMID: 32449922 PMCID: PMC7501826 DOI: 10.1093/jxb/eraa209] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/27/2020] [Indexed: 05/11/2023]
Abstract
Root meristem activity is the most critical process influencing root development. Although several factors that regulate meristem activity have been identified in rice, studies on the enhancement of meristem activity in roots are limited. We identified a T-DNA activation tagging line of a zinc-finger homeobox gene, OsZHD2, which has longer seminal and lateral roots due to increased meristem activity. The phenotypes were confirmed in transgenic plants overexpressing OsZHD2. In addition, the overexpressing plants showed enhanced grain yield under low nutrient and paddy field conditions. OsZHD2 was preferentially expressed in the shoot apical meristem and root tips. Transcriptome analyses and quantitative real-time PCR experiments on roots from the activation tagging line and the wild type showed that genes for ethylene biosynthesis were up-regulated in the activation line. Ethylene levels were higher in the activation lines compared with the wild type. ChIP assay results suggested that OsZHD2 induces ethylene biosynthesis by controlling ACS5 directly. Treatment with ACC (1-aminocyclopropane-1-carboxylic acid), an ethylene precursor, induced the expression of the DR5 reporter at the root tip and stele, whereas treatment with an ethylene biosynthesis inhibitor, AVG (aminoethoxyvinylglycine), decreased that expression in both the wild type and the OsZHD2 overexpression line. These observations suggest that OsZHD2 enhances root meristem activity by influencing ethylene biosynthesis and, in turn, auxin.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Lae-Hyeon Cho
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Wenzhu Yang
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Yunfei Wu
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Woo-Jong Hong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Charlotte Bureau
- Agricultural Research Centre For International Development, Paris, France
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Tao Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide Urrbrae, SA, Australia
| | - Ki-Hong Jung
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Christophe Périn
- Agricultural Research Centre For International Development, Paris, France
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Correspondence:
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Guan L, Li Y, Huang K, Cheng ZM(M. Auxin regulation and MdPIN expression during adventitious root initiation in apple cuttings. HORTICULTURE RESEARCH 2020; 7:143. [PMID: 32922815 PMCID: PMC7459121 DOI: 10.1038/s41438-020-00364-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 05/23/2023]
Abstract
Adventitious root (AR) formation is critical for the efficient propagation of elite horticultural and forestry crops. Despite decades of research, the cellular processes and molecular mechanisms underlying AR induction in woody plants remain obscure. We examined the details of AR formation in apple (Malus domestica) M.9 rootstock, the most widely used dwarf rootstock for intensive production, and investigated the role of polar auxin transport in postembryonic organogenesis. AR formation begins with a series of founder cell divisions and elongation of the interfascicular cambium adjacent to vascular tissues. This process is associated with a relatively high indole acetic acid (IAA) content and hydrolysis of starch grains. Exogenous auxin treatment promoted this cell division, as well as the proliferation and reorganization of the endoplasmic reticulum and Golgi membrane. In contrast, treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) inhibited cell division in the basal region of the cuttings and resulted in abnormal cell divisions during the early stage of AR formation. In addition, PIN-FORMED (PIN) transcripts were differentially expressed throughout the whole AR development process. We also detected upregulation of MdPIN8 and MdPIN10 during induction; upregulation of MdPIN4, MdPIN5, and MdPIN8 during extension; and upregulation of all MdPINs during AR initiation. This research provides an improved understanding of the cellular and molecular underpinnings of the AR process in woody plants.
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Affiliation(s)
- Ling Guan
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, 210014 Nanjing, China
| | - Yingjun Li
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kaihui Huang
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37831 USA
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42
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Li J, Yang Y, Chai M, Ren M, Yuan J, Yang W, Dong Y, Liu B, Jian Q, Wang S, Peng B, Yuan H, Fan H. Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110545. [PMID: 32771158 DOI: 10.1016/j.plantsci.2020.110545] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 05/07/2023]
Abstract
As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.
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Affiliation(s)
- Jintao Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yuna Yang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengmeng Chai
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengdi Ren
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Jingjia Yuan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Wenqian Yang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yu Dong
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - BinWen Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Qingmei Jian
- College of Bioengineering, Jingchu University of Technology, Jingmen, 448000, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Bo Peng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Hongyu Yuan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Haiyan Fan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
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Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci U S A 2020; 117:21242-21250. [PMID: 32817523 PMCID: PMC7474696 DOI: 10.1073/pnas.2005911117] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 (DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.
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Chapman K, Ivanovici A, Taleski M, Sturrock CJ, Ng JLP, Mohd-Radzman NA, Frugier F, Bennett MJ, Mathesius U, Djordjevic MA. CEP receptor signalling controls root system architecture in Arabidopsis and Medicago. THE NEW PHYTOLOGIST 2020; 226:1809-1821. [PMID: 32048296 DOI: 10.1111/nph.16483] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Root system architecture (RSA) influences the effectiveness of resources acquisition from soils but the genetic networks that control RSA remain largely unclear. We used rhizoboxes, X-ray computed tomography, grafting, auxin transport measurements and hormone quantification to demonstrate that Arabidopsis and Medicago CEP (C-TERMINALLY ENCODED PEPTIDE)-CEP RECEPTOR signalling controls RSA, the gravitropic set-point angle (GSA) of lateral roots (LRs), auxin levels and auxin transport. We showed that soil-grown Arabidopsis and Medicago CEP receptor mutants have a narrower RSA, which results from a steeper LR GSA. Grafting showed that CEPR1 in the shoot controls GSA. CEP receptor mutants exhibited an increase in rootward auxin transport and elevated shoot auxin levels. Consistently, the application of auxin to wild-type shoots induced a steeper GSA and auxin transport inhibitors counteracted the CEP receptor mutant's steep GSA phenotype. Concordantly, CEP peptides increased GSA and inhibited rootward auxin transport in wild-type but not in CEP receptor mutants. The results indicated that CEP-CEP receptor-dependent signalling outputs in Arabidopsis and Medicago control overall RSA, LR GSA, shoot auxin levels and rootward auxin transport. We propose that manipulating CEP signalling strength or CEP receptor downstream targets may provide means to alter RSA.
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Affiliation(s)
- Kelly Chapman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Michael Taleski
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Craig J Sturrock
- The Hounsfield Facility, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Jason L P Ng
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nadiatul A Mohd-Radzman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université, Paris Sud, Université, Paris Diderot, INRA, Univ d'Evry, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Song M, Fan X, Chen J, Qu H, Luo L, Xu G. OsNAR2.1 Interaction with OsNIT1 and OsNIT2 Functions in Root-growth Responses to Nitrate and Ammonium. PLANT PHYSIOLOGY 2020; 183:289-303. [PMID: 32071150 PMCID: PMC7210649 DOI: 10.1104/pp.19.01364] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 05/04/2023]
Abstract
The nitrate transport accessory protein OsNAR2 plays a critical role in root-growth responses to nitrate and nitrate acquisition in rice (Oryza sativa). In this study, a pull-down assay combined with yeast two-hybrid and coimmunoprecipitation analyses revealed that OsNAR2.1 interacts with OsNIT1 and OsNIT2. Moreover, an in vitro nitrilase activity assay indicated that indole-3-acetonitrile (IAN) is hydrolyzed to indole-3-acetic acid (IAA) by OsNIT1, the activity of which was enhanced 3- to 4-fold by OsNIT2 and in excess of 5- to 8-fold by OsNAR2.1. Knockout (KO) of OsNAR2 1 was accompanied by repressed expression of both OsNIT1 and OsNIT2, whereas KO of OsNIT1 and OsNIT2 in the osnit1 and osnit2 mutant lines did not affect expression of OsNAR2 1 or the root nitrate acquisition rate. osnit1 and osnit2 displayed decreased primary root length and lateral root density. Double KO of OsNAR2 1 and OsNIT2 caused further decreases in lateral root density under nitrate supply. Ammonium supply repressed OsNAR2 1 expression whereas it upregulated OsNIT1 and OsNIT2 expression. Both osnit1 and osnit2 showed root growth hypersensitivity to external ammonium; however, less root growth sensitivity to external IAN, higher expression of three IAA-amido synthetase genes, and a lower rate of 3H-IAA movement toward the roots were observed. Taken together, we conclude that the interaction of OsNIT1 and OsNIT2 activated by OsNAR2.1 and nitrogen supply is essential for maintaining root growth possibly via altering the IAA ratio of free to conjugate forms and facilitating its transportation.
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Affiliation(s)
- Miaoquan Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingguang Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Le Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
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Teramoto S, Takayasu S, Kitomi Y, Arai-Sanoh Y, Tanabata T, Uga Y. High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography. PLANT METHODS 2020; 16:66. [PMID: 32426023 PMCID: PMC7216661 DOI: 10.1186/s13007-020-00612-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/05/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required. RESULTS We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over 3 weeks. CONCLUSIONS We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method 'RSAvis3D' and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518 Japan
| | - Satoko Takayasu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518 Japan
| | - Yuka Kitomi
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518 Japan
| | - Yumiko Arai-Sanoh
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518 Japan
| | | | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518 Japan
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Li Y, Zhu J, Wu L, Shao Y, Wu Y, Mao C. Functional Divergence of PIN1 Paralogous Genes in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:2720-2732. [PMID: 31410483 DOI: 10.1093/pcp/pcz159] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/07/2019] [Indexed: 05/08/2023]
Abstract
Auxin is a phytohormone that plays an important role in plant growth and development by forming local concentration gradients. The regulation of auxin levels is determined by the activity of auxin efflux carrier protein PIN-formed (PIN). In Arabidopsis thaliana, PIN-formed1 (PIN1) functions in inflorescence and root development. In rice (Oryza sativa L.), there are four PIN1 homologs (OsPIN1a-1d), but their functions remain largely unexplored. Hence, in this study, we created mutant alleles of PIN1 gene-pin1a, pin1b, pin1c, pin1d, pin1a pin1b and pin1c pin1d- using CRISPR/Cas9 technology and used them to study the functions of the four OsPIN1 paralogs in rice. In wild-type rice, all four OsPIN1 genes were relatively highly expressed in the root than in other tissues. Compared with the wild type, the OsPIN1 single mutants had no dramatic phenotypes, but the pin1a pin1b double mutant had shorter shoots and primary roots, fewer crown roots, reduced root gravitropism, longer root hairs and larger panicle branch angle. Furthermore, the pin1c pin1d double mutant showed no observable phenotype at the seedling stage, but showed naked, pin-shape inflorescence at flowering. These data suggest that OsPIN1a and OsPIN1b are involved in root, shoot and inflorescence development in rice, whereas OsPIN1c and OsPIN1d mainly function in panicle formation. Our study provides basic knowledge that will facilitate the study of auxin transport and signaling in rice.
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Affiliation(s)
- Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianshu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingling Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanlin Shao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Sun H, Guo X, Xu F, Wu D, Zhang X, Lou M, Luo F, Xu G, Zhang Y. Overexpression of OsPIN2 Regulates Root Growth and Formation in Response to Phosphate Deficiency in Rice. Int J Mol Sci 2019; 20:ijms20205144. [PMID: 31627334 PMCID: PMC6829224 DOI: 10.3390/ijms20205144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 01/24/2023] Open
Abstract
The response of root architecture to phosphate (P) deficiency is critical in plant growth and development. Auxin is a key regulator of plant root growth in response to P deficiency, but the underlying mechanisms are unclear. In this study, phenotypic and genetic analyses were undertaken to explore the role of OsPIN2, an auxin efflux transporter, in regulating the growth and development of rice roots under normal nutrition condition (control) and low-phosphate condition (LP). Higher expression of OsPIN2 was observed in rice plants under LP compared to the control. Meanwhile, the auxin levels of roots were increased under LP relative to control condition in wild-type (WT) plants. Compared to WT plants, two overexpression (OE) lines had higher auxin levels in the roots under control and LP. LP led to increased seminal roots (SRs) length and the root hairs (RHs) density, but decreased lateral roots (LRs) density in WT plants. However, overexpression of OsPIN2 caused a loss of sensitivity in the root response to P deficiency. The OE lines had a shorter SR length, lower LR density, and greater RH density than WT plants under control. However, the LR and RH densities in the OE lines were similar to those in WT plants under LP. Compared to WT plants, overexpression of OsPIN2 had a shorter root length through decreased root cell elongation under control and LP. Surprisingly, overexpression of OsPIN2 might increase auxin distribution in epidermis of root, resulting in greater RH formation but less LR development in OE plants than in WT plants in the control condition but levels similar of these under LP. These results suggest that higher OsPIN2 expression regulates rice root growth and development maybe by changing auxin distribution in roots under LP condition.
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Affiliation(s)
- Huwei Sun
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xiaoli Guo
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Fugui Xu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Daxia Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xuhong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manman Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feifei Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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Ma J, Pei W, Ma Q, Geng Y, Liu G, Liu J, Cui Y, Zhang X, Wu M, Li X, Li D, Zang X, Song J, Tang S, Zhang J, Yu S, Yu J. QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2663-2676. [PMID: 31236630 DOI: 10.1007/s00122-019-03380-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/14/2019] [Indexed: 05/24/2023]
Abstract
We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Wenfeng Pei
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830001, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yanhui Geng
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Yupeng Cui
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xia Zhang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Dan Li
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - XinShan Zang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Shurong Tang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
- College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.
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50
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Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nat Commun 2019; 10:3480. [PMID: 31375675 PMCID: PMC6677796 DOI: 10.1038/s41467-019-11471-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/05/2019] [Indexed: 01/08/2023] Open
Abstract
An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips along with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land.
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Affiliation(s)
- Yuzhou Zhang
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, China
| | - Xiaojuan Wang
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, China
- College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Xixi Zhang
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
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