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Rong M, Gao SX, Wen D, Xu YH, Wei JH. The LOB domain protein, a novel transcription factor with multiple functions: A review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108922. [PMID: 39038384 DOI: 10.1016/j.plaphy.2024.108922] [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: 05/05/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein, named for its LATERAL ORGAN BOUNDARIES (LOB) domain, is a member of a class of specific transcription factors commonly found in plants and is absent from all other groups of organisms. LBD TFs have been systematically identified in about 35 plant species and are involved in regulating various aspects of plant growth and development. However, research on the signaling network and regulatory functions of LBD TFs is insufficient, and only a few members have been studied. Moreover, a comprehensive review of these existing studies is lacking. In this review, the structure, regulatory mechanism and function of LBD TFs in recent years were reviewed in order to better understand the role of LBD TFs in plant growth and development, and to provide a new perspective for the follow-up study of LBD TFs.
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Affiliation(s)
- Mei Rong
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Shi-Xi Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Dong Wen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yan-Hong Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Jian-He Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, 570311, China.
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2
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Meng J, Li W, Qi F, Yang T, Li N, Wan J, Li X, Jiang Y, Wang C, Huang M, Zhang Y, Chen Y, Teotia S, Tang G, Zhang Z, Tang J. Knockdown of microRNA390 Enhances Maize Brace Root Growth. Int J Mol Sci 2024; 25:6791. [PMID: 38928499 PMCID: PMC11203754 DOI: 10.3390/ijms25126791] [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: 04/09/2024] [Revised: 05/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Brace root architecture is a critical determinant of maize's stalk anchorage and nutrition uptake, influencing root lodging resistance, stress tolerance, and plant growth. To identify the key microRNAs (miRNAs) in control of maize brace root growth, we performed small RNA sequencing using brace root samples at emergence and growth stages. We focused on the genetic modulation of brace root development in maize through manipulation of miR390 and its downstream regulated auxin response factors (ARFs). In the present study, miR167, miR166, miR172, and miR390 were identified to be involved in maize brace root growth in inbred line B73. Utilizing short tandem target mimic (STTM) technology, we further developed maize lines with reduced miR390 expression and analyzed their root architecture compared to wild-type controls. Our findings show that STTM390 maize lines exhibit enhanced brace root length and increased whorl numbers. Gene expression analyses revealed that the suppression of miR390 leads to upregulation of its downstream regulated ARF genes, specifically ZmARF11 and ZmARF26, which may significantly alter root architecture. Additionally, loss-of-function mutants for ZmARF11 and ZmARF26 were characterized to further confirm the role of these genes in brace root growth. These results demonstrate that miR390, ZmARF11, and ZmARF26 play crucial roles in regulating maize brace root growth; the involved complicated molecular mechanisms need to be further explored. This study provides a genetic basis for breeding maize varieties with improved lodging resistance and adaptability to diverse agricultural environments.
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Affiliation(s)
- Juan Meng
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Weiya Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Feiyan Qi
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Xiaoqi Li
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yajuan Jiang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Chenhui Wang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Meilian Huang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yuanyuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Yongqiang Chen
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida 201306, India;
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA;
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (J.M.); (W.L.); (F.Q.); (N.L.); (J.W.); (X.L.); (Y.J.); (C.W.); (M.H.); (Y.Z.); (Y.C.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Hao L, Li S, Dai J, Wang L, Yan Z, Shi Y, Zheng M. Characterization and expression profiles of the ZmLBD gene family in Zea mays. Mol Biol Rep 2024; 51:554. [PMID: 38642178 DOI: 10.1007/s11033-024-09483-9] [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: 01/11/2024] [Accepted: 03/26/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND The Lateral Organ Boundaries Domain (LBD) gene family is a family of plant-specific transcription factors (TFs) that are widely involved in processes such as lateral organ formation, stress response, and nutrient metabolism. However, the function of LBD genes in maize remains poorly understood. METHODS AND RESULTS In this study, a total of 49 ZmLBD genes were identified at the genome-wide level of maize, they were classified into nine branches based on phylogenetic relationships, and all of them were predicted to be nuclear localized. The 49 ZmLBD genes formed eight pairs of segmental duplicates, and members of the same branches' members had similar gene structure and conserved motif composition. The promoters of ZmLBD genes contain multiple types of cis-acting elements. In addition, by constructing the regulatory network of ZmLBD and other genes and miRNAs, 12 and 22 ZmLBDs were found to be involved in the gene regulatory network and miRNA regulatory network, respectively. The expression pattern analysis suggests that ZmLBD genes may be involved in different biological pathways, and drought stress induced the expressions of two inbred lines. CONCLUSIONS The findings enhance our comprehension of the potential roles of the ZmLBD gene family in maize growth and development, which is pivotal for genetic enhancement and breeding efforts pertaining to this significant crop.
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Affiliation(s)
- Lidong Hao
- Postdoctoral Work Station of Gansu Dunhuang Seed Group Co., Ltd, Jiuquan, 735000, Gansu, China
- Post-Doctoral Research Center of Biology, Lanzhou University, Lanzhou, 730000, Gansu, China
- Qionghai Tropical Crops Service Center, Qionghai, 571400, Hainan, China
| | - Shifeng Li
- Research Institute of Gansu Dunhuang Seed Industry Group Co., Ltd, Jiuquan, 735000, Gansu, China
| | - Jun Dai
- Qionghai Tropical Crops Service Center, Qionghai, 571400, Hainan, China.
| | - Li Wang
- Dongfang Agricultural Service Center, Dongfang, 572600, Hainan, China.
| | - Zhibin Yan
- Research Institute of Gansu Dunhuang Seed Industry Group Co., Ltd, Jiuquan, 735000, Gansu, China
| | - Yunqiang Shi
- Suihua Branch of Agricultural Science of Heilongjiang Province, Suihua, 152000, Heilongjiang, China
| | - Meiyu Zheng
- College of Agriculture and Hydraulic Engineering, Suihua University, Suihua, 152000, Heilongjiang, China
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5
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Li P, Zhang Z, Xiao G, Zhao Z, He K, Yang X, Pan Q, Mi G, Jia Z, Yan J, Chen F, Yuan L. Genomic basis determining root system architecture in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:102. [PMID: 38607439 DOI: 10.1007/s00122-024-04606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
KEY MESSAGE A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.
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Affiliation(s)
- Pengcheng Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhihai Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Gui Xiao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zheng Zhao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Kunhui He
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingchun Pan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanjun Chen
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Lixing Yuan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Hostetler AN, Morais de Sousa Tinoco S, Sparks EE. Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:553-562. [PMID: 37798135 DOI: 10.1093/jxb/erad390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [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: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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8
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Wang K, Zhang Z, Sha X, Yu P, Li Y, Zhang D, Liu X, He G, Li Y, Wang T, Guo J, Chen J, Li C. Identification of a new QTL underlying seminal root number in a maize-teosinte population. FRONTIERS IN PLANT SCIENCE 2023; 14:1132017. [PMID: 36824192 PMCID: PMC9941338 DOI: 10.3389/fpls.2023.1132017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Seminal roots play an important role in acquisition of water and nutrients by maize seedlings. Compared with its teosinte ancestor, maize underwent a change in seminal root number (SRN). Although several key genes controlling SRN have been cloned, identification and utilization of new genes from teosinte would be useful for improving maize root architecture. In this study, a maize-teosinte BC2F6 population containing 206 individuals genotyped by resequencing was used to conduct high-resolution quantitative trait locus (QTL) mapping of SRN. A new major QTL on chromosome 7 (qSRN7) was identified. Differentially expressed genes (DEGs) based on RNA-Seq were identified between two inbred lines with no SRN and multiple SRN at two periods of seminal roots primordia formation. A total of 116 DEGs detected in at least one period were identified within the qSRN7 interval. Three DEGs (Zm00001d021572, Zm00001d021579 and Zm00001d021861) associated with SRN were identified through regional association mapping. When compared with reported domestication-related selective sweeps, Zm00001d021572 was selected during maize domestication. Our findings provide important insights into the genetic basis of SRN and identify a promising candidate gene for further studies on SRN.
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Affiliation(s)
- Kailiang Wang
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Zhen Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiaoQian Sha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Yu
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanhua He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Guo
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Jiafa Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Singh Z, Singh H, Garg T, Mushahary KKK, Yadav SR. Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize. PLANT & CELL PHYSIOLOGY 2023; 63:1806-1813. [PMID: 35713294 DOI: 10.1093/pcp/pcac084] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/05/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.
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Affiliation(s)
- Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
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10
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Ren W, Zhao L, Liang J, Wang L, Chen L, Li P, Liu Z, Li X, Zhang Z, Li J, He K, Zhao Z, Ali F, Mi G, Yan J, Zhang F, Chen F, Yuan L, Pan Q. Genome-wide dissection of changes in maize root system architecture during modern breeding. NATURE PLANTS 2022; 8:1408-1422. [PMID: 36396706 DOI: 10.1038/s41477-022-01274-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 10/12/2022] [Indexed: 05/12/2023]
Abstract
Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.
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Affiliation(s)
- Wei Ren
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Longfei Zhao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jiaxing Liang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Lifeng Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Limei Chen
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Pengcheng Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhigang Liu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Xiaojie Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhihai Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jieping Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Kunhui He
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Zheng Zhao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Farhan Ali
- Cereal Crops Research Institute, Pirsabak, Nowshera, Pakistan
| | - Guohua Mi
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fusuo Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Fanjun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
| | - Lixing Yuan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
| | - Qingchun Pan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
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11
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Feng X, Xiong J, Zhang W, Guan H, Zheng D, Xiong H, Jia L, Hu Y, Zhou H, Wen Y, Zhang X, Wu F, Wang Q, Xu J, Lu Y. ZmLBD5, a class-II LBD gene, negatively regulates drought tolerance by impairing abscisic acid synthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1364-1376. [PMID: 36305873 DOI: 10.1111/tpj.16015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors. Class-I LBD genes have been widely demonstrated to play pivotal roles in organ development; however, knowledge on class-II genes remains limited. Here, we report that ZmLBD5, a class-II LBD gene, is involved in the regulation of maize (Zea mays) growth and the drought response by affecting gibberellin (GA) and abscisic acid (ABA) synthesis. ZmLBD5 is mainly involved in regulation of the TPS-KS-GA2ox gene module, which is comprised of key enzyme-encoding genes involved in GA and ABA biosynthesis. ABA insufficiency increases stomatal density and aperture in overexpression plants and causes a drought-sensitive phenotype by promoting water transpiration. Increased GA1 levels promotes seedling growth in overexpression plants. Accordingly, CRISPR/Cas9 knockout lbd5 seedlings are dwarf but drought-tolerant. Moreover, lbd5 has a higher grain yield under drought stress conditions and shows no penalty in well-watered conditions compared to the wild type. On the whole, ZmLBD5 is a negative regulator of maize drought tolerance, and it is a potentially useful target for drought resistance breeding.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Sichuan, 611130, China
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Jing Xiong
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Weixiao Zhang
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Huarui Guan
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Dan Zheng
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Hao Xiong
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Li Jia
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Yue Hu
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Hanmei Zhou
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Ying Wen
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Xuemei Zhang
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Fengkai Wu
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Qingjun Wang
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Jie Xu
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Sichuan, 611130, China
- Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
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12
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Urfan M, Hakla HR, Sharma S, Khajuria M, Satbhai SB, Vyas D, Bhougal S, Yadav NS, Pal S. Paclobutrazol improves surface water use efficiency by regulating allometric trait behavior in maize. CHEMOSPHERE 2022; 307:135958. [PMID: 35952796 DOI: 10.1016/j.chemosphere.2022.135958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Paclobutrazol (PBZ) role in drought management of maize is least understood. In maize, root traits are linked with surface water management. Over three years, early and terminal deficit irrigation (EDI and TDI) with or without PBZ were imposed on DKC-9144 and PG-2475 maize varieties. Several allometric parameters viz. stem height, stem diameter, leaf area and root traits along with physiological processes were measured. Implication of these parameters in the management of soil surface irrigation in terms of water use efficiency (WUE) was demonstrated in maize. Increased number of lateral roots and root number density in DKC-9144 provided more surface area for water absorption for better management of EDI. Root growth rates showed a similar pattern with root length, root surface areas, and root numbers in EDI. Elevated expressions of ZmRTCL, ZmRTCS and ZmARF34 in EDI and EDI plus PBZ were associated with seminal roots and root laterals initiation. Under TDI alone or in combination with PBZ, root lengths (BRL, CRL, SRL) and root surface areas varied in DKC-9144 and PG-2475 over control. Furthermore, correlation analysis showed that decrease in WUE under TDI was significantly associated with a reduction in stem thickness and leaf surface area. For WUE_N in TDI and PBZ plus TDI, structural equation modelling proposed, brace root surface area (BRSA_N) as a positive contributor, while a negative contributor was seminal root surface area (SRSA_N). Present study explained the importance of specific root traits and their association with other allometric parameters for improving WUE in DKC-9144 variety of maize and the crop in general.
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Affiliation(s)
- Mohammad Urfan
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Haroon Rashid Hakla
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Shubham Sharma
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Manu Khajuria
- Biodiversity and Applied Botany Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
| | - Santosh B Satbhai
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, SAS Nagar, Punjab, 140406, India.
| | - Dhiraj Vyas
- Biodiversity and Applied Botany Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
| | - Sunil Bhougal
- Department of Statistics, University of Jammu, Jammu, 180006, India.
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, 403587, Canada.
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
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13
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Qin T, Kazim A, Wang Y, Richard D, Yao P, Bi Z, Liu Y, Sun C, Bai J. Root-Related Genes in Crops and Their Application under Drought Stress Resistance—A Review. Int J Mol Sci 2022; 23:ijms231911477. [PMID: 36232779 PMCID: PMC9569943 DOI: 10.3390/ijms231911477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Crop growth and development are frequently affected by biotic and abiotic stresses. The adaptation of crops to stress is mostly achieved by regulating specific genes. The root system is the primary organ for nutrient and water uptake, and has an important role in drought stress response. The improvement of stress tolerance to increase crop yield potential and yield stability is a traditional goal of breeders in cultivar development using integrated breeding methods. An improved understanding of genes that control root development will enable the formulation of strategies to incorporate stress-tolerant genes into breeding for complex agronomic traits and provide opportunities for developing stress-tolerant germplasm. We screened the genes associated with root growth and development from diverse plants including Arabidopsis, rice, maize, pepper and tomato. This paper provides a theoretical basis for the application of root-related genes in molecular breeding to achieve crop drought tolerance by the improvement of root architecture.
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Affiliation(s)
- Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ali Kazim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Yihao Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Dormatey Richard
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (C.S.); (J.B.); Tel.: +86-189-9319-8496 (C.S.); +86-181-0942-4020 (J.B.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (C.S.); (J.B.); Tel.: +86-189-9319-8496 (C.S.); +86-181-0942-4020 (J.B.)
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14
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Gonin M, Jeong K, Coudert Y, Lavarenne J, Hoang GT, Bes M, To HTM, Thiaw MN, Do TV, Moukouanga D, Guyomarc'h S, Bellande K, Brossier J, Parizot B, Nguyen HT, Beeckman T, Bergougnoux V, Rouster J, Sallaud C, Laplaze L, Champion A, Gantet P. CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:546-566. [PMID: 35596715 PMCID: PMC9542200 DOI: 10.1111/tpj.15838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
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Affiliation(s)
- Mathieu Gonin
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kwanho Jeong
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyon69007France
| | - Jeremy Lavarenne
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Martine Bes
- CIRAD, UMR AGAPF‐34398MontpellierFrance
- UMR AGAPUniversité de Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, LMIRICE2Vietnam Academy of Science and Technology11300HanoiVietnam
| | - Marie‐Rose Ndella Thiaw
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Toan Van Do
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Daniel Moukouanga
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Soazig Guyomarc'h
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kevin Bellande
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Jean‐Rémy Brossier
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Boris Parizot
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Hieu Trang Nguyen
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jacques Rouster
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Christophe Sallaud
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Laurent Laplaze
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Antony Champion
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Pascal Gantet
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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15
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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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16
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Omary M, Gil-Yarom N, Yahav C, Steiner E, Hendelman A, Efroni I. A conserved superlocus regulates above- and belowground root initiation. Science 2022; 375:eabf4368. [PMID: 35239373 DOI: 10.1101/2020.11.11.377937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evyatar Steiner
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Idan Efroni
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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17
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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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18
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McReynolds MR, Dash L, Montes C, Draves MA, Lang MG, Walley JW, Kelley DR. Temporal and spatial auxin responsive networks in maize primary roots. QUANTITATIVE PLANT BIOLOGY 2022; 3:e21. [PMID: 37077976 PMCID: PMC10095944 DOI: 10.1017/qpb.2022.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 05/03/2023]
Abstract
Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin-regulated networks underlying maize root development, we have characterized auxin-responsive transcription across two time points (30 and 120 min) and four regions of the primary root: the meristematic zone, elongation zone, cortex and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin-regulated genes are region unique and are predominantly observed in differentiated tissues compared with the root meristem. Auxin gene regulatory networks were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin-Response Factor subnetworks were generated to identify target genes that exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.
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Affiliation(s)
- Maxwell R. McReynolds
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Linkan Dash
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Melissa A. Draves
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Michelle G. Lang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
- Corteva Agriscience, Johnston, Iowa50131, USA
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
- Authors for correspondence: D. R. Kelley and J. W. Walley, E-mail: ;
| | - Dior R. Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
- Authors for correspondence: D. R. Kelley and J. W. Walley, E-mail: ;
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19
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Teng R, Wu Z, Xu S, Hou H, Zhang D, Chen F, Teng N. A Novel Lateral Organ Boundary-domain Factor CmLBD2 Positively Regulates Pollen Development by Activating CmACOS5 in Chrysanthemum morifolium. PLANT & CELL PHYSIOLOGY 2021; 62:1687-1701. [PMID: 34370862 DOI: 10.1093/pcp/pcab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Male sterility, as a common reproductive characteristic in plants, plays an important role in breeding, in which pollen abortion is a key factor leading to male sterility. Here, based on a low expression level gene CmACOS5 in transcriptome of pollen abortive chrysanthemum, a new transcription factor CmLBD2 of the Lateral Organ Boundaries Domain family, which could bind the promoter of CmACOS5 by yeast one-hybrid library was screened. This study revealed the origin and expression pattern of CmLBD2 in chrysanthemum and verified the functions of two genes in pollen development by transgenic means. Inhibiting the expression of CmACOS5 or CmLBD2 can lead to a large reduction in pollen and even abortion in chrysanthemum. Using yeast one-/two-hybrid, electrophoretic mobility shift assays, and luciferase reporter assays, it was verified that CmLBD2 directly binds to the promoter of CmACOS5. These results suggest that LBD2 is a novel, key transcription factor regulating pollen development. This result will provide a new research background for enriching the function of LBD family proteins and also lay a new foundation for the breeding of male sterile lines and the mechanism of pollen development.
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Affiliation(s)
- Renda Teng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Sujuan Xu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Huizhong Hou
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Dehua Zhang
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
| | - Fadi Chen
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Nianjun Teng
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Graduate Workstation of Nanjing Agriculture University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing 210043, China
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20
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Wang Y, Sun H, Wang H, Yang X, Xu Y, Yang Z, Xu C, Li P. Integrating transcriptome, co-expression and QTL-seq analysis reveals that primary root growth in maize is regulated via flavonoid biosynthesis and auxin signal transduction. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4773-4795. [PMID: 33909071 DOI: 10.1093/jxb/erab177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 04/24/2021] [Indexed: 05/28/2023]
Abstract
The primary root is critical for early seedling growth and survival. To understand the molecular mechanisms governing primary root development, we performed a dynamic transcriptome analysis of two maize (Zea mays) inbred lines with contrasting primary root length at nine time points over a 12-day period. A total of 18 702 genes were differentially expressed between two lines or different time points. Gene enrichment, phytohormone content determination, and metabolomics analysis showed that auxin biosynthesis and signal transduction, as well as the phenylpropanoid and flavonoid biosynthesis pathways, were associated with root development. Co-expression network analysis revealed that eight modules were associated with lines/stages, as well as primary or lateral root length. In root-related modules, flavonoid metabolism accompanied by auxin biosynthesis and signal transduction constituted a complex gene regulatory network during primary root development. Two candidate genes (rootless concerning crown and seminal roots, rtcs and Zm00001d012781) involved in auxin signaling and flavonoid biosynthesis were identified by co-expression network analysis, QTL-seq and functional annotation. These results increase our understanding of the regulatory network controlling the development of primary and lateral root length, and provide a valuable genetic resource for improvement of root performance in maize.
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Affiliation(s)
- Yunyun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Hui Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xiaoyi Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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21
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Ober ES, Alahmad S, Cockram J, Forestan C, Hickey LT, Kant J, Maccaferri M, Marr E, Milner M, Pinto F, Rambla C, Reynolds M, Salvi S, Sciara G, Snowdon RJ, Thomelin P, Tuberosa R, Uauy C, Voss-Fels KP, Wallington E, Watt M. Wheat root systems as a breeding target for climate resilience. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1645-1662. [PMID: 33900415 PMCID: PMC8206059 DOI: 10.1007/s00122-021-03819-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
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Affiliation(s)
- Eric S Ober
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Cristian Forestan
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Josefine Kant
- Forschungszentrum Jülich, IBG-2, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Emily Marr
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Charlotte Rambla
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Kai P Voss-Fels
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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22
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Hostetler AN, Khangura RS, Dilkes BP, Sparks EE. Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101985. [PMID: 33418403 DOI: 10.1016/j.pbi.2020.101985] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 05/28/2023]
Abstract
Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, United States
| | - Rajdeep S Khangura
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, United States.
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23
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Zheng C, Shen F, Wang Y, Wu T, Xu X, Zhang X, Han Z. Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics 2020; 21:852. [PMID: 33261554 PMCID: PMC7709433 DOI: 10.1186/s12864-020-07257-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Results Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°. Conclusions Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.
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Affiliation(s)
- Caixia Zheng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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24
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Barros VA, Chandnani R, de Sousa SM, Maciel LS, Tokizawa M, Guimaraes CT, Magalhaes JV, Kochian LV. Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils. FRONTIERS IN PLANT SCIENCE 2020; 11:565339. [PMID: 33281841 PMCID: PMC7688899 DOI: 10.3389/fpls.2020.565339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 06/01/2023]
Abstract
Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.
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Affiliation(s)
- Vanessa A. Barros
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Laiane S. Maciel
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mutsutomo Tokizawa
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Jurandir V. Magalhaes
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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25
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Mhimdi M, Pérez-Pérez JM. Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics? FRONTIERS IN PLANT SCIENCE 2020; 11:582020. [PMID: 33123185 PMCID: PMC7573222 DOI: 10.3389/fpls.2020.582020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/18/2020] [Indexed: 05/23/2023]
Abstract
Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.
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26
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Ma L, Qing C, Frei U, Shen Y, Lübberstedt T. Association mapping for root system architecture traits under two nitrogen conditions in germplasm enhancement of maize doubled haploid lines. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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27
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Janiak A, Kwasniewski M, Sowa M, Kuczyńska A, Mikołajczak K, Ogrodowicz P, Szarejko I. Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms. Int J Mol Sci 2019; 20:ijms20246139. [PMID: 31817496 PMCID: PMC6940957 DOI: 10.3390/ijms20246139] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Root systems play a pivotal role in coupling with drought stress, which is accompanied with a substantial transcriptome rebuilding in the root tissues. Here, we present the results of global gene expression profiling of roots of two barley genotypes with contrasting abilities to cope with drought that were subjected to a mild level of the stress. We concentrate our analysis on gene expression regulation processes, which allowed the identification of 88 genes from 39 families involved in transcriptional regulation in roots upon mild drought. They include 13 genes encoding transcription factors (TFs) from AP2 family represented by ERFs, DREB, or B3 domain-containing TFs, eight WRKYs, six NACs, five of the HD-domain, MYB or MYB-related, bHLH and bZIP TFs. Also, the representatives of C3H, CPP, GRAS, LOB-domain, TCP, Tiffy, Tubby, and NF-Ys TFs, among others were found to be regulated by the mild drought in barley roots. We found that drought tolerance is accompanied with a lower number of gene expression changes than the amount observed in a susceptible genotype. The better drought acclimation may be related to the activation of transcription factors involved in the maintenance of primary root growth and in the epigenetic control of chromatin and DNA methylation. In addition, our analysis pointed to fives TFs from ERF, LOB, NAC, WRKY and bHLH families that may be important in the mild but not the severe drought response of barley roots.
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Affiliation(s)
- Agnieszka Janiak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
- Correspondence: ; Tel.: +0048-32-2009-457
| | - Miroslaw Kwasniewski
- Center of Bioinformatics and Data Analysis, Medical University in Białystok, 15-269 Białystok, Poland
| | - Marta Sowa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | | | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
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Shorinola O, Kaye R, Golan G, Peleg Z, Kepinski S, Uauy C. Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform. G3 (BETHESDA, MD.) 2019; 9:2799-2809. [PMID: 31352407 PMCID: PMC6723138 DOI: 10.1534/g3.119.400537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022]
Abstract
Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.
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Affiliation(s)
- Oluwaseyi Shorinola
- Bioscience Eastern and Central Africa - International Livestock Research Institute, Nairobi, PO Box 30709, Kenya
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan Kaye
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Li P, Pan T, Wang H, Wei J, Chen M, Hu X, Zhao Y, Yang X, Yin S, Xu Y, Fang H, Liu J, Xu C, Yang Z. Natural variation of ZmHKT1 affects root morphology in maize at the seedling stage. PLANTA 2019; 249:879-889. [PMID: 30460404 DOI: 10.1007/s00425-018-3043-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/12/2018] [Indexed: 05/25/2023]
Abstract
Eight variants in ZmHKT1 promoter were significantly associated with root diameter, four haplotypes based on these significant variants were found, and Hap2 has the largest root diameter. Roots play an important role in uptake of water, nutrients and plant anchorage. Identification of gene and corresponding SNPs associated with root traits would enable develop maize lines with better root traits that might help to improve capacity for absorbing nutrients and water acquisition. The genomic sequences of a salt tolerance gene ZmHKT1 was resequenced in 349 maize inbred lines, and the association between nucleotide polymorphisms and seedling root traits was detected. A total of 269 variants in ZmHKT1 were identified, including 226 single nucleotide polymorphisms and 43 insertions and deletions. The gene displayed high level of nucleotide diversity, especially in non-genic regions. A total of 19 variations in untranslated region of ZmHKT1 were found to be associated with six seedling traits. Eight variants in promoter region were significantly associated with average root diameter (ARD), four haplotypes were found based on these significant variants, and Hap2 has the largest ARD. Two SNPs in high-linkage disequilibrium (SNP-415 and SNP 2169) with pleiotropic effects were significantly associated with plant height, root surface area, root volume, and shoot dry weight. This result revealed that ZmHKT1 was an important contributor to the phenotypic variations of seedling root traits in maize, these significant variants could use to develop functional markers to improve root traits.
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Affiliation(s)
- Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Ting Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jie Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Minjun Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaohong Hu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyi Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Shuangyi Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Huimin Fang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
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Li J, Chen F, Li Y, Li P, Wang Y, Mi G, Yuan L. ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development. FRONTIERS IN PLANT SCIENCE 2019; 10:820. [PMID: 31333689 PMCID: PMC6621205 DOI: 10.3389/fpls.2019.00820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/06/2019] [Indexed: 05/12/2023]
Abstract
In maize, shoot-borne roots dominate the whole root system and play essential roles in water and nutrient acquisition and lodging tolerance. Shoot-borne roots initiate at shoot nodes, including crown roots from the belowground nodes and brace roots from aboveground nodes. In contrast to crown roots, few genes for brace roots development have been identified. Here, we characterized a maize AP2/ERF transcription factor, ZmRAP2.7, to be involved in brace roots development. ZmRAP2.7 expressed in all types of roots, and the encoded protein localized in the nucleus with transcriptional activation activity. A maize transposon insert mutant RAP2.7-Mu defective in ZmRAP2.7 expression revealed a decreased number of brace roots but not crown roots. Maize Corngrass1 mutant, which showed an elevated expression of ZmRAP2.7, however, revealed an increased number of brace roots. The ZmRAP2.7-based association analysis in a maize panel further identified a SNP marker at the fifth exon of gene to be associated with number of brace roots. These results uncovered a function of ZmRAP2.7 in brace roots development and provided the valuable gene and allele for genetic improvement of maize root systems.
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Affiliation(s)
- Jieping Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Plant Science, School of Life Sciences, Henan University, Kaifeng, China
| | - Fanjun Chen
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yanqing Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Pengcheng Li
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics, Co-Innovation Center for Modern Production Technology of Grain Crops, MOE, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yuanqing Wang
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, MOE, Department of Plant Nutrition, College Resources and Environmental Sciences, China Agricultural University, Beijing, China
- *Correspondence: Lixing Yuan,
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Shi J, Drummond BJ, Habben JE, Brugire N, Weers BP, Hakimi SM, Lafitte HR, Schussler JR, Mo H, Beatty M, Zastrow-Hayes G, O'Neill D. Ectopic expression of ARGOS8 reveals a role for ethylene in root-lodging resistance in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:378-390. [PMID: 30326542 PMCID: PMC7379592 DOI: 10.1111/tpj.14131] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 05/22/2023]
Abstract
Ethylene plays a critical role in many diverse processes in plant development. Recent studies have demonstrated that overexpression of the maize ARGOS8 gene reduces the plant's response to ethylene by decreasing ethylene signaling and enhances grain yield in transgenic maize plants. The objective of this study was to determine the effects of ethylene on the development of nodal roots, which are primarily responsible for root-lodging resistance in maize. Exogenous application of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) was found to promote the emergence of nodal roots. Transcriptome analysis of nodal tissues revealed that the expression of genes involved in metabolic processes and cell wall biogenesis was upregulated in response to ACC treatment, supporting the notion that ethylene is a positive regulator for the outgrowth of young root primordia. In BSV::ARGOS8 transgenic plants with reduced ethylene sensitivity due to constitutive overexpression of ARGOS8, nodal root emergence was delayed and the promotional effect of ACC on nodal root emergence decreased. Field tests showed that the BSV::ARGOS8 plants had higher root lodging relative to non-transgenic controls. When ARGOS8 expression was controlled by the developmentally regulated promoter FTM1, which conferred ARGOS8 overexpression in adult plants but not in the nodal roots and nodes in juvenile plants, the FTM1::ARGOS8 plants had no significant difference in root lodging compared with the wild type but produced a higher grain yield. These results suggest that ethylene has a role in promoting nodal root emergence and that a delay in nodal root development has a negative effect on root-lodging resistance in maize.
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Affiliation(s)
- Jinrui Shi
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Bruce J Drummond
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Jeffrey E Habben
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Norbert Brugire
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Ben P Weers
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Salim M Hakimi
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - H Renee Lafitte
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Jeffrey R Schussler
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Hua Mo
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Mary Beatty
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Gina Zastrow-Hayes
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Dennis O'Neill
- Corteva Agriscience, Agriculture Division of DowDuPont, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
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32
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Chen WF, Wei XB, Rety S, Huang LY, Liu NN, Dou SX, Xi XG. Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat. J Biol Chem 2018; 294:142-156. [PMID: 30425099 DOI: 10.1074/jbc.ra118.003956] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/10/2018] [Indexed: 01/13/2023] Open
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.
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Affiliation(s)
- Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Bin Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Stephane Rety
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
| | - Ling-Yun Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61 Avenue du Président Wilson, F-94235 Cachan, France.
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33
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Bray AL, Topp CN. The Quantitative Genetic Control of Root Architecture in Maize. PLANT & CELL PHYSIOLOGY 2018; 59:1919-1930. [PMID: 30020530 PMCID: PMC6178961 DOI: 10.1093/pcp/pcy141] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 05/07/2023]
Abstract
Roots remain an underexplored frontier in plant genetics despite their well-known influence on plant development, agricultural performance and competition in the wild. Visualizing and measuring root structures and their growth is vastly more difficult than characterizing aboveground parts of the plant and is often simply avoided. The majority of research on maize root systems has focused on their anatomy, physiology, development and soil interaction, but much less is known about the genetics that control quantitative traits. In maize, seven root development genes have been cloned using mutagenesis, but no genes underlying the many root-related quantitative trait loci (QTLs) have been identified. In this review, we discuss whether the maize mutants known to control root development may also influence quantitative aspects of root architecture, including the extent to which they overlap with the most recent maize root trait QTLs. We highlight specific challenges and anticipate the impacts that emerging technologies, especially computational approaches, may have toward the identification of genes controlling root quantitative traits.
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Affiliation(s)
- Adam L Bray
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christopher N Topp
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Corresponding author: E-mail, ; Fax, 314 587 1501
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Liu W, Yu J, Ge Y, Qin P, Xu L. Pivotal role of LBD16 in root and root-like organ initiation. Cell Mol Life Sci 2018; 75:3329-3338. [PMID: 29943076 PMCID: PMC11105430 DOI: 10.1007/s00018-018-2861-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/17/2018] [Accepted: 06/21/2018] [Indexed: 12/27/2022]
Abstract
In the post-embryonic stage of Arabidopsis thaliana, roots can be initiated from the vascular region of the existing roots or non-root organs; they are designated as lateral roots (LRs) and adventitious roots (ARs), respectively. Some root-like organs can also be initiated from the vasculature. In tissue culture, auxin-induced callus, which is a group of pluripotent root-primordium-like cells, is formed via the rooting pathway. The formation of feeding structures from the vasculature induced by root-knot nematodes also borrows the rooting pathway. In this review, we summarize and discuss recent progress on the role of LATERAL ORGAN BOUNDARIES DOMAIN16 (LBD16; also known as ASYMMETRIC LEAVES2-LIKE18, ASL18), a member of the LBD/ASL gene family encoding plant-specific transcription factors, in roots and root-like organ initiation. Different root and root-like organ initiation processes have distinct priming mechanisms to specify founder cells. All these priming mechanisms converge to activate LBD16 expression in the primed founder cells. The activation of LBD16 expression leads to organ initiation via promotion of cell division and establishment of root-primordium identity. Therefore, LBD16 might play a common and pivotal role in root and root-like organ initiation.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jie Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yachao Ge
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Qin
- Department of Instrument Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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Hochholdinger F, Marcon C, Baldauf JA, Yu P, Frey FP. Proteomics of Maize Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:143. [PMID: 29556242 PMCID: PMC5844967 DOI: 10.3389/fpls.2018.00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.
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36
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Hochholdinger F, Yu P, Marcon C. Genetic Control of Root System Development in Maize. TRENDS IN PLANT SCIENCE 2018; 23:79-88. [PMID: 29170008 DOI: 10.1016/j.tplants.2017.10.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/21/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
The maize root system comprises structurally and functionally different root types. Mutant analyses have revealed that root-type-specific genetic regulators intrinsically determine the maize root system architecture. Molecular cloning of these genes has demonstrated that key elements of auxin signal transduction, such as LOB domain (LBD) and Aux/IAA proteins, are instrumental for seminal, shoot-borne, and lateral root initiation. Moreover, genetic analyses have demonstrated that genes related to exocytotic vesicle docking, cell wall loosening, and cellulose synthesis and organization control root hair elongation. The identification of upstream regulators, protein interaction partners, and downstream targets of these genes together with cell-type-specific transcriptome analyses have provided novel insights into the regulatory networks controlling root development and architecture in maize.
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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.
| | - Peng Yu
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Caroline Marcon
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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37
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Xu C, Fu X, Liu R, Guo L, Ran L, Li C, Tian Q, Jiao B, Wang B, Luo K. PtoMYB170 positively regulates lignin deposition during wood formation in poplar and confers drought tolerance in transgenic Arabidopsis. TREE PHYSIOLOGY 2017; 37:1713-1726. [PMID: 28985414 DOI: 10.1093/treephys/tpx093] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/22/2017] [Indexed: 05/20/2023]
Abstract
Wood formation is a complex developmental process under multi-level transcriptional control executed by a large set of transcription factors. However, only limited members have been characterized to be key regulators of lignin biosynthesis in poplar. Here we report the conserved and unique functions of PtoMYB170, a transcription factor identified from Populus tomentosa (Chinese white poplar), in lignin deposition and drought tolerance in comparison with its duplicate paralog PtoMYB216. PtoMYB170 is preferentially expressed in young leaves and xylem tissues. Overexpression of PtoMYB170 in transgenic poplar plants resulted in stronger lignification and more thickened secondary wall in xylem compared with wild-type plants, whereas the CRISPR/Cas9-generated mutation of PtoMYB170 weakened lignin deposition, thereby leading to a more flexible and collapsed xylem phenotype. Transient expression experiments demonstrated that PtoMYB170 specifically activated the expression of lignin biosynthetic genes, consistent with the function of PtoMYB216. However, GUS staining assays revealed that PtoMYB170 was specifically expressed in guard cells of transgenic Arabidopsis while PtoMYB216 was not. Heterologous expression of PtoMYB170 in Arabidopsis enhanced stomatal closure in the dark and resulted in drought tolerance of the transgenic plants through reduced water loss, indicating a diversified role from PtoMYB216. These results revealed the PtoMYB170-dependent positive transcriptional regulation on lignin deposition in poplar and its coordinated function in enhancing drought tolerance by promoting dark-induced stomatal closure.
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Affiliation(s)
- Changzheng Xu
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Xiaokang Fu
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Rui Liu
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Li Guo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Lingyu Ran
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Chaofeng Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008 Xining, China
| | - Qiaoyan Tian
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Bo Jiao
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Bangjun Wang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
| | - Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, 400715 Chongqing, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008 Xining, China
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Jeon E, Young Kang N, Cho C, Joon Seo P, Chung Suh M, Kim J. LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:2190-2201. [PMID: 29040694 DOI: 10.1093/pcp/pcx153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
The LATERAL ORGAN BOUNDARIES (LOB) DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) gene family members play key roles in diverse aspects of plant development. Previous studies have shown that LBD16, 18, 29 and 33 are critical for integrating the plant hormone auxin to control lateral root development in Arabidopsis thaliana. In the present study, we show that LBD14 is expressed exclusively in the root where it promotes lateral root (LR) emergence. Repression of LBD14 expression by ABA correlates with the inhibitory effects of ABA on LR emergence. Transient gene expression assays with Arabidopsis protoplasts demonstrated that LBD14 is a nuclear-localized transcriptional activator. The knock-down of LBD14 expression by RNA interference (RNAi) resulted in reduced LR formation by delaying both LR primordium development and LR emergence, whereas overexpression of LBD14 in Arabidopsis enhances LR formation. We show that ABA (but not other plant hormones such as auxin, brassinosteroids and cytokinin) specifically down-regulated β-glucuronidase (GUS) expression under the control of the LBD14 promoter in transgenic Arabidopsis during LR development from initiation to emergence and endogenous LBD14 transcript levels in the root. Moreover, RNAi of LBD14 enhanced the LR suppression in response to ABA, whereas LBD14 overexpression did not alter the ABA-mediated suppression of LR formation. Taken together, these results suggest that LBD14 promoting LR formation is one of the critical factors regulated by ABA to inhibit LR growth, contributing to the regulation of the Arabidopsis root system architecture in response to ABA.
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Affiliation(s)
- Eunkyeong Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Na Young Kang
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Korea
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Wang J, Pei L, Jin Z, Zhang K, Zhang J. Overexpression of the protein phosphatase 2A regulatory subunit a gene ZmPP2AA1 improves low phosphate tolerance by remodeling the root system architecture of maize. PLoS One 2017; 12:e0176538. [PMID: 28448624 PMCID: PMC5407761 DOI: 10.1371/journal.pone.0176538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/12/2017] [Indexed: 11/21/2022] Open
Abstract
Phosphate (Pi) limitation is a constraint for plant growth and development in many natural and agricultural ecosystems. In this study, a gene encoding Zea mays L. protein phosphatase 2A regulatory subunit A, designated ZmPP2AA1, was induced in roots by low Pi availability. The function of the ZmPP2AA1 gene in maize was analyzed using overexpression and RNA interference. ZmPP2AA1 modulated root gravitropism, negatively regulated primary root (PR) growth, and stimulated the development of lateral roots (LRs). A detailed characterization of the root system architecture (RSA) in response to different Pi concentrations with or without indole-3-acetic acid and 1-N-naphthylphthalamic acid revealed that auxin was involved in the RSA response to low Pi availability. Overexpression of ZmPP2AA1 enhanced tolerance to Pi starvation in transgenic maize in hydroponic and soil pot experiments. An increased dry weight (DW), root-to-shoot ratio, and total P content and concentration, along with a delayed and reduced accumulation of anthocyanin in overexpressing transgenic maize plants coincided with their highly branched root system and increased Pi uptake capability under low Pi conditions. Inflorescence development of the ZmPP2AA1 overexpressing line was less affected by low Pi stress, resulting in higher grain yield per plant under Pi deprivation. These data reveal the biological function of ZmPP2AA1, provide insights into a linkage between auxin and low Pi responses, and drive new strategies for the efficient utilization of Pi by maize.
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Affiliation(s)
- Jiemin Wang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Laming Pei
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
- Department of Biotechnology, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhe Jin
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Kewei Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Juren Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
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Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F. Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:403-414. [PMID: 28204533 PMCID: PMC5444478 DOI: 10.1093/jxb/erw422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise comparisons of rtcs and wild-type embryo transcriptomes identified 131 transcription factors among 3526 differentially expressed genes [false discovery rate (FDR) <5% and |log2Fc|≥1]. Among those, functional annotation highlighted genes involved in cell cycle control and phytohormone action, particularly auxin signaling. Moreover, in silico promoter analyses identified putative RTCS target genes associated with transcription factor action and hormone metabolism and signaling. Significantly, non-syntenic genes that emerged after the separation of maize and sorghum were over-represented among genes displaying RTCS-dependent expression during seminal root primordia formation. This might suggest that these non-syntenic genes came under the transcriptional control of the syntenic gene rtcs during seminal root evolution. Taken together, this study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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Genome-Wide Identification, Evolutionary Analysis and Expression Profiles of LATERAL ORGAN BOUNDARIES DOMAIN Gene Family in Lotus japonicus and Medicago truncatula. PLoS One 2016; 11:e0161901. [PMID: 27560982 PMCID: PMC4999203 DOI: 10.1371/journal.pone.0161901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022] Open
Abstract
The LATERAL ORGANBOUNDARIESDOMAIN (LBD) gene family has been well-studied in Arabidopsis and play crucial roles in the diverse growth and development processes including establishment and maintenance of boundary of developmental lateral organs. In this study we identified and characterized 38 LBD genes in Lotus japonicus (LjLBD) and 57 LBD genes in Medicago truncatula (MtLBD), both of which are model legume plants that have some specific development features absent in Arabidopsis. The phylogenetic relationships, their locations in the genome, genes structure and conserved motifs were examined. The results revealed that all LjLBD and MtLBD genes could be distinctly divided into two classes: Class I and II. The evolutionary analysis showed that Type I functional divergence with some significantly site-specific shifts may be the main force for the divergence between Class I and Class II. In addition, the expression patterns of LjLBD genes uncovered the diverse functions in plant development. Interestingly, we found that two LjLBD proteins that were highly expressed during compound leaf and pulvinus development, can interact via yeast two-hybrid assays. Taken together, our findings provide an evolutionary and genetic foundation in further understanding the molecular basis of LBD gene family in general, specifically in L. japonicus and M. truncatula.
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Hochholdinger F. Untapping root system architecture for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4431-3. [PMID: 27493225 PMCID: PMC4973748 DOI: 10.1093/jxb/erw262] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Frank Hochholdinger
- Institute for Crop Science and Resource Conservation (INRES), Faculty of Agriculture, University of Bonn, 53177 Bonn, Germany
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Li B, Liu D, Li Q, Mao X, Li A, Wang J, Chang X, Jing R. Overexpression of wheat gene TaMOR improves root system architecture and grain yield in Oryza sativa. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4155-67. [PMID: 27229732 PMCID: PMC5301925 DOI: 10.1093/jxb/erw193] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Improved root architecture is an effective strategy to increase crop yield. We demonstrate that overexpression of transcription factor gene MORE ROOT (TaMOR) from wheat (Triticum aestivum L.) results in more roots and higher grain yield in rice (Oryza sativa). TaMOR, encoding a plant-specific transcription factor belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) protein family, is highly conserved in wheat and its wild relatives. In this study, tissue expression patterns indicated that TaMOR mainly localizes to root initiation sites. The consistent gene expression pattern suggests that TaMOR is involved in root initiation. Exogenous auxin treatment induced TaMOR expression without de novo protein biosynthesis. Both in vivo and in vitro experiments demonstrated that TaMOR interacts with TaMOR-related protein TaMRRP, which contains a four-tandem-pentatricopeptide repeat motif. Overexpression of TaMOR led to more lateral roots in Arabidopsis thaliana, and TaMOR-overexpressing rice plants had more crown roots, a longer main panicle, a higher number of primary branches on the main panicle, a higher grain number per plant, and higher yield per plant than the plants of wild type. In general, TaMOR-D-overexpressing lines had larger root systems in Arabidopsis and rice, and produce a higher grain yield per plant. TaMOR therefore offers an opportunity to improve root architecture and increase yield in crop plants.
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Affiliation(s)
- Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Zhang W, Zhao G, Gao L, Kong X, Guo Z, Wu B, Jia J. Functional Studies of Heading Date-Related Gene TaPRR73, a Paralog of Ppd1 in Common Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:772. [PMID: 27313595 PMCID: PMC4887500 DOI: 10.3389/fpls.2016.00772] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/17/2016] [Indexed: 05/29/2023]
Abstract
Photoperiod response-related genes play a crucial role in duration of the plant growth. In this study, we focused on TaPRR73, a paralog of "Green Revolution" gene Ppd1 (TaPRR37). We found that overexpression of the truncated TaPRR73 form lacking part of the N-terminal PR domain in transgenic rice promoted heading under long day conditions. Association analysis in common wheat verified that TaPRR73 was an important agronomic photoperiod response gene that significantly affected heading date and plant height; expression analysis proved that specific alleles of TaPRR73-A1 had highly expressed levels in earlier heading lines; the distribution of haplotypes indicated that one of these alleles had been selected in breeding programs. Our results demonstrated that TaPRR73 contributed to regulation of heading date in wheat and could be useful in wheat breeding and in broadening adaptation of the crop to new regions.
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Affiliation(s)
- Wenping Zhang
- Triticease Research Institute, Sichuan Agricultural UniversityChengdu, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Guangyao Zhao
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Lifeng Gao
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xiuying Kong
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhiai Guo
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Bihua Wu
- Triticease Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Jizeng Jia
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop science, Chinese Academy of Agricultural SciencesBeijing, China
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Li P, Zhuang Z, Cai H, Cheng S, Soomro AA, Liu Z, Gu R, Mi G, Yuan L, Chen F. Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:242-53. [PMID: 26269087 DOI: 10.1111/jipb.12384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/10/2015] [Indexed: 05/26/2023]
Abstract
Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.
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Affiliation(s)
- Pengcheng Li
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhongjuan Zhuang
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Leading Bio-agricultural Co., Ltd., Qinhuangdao, 066000, China
| | - Hongguang Cai
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Shuai Cheng
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ayaz Ali Soomro
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhigang Liu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Riliang Gu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Fanjun Chen
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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Salvi S, Giuliani S, Ricciolini C, Carraro N, Maccaferri M, Presterl T, Ouzunova M, Tuberosa R. Two major quantitative trait loci controlling the number of seminal roots in maize co-map with the root developmental genes rtcs and rum1. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1149-59. [PMID: 26880748 PMCID: PMC4753855 DOI: 10.1093/jxb/erw011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genetic dissection of root architecture and functions allows for a more effective and informed design of novel root ideotypes and paves the way to evaluate their effects on crop resilience to a number of abiotic stresses. In maize, limited attention has been devoted to the genetic analysis of root architecture diversity at the early stage. The difference in embryonic (including seminal and primary) root architecture between the maize reference line B73 (which mostly develops three seminal roots) and the landrace Gaspé Flint (with virtually no seminal roots) was genetically dissected using a collection of introgression lines grown in paper rolls and pots. Quantitative trait locus (QTL) analysis identified three QTLs controlling seminal root number (SRN) on chromosome bins 1.02, 3.07, and 8.04-8.05, which collectively explained 66% of the phenotypic variation. In all three cases, Gaspé Flint contributed the allele for lower SRN. Primary root dry weight was negatively correlated with SRN (r= -0.52), and QTLs for primary root size co-mapped with SRN QTLs, suggesting a pleiotropic effect of SRN QTLs on the primary root, most probably caused by competition for seed resources. Interestingly, two out of three SRN QTLs co-mapped with the only two known maize genes (rtcs and rum1) affecting the number of seminal roots. The strong additive effect of the three QTLs and the development of near isogenic lines for each QTL in the elite B73 background provide unique opportunities to characterize functionally the genes involved in root development and to evaluate how root architecture affects seedling establishment, early development, and eventually yield in maize.
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Affiliation(s)
- Silvio Salvi
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Silvia Giuliani
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | - Nicola Carraro
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Marco Maccaferri
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Roberto Tuberosa
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
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Xu C, Luo F, Hochholdinger F. LOB Domain Proteins: Beyond Lateral Organ Boundaries. TRENDS IN PLANT SCIENCE 2016; 21:159-167. [PMID: 26616195 DOI: 10.1016/j.tplants.2015.10.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/28/2015] [Accepted: 10/15/2015] [Indexed: 05/07/2023]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins defined by a conserved LATERAL ORGAN BOUNDARIES (LOB) domain are key regulators of plant organ development. Recent studies have expanded their functional diversity beyond the definition of lateral organ boundaries to pollen development, plant regeneration, photomorphogenesis, pathogen response, and specific developmental functions in non-model plants, such as poplar and legumes. The identification of a range of upstream regulators, protein partners, and downstream targets of LBD family members has unraveled the molecular networks of LBD-dependent processes. Moreover, it has been demonstrated that LBD proteins have essential roles in integrating developmental changes in response to phytohormone signaling or environmental cues. As we discuss here, these novel discoveries of LBD functions and their molecular contexts promote a better understanding of this plant-specific transcription factor family.
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Affiliation(s)
- Changzheng Xu
- Southwest University, College of Environment and Resources, Research Centre of Bioenergy and Bioremediation (RCBB), 400715 Chongqing, China; Southwest University, College of Environment and Resources, Centre of Excellence for Soil Biology (CRE), 400715, Chongqing, China.
| | - Feng Luo
- Southwest University, College of Environment and Resources, Research Centre of Bioenergy and Bioremediation (RCBB), 400715 Chongqing, China
| | - Frank Hochholdinger
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, 53113 Bonn, Germany.
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Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F. Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1123-35. [PMID: 26628518 PMCID: PMC4753849 DOI: 10.1093/jxb/erv513] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, D-93053 Regensburg, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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