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Kirschner GK, Hochholdinger F, Salvi S, Bennett MJ, Huang G, Bhosale RA. Genetic regulation of the root angle in cereals. TRENDS IN PLANT SCIENCE 2024; 29:814-822. [PMID: 38402016 DOI: 10.1016/j.tplants.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
The root angle plays a critical role in efficiently capturing nutrients and water from different soil layers. Steeper root angles enable access to mobile water and nitrogen from deeper soil layers, whereas shallow root angles facilitate the capture of immobile phosphorus from the topsoil. Thus, understanding the genetic regulation of the root angle is crucial for breeding crop varieties that can efficiently capture resources and enhance yield. Moreover, this understanding can contribute to developing varieties that effectively sequester carbon in deeper soil layers, supporting global carbon mitigation efforts. Here we review and consolidate significant recent discoveries regarding the molecular components controlling root angle in cereal crop species and outline the remaining research gaps in this field.
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Affiliation(s)
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, LE12 5RD Nottingham, UK
| | - Guoqiang Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Rahul A Bhosale
- School of Biosciences, University of Nottingham, LE12 5RD Nottingham, UK; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
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2
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Alrajhi A, Alharbi S, Beecham S, Alotaibi F. Regulation of root growth and elongation in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1397337. [PMID: 38835859 PMCID: PMC11148372 DOI: 10.3389/fpls.2024.1397337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
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Affiliation(s)
- Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Saif Alharbi
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Saudi Arabia
| | - Simon Beecham
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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3
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Chen X, Tang Y, Duan Q, Hu J. Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat. PLoS One 2023; 18:e0279353. [PMID: 37418496 PMCID: PMC10328375 DOI: 10.1371/journal.pone.0279353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 12/06/2022] [Indexed: 07/09/2023] Open
Abstract
Plant roots are essential for water and nutrient absorption, anchoring, mechanical support, metabolite storage and interaction with the surrounding soil environment. A comprehensive understanding of root traits provides an opportunity to build ideal roots architectural system that provides improved stability and yield advantage in adverse target environments caused by soil quality degradation, climate change, etc. However, we hypothesize that quantitative indicators characterizing root system are still need to be supplemented. Features describing root growth and distribution, until now, belong mostly to 2D indicators or reflect changes in the root system with a depth of soil layers but are rarely considered in a spatial region along the circumferential direction. We proposed five new indicators to quantify the dynamics of the root system architecture (RSA) along its eight-part circumferential orientations with visualization technology which consists of in-situ field root samplings, RSA digitization, and reconstruction according to previous research based on field experiments that conducted on paddy-wheat cultivation land with three fertilization rates. The experimental results showed that the growth space of paddy-wheat root is mainly restricted to a cylinder with a diameter of 180 mm and height of 200 mm at the seedlings stage. There were slow fluctuating trends in growth by the mean values of five new indicators within a single volume of soil. The fluctuation of five new indicators was indicated in each sampling time, which decreased gradually with time. Furthermore, treatment of N70 and N130 could similarly impact root spatial heterogeneity. Therefore, we concluded that the five new indicators could quantify the spatial dynamics of the root system of paddy-wheat at the seedling stage of cultivation. It is of great significance to the comprehensive quantification of crop roots in targeted breeding programs and the methods innovation of field crop root research.
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Affiliation(s)
- Xinxin Chen
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Yongli Tang
- Nanjing Agricultural Equipment Extension Center, Nanjing, China
| | - Qingfei Duan
- College of Engineering, Nanjing Agricultural University, Nanjing, China
| | - Jianping Hu
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
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Xue H, Dong Y, Li Z, Wang J, Yuan X, He F, Li Z, Gao X, Liu J. Transcriptome analysis reveals the molecular mechanisms by which carbon dots regulate the growth of Chlamydomonas reinhardtii. J Colloid Interface Sci 2023; 649:22-35. [PMID: 37331107 DOI: 10.1016/j.jcis.2023.06.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/20/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
Carbon dots (CDs) have attracted increasing attention for their ability to artificially improve photosynthesis. Microalgal bioproducts have emerged as promising sources of sustainable nutrition and energy. However, the gene regulation mechanism of CDs on microalgae remains unexplored. The study synthesized red-emitting CDs and applied them to Chlamydomonas reinhardtii. Results showed that 0.5 mg/L-CDs acted as light supplements to promote cell division and biomass in C. reinhardtii. CDs improved the energy transfer of PS II, photochemical efficiency of PS II, and photosynthetic electron transfer. The pigment content and carbohydrate production slightly increased, while protein and lipid contents significantly increased (by 28.4% and 27.7%, respectively) in a short cultivation time. Transcriptome analysis identified 1166 differentially expressed genes. CDs resulted in faster cell growth by up-regulating the expression of genes associated with cell growth and death, promoting sister chromatid separation, accelerating the mitotic process and shortening the cell cycle. CDs improved the ability of energy conversion by up-regulating photosynthetic electron transfer-related genes. Carbohydrate metabolism-related genes were regulated and provided more available pyruvate for the citrate cycle. The study provides evidence for the genetic regulation of microalgal bioresources by artificially synthesized CDs.
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Affiliation(s)
- Huidan Xue
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710012, China.
| | - Yibei Dong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhihuan Li
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jing Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Xiaolong Yuan
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Fei He
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhengke Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Xiang Gao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jianxi Liu
- State Key Laboratory of Solidification Processing, Center of Advanced Lubrication and Seal Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an 710072, China.
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5
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Ren M, Li Y, Zhu J, Zhao K, Wu Z, Mao C. Phenotypes and Molecular Mechanisms Underlying the Root Response to Phosphate Deprivation in Plants. Int J Mol Sci 2023; 24:ijms24065107. [PMID: 36982176 PMCID: PMC10049108 DOI: 10.3390/ijms24065107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Phosphorus (P) is an essential macronutrient for plant growth. The roots are the main organ for nutrient and water absorption in plants, and they adapt to low-P soils by altering their architecture for enhancing absorption of inorganic phosphate (Pi). This review summarizes the physiological and molecular mechanisms underlying the developmental responses of roots to Pi starvation, including the primary root, lateral root, root hair, and root growth angle, in the dicot model plant Arabidopsis thaliana and the monocot model plant rice (Oryza sativa). The importance of different root traits and genes for breeding P-efficient roots in rice varieties for Pi-deficient soils are also discussed, which we hope will benefit the genetic improvement of Pi uptake, Pi-use efficiency, and crop yields.
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Affiliation(s)
- Meiyan Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianshu Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Keju Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhongchang Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572100, China
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6
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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Li L, Chen X. Auxin regulation on crop: from mechanisms to opportunities in soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:16. [PMID: 37313296 PMCID: PMC10248601 DOI: 10.1007/s11032-023-01361-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/10/2023] [Indexed: 06/15/2023]
Abstract
Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) breeding.
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Affiliation(s)
- Linfang Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Wu Q, Wu J, Hu P, Zhang W, Ma Y, Yu K, Guo Y, Cao J, Li H, Li B, Yao Y, Cao H, Zhang W. Quantification of the three-dimensional root system architecture using an automated rotating imaging system. PLANT METHODS 2023; 19:11. [PMID: 36732764 PMCID: PMC9896698 DOI: 10.1186/s13007-023-00988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Crop breeding based on root system architecture (RSA) optimization is an essential factor for improving crop production in developing countries. Identification, evaluation, and selection of root traits of soil-grown crops require innovations that enable high-throughput and accurate quantification of three-dimensional (3D) RSA of crops over developmental time. RESULTS We proposed an automated imaging system and 3D imaging data processing pipeline to quantify the 3D RSA of soil-grown individual plants across seedlings to the mature stage. A multi-view automated imaging system composed of a rotary table and an imaging arm with 12 cameras mounted with a combination of fan-shaped and vertical distribution was developed to obtain 3D image data of roots grown on a customized root support mesh. A 3D imaging data processing pipeline was developed to quantify the 3D RSA based on the point cloud generated from multi-view images. The global architecture of root systems can be quantified automatically. Detailed analysis of the reconstructed 3D root model also allowed us to investigate the Spatio-temporal distribution of roots. A method combining horizontal slicing and iterative erosion and dilation was developed to automatically segment different root types, and identify local root traits (e.g., length, diameter of the main root, and length, diameter, initial angle, and the number of nodal roots or lateral roots). One maize (Zea mays L.) cultivar and two rapeseed (Brassica napus L.) cultivars at different growth stages were selected to test the performance of the automated imaging system and 3D imaging data processing pipeline. CONCLUSIONS The results demonstrated the capabilities of the proposed imaging and analytical system for high-throughput phenotyping of root traits for both monocotyledons and dicotyledons across growth stages. The proposed system offers a potential tool to further explore the 3D RSA for improving root traits and agronomic qualities of crops.
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Affiliation(s)
- Qian Wu
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Jie Wu
- Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Pengcheng Hu
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Weixin Zhang
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kun Yu
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yan Guo
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jing Cao
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Huayong Li
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Baiming Li
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuyang Yao
- College of Electronics & Information Engineering, Nanjing University of Information Science and Technology, Nanjing, 210044, Jiangsu, China
| | - Hongxin Cao
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
| | - Wenyu Zhang
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Bhattacharya S, Gröne F, Przesdzink F, Ziffer-Berger J, Barazani O, Mummenhoff K, Kappert N. 'Root of all success': Plasticity in root architecture of invasive wild radish for adaptive benefit. FRONTIERS IN PLANT SCIENCE 2022; 13:1035089. [PMID: 36466265 PMCID: PMC9709435 DOI: 10.3389/fpls.2022.1035089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Successful plant establishment in a particular environment depends on the root architecture of the seedlings and the extent of edaphic resource utilization. However, diverse habitats often pose a predicament on the suitability of the fundamental root structure of a species that evolved over a long period. We hypothesized that the plasticity in the genetically controlled root architecture in variable habitats provides an adaptive advantage to worldwide-distributed wild radish (Raphanus raphanistrum, Rr) over its close relative (R. pugioniformis, Rp) that remained endemic to the East Mediterranean region. To test the hypothesis, we performed a reciprocal comparative analysis between the two species, growing in a common garden experiment on their native soils (Hamra/Sandy for Rr, Terra Rossa for Rp) and complementary controlled experiments mimicking the major soil compositions. Additionally, we analyzed the root growth kinetics via semi-automated digital profiling and compared the architecture between Rr and Rp. In both experiments, the primary roots of Rr were significantly longer, developed fewer lateral roots, and showed slower growth kinetics than Rp. Multivariate analyses of seven significant root architecture variables revealed that Rr could successfully adapt to different surrogate growth conditions by only modulating their main root length and number of lateral roots. In contrast, Rp needs to modify several other root parameters, which are very resource-intensive, to grow on non-native soil. Altogether the findings suggest an evo-devo adaptive advantage for Rr as it can potentially establish in various habitats with the minimal tweak of key root parameters, hence allocating resources for other developmental requirements.
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Affiliation(s)
| | - Franziska Gröne
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Felix Przesdzink
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Jotham Ziffer-Berger
- Department of Biology, Levinsky College of Education, Tel-Aviv, Israel
- Herbarium, Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Oz Barazani
- Institute of Plant Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Klaus Mummenhoff
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Niels Kappert
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
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P. Pais I, Moreira R, Semedo JN, Reboredo FH, Lidon FC, Coutinho J, Maçãs B, Scotti-Campos P. Phenotypic Diversity of Seminal Root Traits in Bread Wheat Germplasm from Different Origins. PLANTS (BASEL, SWITZERLAND) 2022; 11:2842. [PMID: 36365295 PMCID: PMC9657832 DOI: 10.3390/plants11212842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major staple crop, and more adapted varieties are needed to ensure productivity under unpredictable stress scenarios resulting from climate changes. In the development of new genotypes, root system traits are essential since roots have a key function in water and nutrient uptake, and root architecture determines the plant's ability to spatially explore the soil resources. Genetic variation in wheat root system may be assessed at the early stages of development. This study evaluates in vitro and at the seedling stage, the genetic diversity of root growth angle (RGA), seminal root number (SRN), and radicle length (RadL) in 30 bread wheat genotypes from different origins and belonging to distinct evolutive or breeding groups. SRN and RadL were analyzed at 1, 2, 3 and 6 days after sowing (DAS) and RGA was measured through the angle between the first pair of seminal roots. A large variability was found in RGA values that ranged from 63° to 122°. Although differences were found between genotypes within the same groups, the narrower angles tended to occur among landraces, while the higher RGA values were observed in advanced lines and Australian varieties. Differences were also observed as regards the SRN (1.0-3.0, 2.7-4.7, 3.2-5.0 and 4.4-6.3 at 1, 2, 3 and 6 DAS, respectively) and RadL (0.1-1.5, 2.1-5.0, 4.0-7.5 and 5.1-13.7 cm at 1, 2, 3 and 6 DAS, respectively). Genetic variability in root traits at seedling stage allows more rapid selection of genotypes better adapted to environmental and soil constraints, necessary to Portuguese Wheat Breeding Program. It will also contribute to the definition of wheat ideotypes with improved performance under Mediterranean climate conditions.
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Affiliation(s)
- Isabel P. Pais
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Moreira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
| | - José N. Semedo
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Fernando H. Reboredo
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Earth Sciences Department, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Fernando C. Lidon
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Earth Sciences Department, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Coutinho
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estrada Gil Vaz, Ap. 6, 7350-901 Elvas, Portugal
| | - Benvindo Maçãs
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estrada Gil Vaz, Ap. 6, 7350-901 Elvas, Portugal
| | - Paula Scotti-Campos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Chi Y, Tam NFY, Li WC, Ye Z. Multiple geochemical and microbial processes regulated by redox and organic matter control the vertical heterogeneity of As and Cd in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156229. [PMID: 35643135 DOI: 10.1016/j.scitotenv.2022.156229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/21/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
The heterogeneity of arsenic (As) and cadmium (Cd) in paddy soils seriously hinders the assessment of contamination status and prediction of rice uptake. Their vertical patterns across different environmental conditions and the underlying mechanisms remain largely unexplored. In this study, maximum vertical differences of bioavailable As and Cd within 0-30 cm depth in paddy soils were 4.1-fold and four orders of magnitude, respectively. The vertical patterns of As and Cd followed the vertical redox gradient in long-term reduced paddies, but were shaped by the vertical pH gradient derived from acidic wastewater irrigation in partly oxidized soils. Iron(III)- and sulfate-reducing bacteria played key roles in the formation of vertical pH gradient and the immobilization of As and Cd by iron (hydr)oxides and sulfides under varied redox conditions. Soil redox and organic matter determined the transition between these two mechanisms via regulating microbial iron(III) and sulfate reduction processes. The work proposes that soil vertical As and Cd patterns directly affect the accumulation of As and Cd in different rice cultivars with different vertical root patterns. This is the first study elucidating the controlling mechanisms governing the vertical As and Cd patterns in paddy fields, providing important references to identify, manage and remediate contaminated paddy fields.
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Affiliation(s)
- Yihan Chi
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; Department of Science and Environmental Studies, the Education University of Hong Kong, Hong Kong, China
| | - Nora Fung-Yee Tam
- School of Science and Technology, The Hong Kong Metropolitan University, Kowloon, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.
| | - Wai Chin Li
- Department of Science and Environmental Studies, the Education University of Hong Kong, Hong Kong, China.
| | - Zhihong Ye
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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12
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Teramoto S, Yamasaki M, Uga Y. Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies. BREEDING SCIENCE 2022; 72:222-231. [PMID: 36408322 PMCID: PMC9653191 DOI: 10.1270/jsbbs.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/10/2022] [Indexed: 06/16/2023]
Abstract
To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo 675-2103, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
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13
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Kořínková N, Fontana IM, Nguyen TD, Pouramini P, Bergougnoux V, Hensel G. Enhancing cereal productivity by genetic modification of root architecture. Biotechnol J 2022; 17:e2100505. [PMID: 35537849 DOI: 10.1002/biot.202100505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/23/2022] [Indexed: 11/06/2022]
Abstract
Food security is one of the main topics of today's agriculture, primarily due to increasingly challenging environmental conditions. As most of humankind has a daily intake of cereal grains, current breeding programs focus on these crop plants. Customised endonucleases have been included in the breeders' toolbox after successfully demonstrating their use. Due to technological restrictions, the main focus of the new technology was on above-ground plant organs. In contrast, the essential below ground components were given only limited attention. In the present review, the knowledge of the root system architecture in cereals and the role of phytohormones during their establishment is summarized, and the underlying molecular mechanisms are outlined. The review summarizes how the use of CRISPR-based genome editing methodology can improve the root system architecture to enhance crop production genetically. Finally, future research directions involving this knowledge and technical advances are suggested. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nikola Kořínková
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Irene M Fontana
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Thu D Nguyen
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371
| | - Pouneh Pouramini
- Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Reproductive Biology, D-06466 Seeland OT, Gatersleben
| | - Véronique Bergougnoux
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371
| | - Goetz Hensel
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, CZ-78371.,Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, D-40225, Dusseldorf
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14
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Isolation and Molecular Characterisation of TtDro1A and TtDro1B Genes from Triticum turgidum Subspecies durum and turgidum, Study of Their Influences on Seedling Root Angles. PLANTS 2022; 11:plants11060821. [PMID: 35336704 PMCID: PMC8954752 DOI: 10.3390/plants11060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Durum wheat (Triticum turgidum, 2n = 4x = AABB) includes several subspecies with differential characteristics in their root system architecture (RSA). Subspecies durum has longer and more vertical roots, while subspecies turgidum has smaller and shallower roots. The homeologous genes TtDro1A and TtDro1B of both subspecies have been identified and found to differ in their sizes, sequences and the proteins they encode. To determine whether there is a relationship between the level of expression of these two genes and the angle adopted by the roots of durum wheat seedlings, their expressions has been studied by RT-qPCR, both in the primary seminal root and in the other seminal roots. The results of the analyses showed that the TtDro1A gene is expressed 1.4 times more in the primary seminal root than in the other seminal roots. Furthermore, this gene is expressed 2.49 to 8.76 times more than TtDro1B depending on root type (primary or seminal) and subspecies. There are positive correlations between the expression ratio of both genes (TtDro1A/TtDro1B) and the mean of all root angles, the most vertical root angle and the most horizontal root angle of the seedlings. The higher the expression of TtDro1B gene, the lower the root growth angles.
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15
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Galindo-Castañeda T, Lynch JP, Six J, Hartmann M. Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms. FRONTIERS IN PLANT SCIENCE 2022; 13:827369. [PMID: 35356114 PMCID: PMC8959776 DOI: 10.3389/fpls.2022.827369] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 05/14/2023]
Abstract
Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.
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Affiliation(s)
- Tania Galindo-Castañeda
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Johan Six
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
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16
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Teramoto S, Uga Y. Improving the efficiency of plant root system phenotyping through digitization and automation. BREEDING SCIENCE 2022; 72:48-55. [PMID: 36045896 PMCID: PMC8987843 DOI: 10.1270/jsbbs.21053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/11/2021] [Indexed: 05/19/2023]
Abstract
Root system architecture (RSA) determines unevenly distributed water and nutrient availability in soil. Genetic improvement of RSA, therefore, is related to crop production. However, RSA phenotyping has been carried out less frequently than above-ground phenotyping because measuring roots in the soil is difficult and labor intensive. Recent advancements have led to the digitalization of plant measurements; this digital phenotyping has been widely used for measurements of both above-ground and RSA traits. Digital phenotyping for RSA is slower and more difficult than for above-ground traits because the roots are hidden underground. In this review, we summarized recent trends in digital phenotyping for RSA traits. We classified the sample types into three categories: soil block containing roots, section of soil block, and root sample. Examples of the use of digital phenotyping are presented for each category. We also discussed room for improvement in digital phenotyping in each category.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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17
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Liu Y, von Wirén N. Integration of nutrient and water availabilities via auxin into the root developmental program. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102117. [PMID: 34624806 DOI: 10.1016/j.pbi.2021.102117] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
In most soils, the spatial distribution of nutrients and water in the rooting zone of plants is heterogeneous and changes over time. To access localized resources more efficiently, plants induce foraging responses by modulating individual morphological root traits, such as the length of the primary root or the number and length of lateral roots. These adaptive responses require the integration of exogenous and endogenous nutrient- or water-related signals into the root developmental program. Recent studies corroborated a central role of auxin in shaping root architectural traits in response to fluctuating nutrient and water availabilities. In this review, we highlight current knowledge on nutrient- and water-related developmental processes that impact root foraging and involve auxin as a central player. A deeper understanding and exploitation of these auxin-related processes and mechanisms promises advances in crop breeding for higher resource efficiency.
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Affiliation(s)
- Ying Liu
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Stadt Seeland, OT Gatersleben, Germany.
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18
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Chin S, Blancaflor EB. Plant Gravitropism: From Mechanistic Insights into Plant Function on Earth to Plants Colonizing Other Worlds. Methods Mol Biol 2022; 2368:1-41. [PMID: 34647245 DOI: 10.1007/978-1-0716-1677-2_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gravitropism, the growth of roots and shoots toward or away from the direction of gravity, has been studied for centuries. Such studies have not only led to a better understanding of the gravitropic process itself, but also paved new paths leading to deeper mechanistic insights into a wide range of research areas. These include hormone biology, cell signal transduction, regulation of gene expression, plant evolution, and plant interactions with a variety of environmental stimuli. In addition to contributions to basic knowledge about how plants function, there is accumulating evidence that gravitropism confers adaptive advantages to crops, particularly under marginal agricultural soils. Therefore, gravitropism is emerging as a breeding target for enhancing agricultural productivity. Moreover, research on gravitropism has spawned several studies on plant growth in microgravity that have enabled researchers to uncouple the effects of gravity from other tropisms. Although rapid progress on understanding gravitropism witnessed during the past decade continues to be driven by traditional molecular, physiological, and cell biological tools, these tools have been enriched by technological innovations in next-generation omics platforms and microgravity analog facilities. In this chapter, we review the field of gravitropism by highlighting recent landmark studies that have provided unique insights into this classic research topic while also discussing potential contributions to agriculture on Earth and beyond.
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Affiliation(s)
- Sabrina Chin
- Department of Botany, University of Wisconsin, Madison, WI, USA.
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19
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Schäfer ED, Ajmera I, Farcot E, Owen MR, Band LR, Lynch JP. In silico evidence for the utility of parsimonious root phenotypes for improved vegetative growth and carbon sequestration under drought. FRONTIERS IN PLANT SCIENCE 2022; 13:1010165. [PMID: 36466274 PMCID: PMC9713484 DOI: 10.3389/fpls.2022.1010165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/03/2022] [Indexed: 05/11/2023]
Abstract
Drought is a primary constraint to crop yields and climate change is expected to increase the frequency and severity of drought stress in the future. It has been hypothesized that crops can be made more resistant to drought and better able to sequester atmospheric carbon in the soil by selecting appropriate root phenotypes. We introduce OpenSimRoot_v2, an upgraded version of the functional-structural plant/soil model OpenSimRoot, and use it to test the utility of a maize root phenotype with fewer and steeper axial roots, reduced lateral root branching density, and more aerenchyma formation (i.e. the 'Steep, Cheap, and Deep' (SCD) ideotype) and different combinations of underlying SCD root phene states under rainfed and drought conditions in three distinct maize growing pedoclimatic environments in the USA, Nigeria, and Mexico. In all environments where plants are subjected to drought stress the SCD ideotype as well as several intermediate phenotypes lead to greater shoot biomass after 42 days. As an additional advantage, the amount of carbon deposited below 50 cm in the soil is twice as great for the SCD phenotype as for the reference phenotype in 5 out of 6 simulated environments. We conclude that crop growth and deep soil carbon deposition can be improved by breeding maize plants with fewer axial roots, reduced lateral root branching density, and more aerenchyma formation.
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Affiliation(s)
- Ernst D. Schäfer
- Department of Plant Science, Pennysylvania State University, State College, PA, United States
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ishan Ajmera
- Department of Plant Science, Pennysylvania State University, State College, PA, United States
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Markus R. Owen
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Leah R. Band
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan P. Lynch
- Department of Plant Science, Pennysylvania State University, State College, PA, United States
- *Correspondence: Jonathan P. Lynch,
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20
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Daryani P, Darzi Ramandi H, Dezhsetan S, Mirdar Mansuri R, Hosseini Salekdeh G, Shobbar ZS. Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:81-106. [PMID: 34623472 DOI: 10.1007/s00122-021-03953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
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Affiliation(s)
- Parisa Daryani
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Dezhsetan
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran.
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21
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Wang Y, Xie Z, Wang X, Peng X, Zheng J. Fluorescent carbon-dots enhance light harvesting and photosynthesis by overexpressing PsbP and PsiK genes. J Nanobiotechnology 2021; 19:260. [PMID: 34454524 PMCID: PMC8403421 DOI: 10.1186/s12951-021-01005-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Fluorescent carbon-dots (CDs) with multifaceted advantages have provided hope for improvement of crop growth. Near infrared (NIR) CDs would be more competitive and promising than short-wavelength emissive CDs, which are not directly utilized by chloroplast. The molecular targets and underlying mechanism of these stimulative effects are rarely mentioned. RESULTS NIR-CDs with good mono-dispersity and hydrophily were easily prepared by a one-step microwave-assisted carbonization manner, which showed obvious UV absorptive and far-red emissive properties. The chloroplast-CDs complexes could accelerate the electron transfer from photosystem II (PS II) to photosystem I (PS I). NIR-CDs exhibited a concentration-dependent promotion effect on N. benthamiana growth by strengthening photosynthesis. We firstly demonstrated that potential mechanisms behind the photosynthesis-stimulating activity might be related to up-regulated expression of the photosynthesis and chloroplast synthesis related genes, among which PsbP and PsiK genes are the key regulators. CONCLUSION These results illustrated that NIR-CDs showed great potential in the applications to increase crop yields through ultraviolet light harvesting and elevated photosynthesis efficiency. This work would provide a theoretical basis for the understanding and applications of the luminescent nanomaterials (not limited to CDs) in the sunlight conversion-related sustainable agriculture.
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Affiliation(s)
- Yuhui Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, People's Republic of China
| | - Zhuomi Xie
- Ningbo Research Institute of Zhejiang University, Ningbo, 315100, People's Republic of China
- Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Xiuhua Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, People's Republic of China
| | - Xin Peng
- Ningbo Research Institute of Zhejiang University, Ningbo, 315100, People's Republic of China.
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, People's Republic of China.
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22
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Identification of Markers for Root Traits Related to Drought Tolerance Using Traditional Rice Germplasm. Mol Biotechnol 2021; 63:1280-1292. [PMID: 34398447 DOI: 10.1007/s12033-021-00380-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022]
Abstract
Drought is one of the important constraints affecting rice productivity worldwide. The vigorous shoot and deep root system help to improve drought resistance. In present era, genome-wide association study (GWAS) is the preferred method for mapping of QTLs for complex traits such as root and drought tolerance traits. In the present study, 114 rice genotypes were evaluated for various root and shoot traits under water stress conditions. All genotypes showed a significant amount of variation for various root and shoot traits. Correlation analysis revealed that high dry shoot weight and fresh shoot weight is associated with root length, root volume, fresh root weight and dry root weight. A total of 11 significant marker-trait associations were detected for various root, shoot and drought tolerance traits with the coefficient of determination (R2) ranging from 18.99 to 53.41%. Marker RM252 and RM212 showed association with three root traits which suggests their scope for improvement of root system. In the present study, a novel QTL was detected for root length associated with RM127, explaining 19.30% of variation. The marker alleles with increasing phenotypic effects for root and drought-tolerant traits can be exploited for improvement of root and drought tolerance traits using marker-assisted selection.
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23
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Wang H, Tang X, Yang X, Fan Y, Xu Y, Li P, Xu C, Yang Z. Exploiting natural variation in crown root traits via genome-wide association studies in maize. BMC PLANT BIOLOGY 2021; 21:346. [PMID: 34301195 PMCID: PMC8299645 DOI: 10.1186/s12870-021-03127-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/12/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear. METHODS In this study, the CRA, CRD, and CRN of 316 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using two single-locus methods (GLM and MLM) and three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA) with 140,421 SNP. RESULTS A total of 38 QTL including 126 SNPs were detected for CRA, CRD, and CRN. Additionally, 113 candidate genes within 50 kb of the significant SNPs were identified. Combining the gene annotation information and the expression profiles, 3 genes including GRMZM2G141205 (IAA), GRMZM2G138511 (HSP) and GRMZM2G175910 (cytokinin-O-glucosyltransferase) were selected as potentially candidate genes related to crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN in different environments. Four haplotypes were detected based on these significant variants, and Hap1 has more CRN. CONCLUSIONS These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions.
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Affiliation(s)
- 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, Yangzhou, 225009, China
| | - Xiao Tang
- 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, Yangzhou, 225009, China
| | - Xiaoyi Yang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Fan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yang Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Pengcheng Li
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, 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, 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, Yangzhou, 225009, China.
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Li C, Li L, Reynolds MP, Wang J, Chang X, Mao X, Jing R. Recognizing the hidden half in wheat: root system attributes associated with drought tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5117-5133. [PMID: 33783492 DOI: 10.1093/jxb/erab124] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/09/2023]
Abstract
Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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25
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Panda S, Majhi PK, Anandan A, Mahender A, Veludandi S, Bastia D, Guttala SB, Singh SK, Saha S, Ali J. Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:6058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
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Affiliation(s)
- Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India;
| | - Prasanta Kumar Majhi
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University (B.H.U.), Varanasi 221005, Uttar Pradesh, India; (P.K.M.); (S.K.S.)
| | - Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines;
| | - Sumanth Veludandi
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
| | - Debendranath Bastia
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India;
| | - Suresh Babu Guttala
- Department of Genetics and Plant Breeding, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj 211007, Uttar Pradesh, India;
| | - Shravan Kumar Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University (B.H.U.), Varanasi 221005, Uttar Pradesh, India; (P.K.M.); (S.K.S.)
| | - Sanjoy Saha
- Crop Production Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India;
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines;
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26
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Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. PLANT, CELL & ENVIRONMENT 2021; 44:1846-1857. [PMID: 33576018 DOI: 10.1111/pce.14029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin-responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with a high and auxin-mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin-responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1-mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis-based insertion of the INDITTO2 transposon into the DRO1 promoter of the non-adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.
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Affiliation(s)
- Yiting Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
- Shanxi Agricultural University/Shanxi Academy of Agricultural Sciences. The Industrial Crop Institute, Fenyang, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Dong Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Baolin Yao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Si Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Li Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Jie Qian
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xuan Zhou
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Li Han
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Shuanglu Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Canrong Ma
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yanfang Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Chongyu Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qian Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Saijie Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Lina Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xi Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Youchun Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Hao Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Jing Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qiong Luo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Lichi Li
- International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Sheng Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Zhili Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Lei Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chengyun Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
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27
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Oo AZ, Tsujimoto Y, Mukai M, Nishigaki T, Takai T, Uga Y. Synergy between a shallow root system with a DRO1 homologue and localized P application improves P uptake of lowland rice. Sci Rep 2021; 11:9484. [PMID: 33947950 PMCID: PMC8096825 DOI: 10.1038/s41598-021-89129-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/21/2021] [Indexed: 11/09/2022] Open
Abstract
Improved phosphorus (P) use efficiency for crop production is needed, given the depletion of phosphorus ore deposits, and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has been little understood. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots after placing P near the roots at transplanting (P-dipping). The experiment identified that the P-dipping created an available P hotspot at the plant base of the soil surface layer where the qsor1-NIL had the greatest root biomass and root surface area despite no genotyipic differences in total values, whereby the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The superior surface root development of qsor1-NIL could have facilitated P uptakes from the P hotspot, implying that P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.
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Affiliation(s)
- Aung Zaw Oo
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Yasuhiro Tsujimoto
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan.
| | - Mana Mukai
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Tomohiro Nishigaki
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Toshiyuki Takai
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2, Kan-nondai, Tsukuba, Ibaraki, 3058518, Japan
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28
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1101/2020.12.11.421685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 05/26/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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29
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1111/tpj.15226] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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30
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Mohan A, Grant NP, Schillinger WF, Gill KS. Characterizing reduced height wheat mutants for traits affecting abiotic stress and photosynthesis during seedling growth. PHYSIOLOGIA PLANTARUM 2021; 172:233-246. [PMID: 33421138 DOI: 10.1111/ppl.13321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Most high-yielding, semidwarf wheat (Triticum aestivum L.) grown around the world contains either Rht1 or Rht2 genes. The success of these high-yielding cultivars is greatest in the most productive farming environments but provide marginal benefits in less favorable growing conditions such as shallow soils and low-precipitation dryland farming. Further, growing evidence suggests semidwarf genes not only affect early seedling growth but limit grain yield, especially under abiotic stress conditions. There are 23 other reduced-height mutants reported in wheat, most of which have not been functionally characterized. We evaluated these mutants along with their parents for several traits affecting seedling emergence, early seedling growth, and photosynthetic efficiency. Two- to seven-fold differences in coleoptile length, first leaf length, root length, and root angle were observed among the genotypes. Most of the mutations had a positive effect on root length, while the root angle narrowed. Coleoptile and first leaf lengths were strongly correlated with emergence. A specialized deep planting experiment identified Rht5, Rht6, Rht8, and Rht13 with significantly improved seedling emergence compared to the parent. Among the mutants, Rht4, Rht19, and Rht12 ranked highest for photosynthetic traits while Rht9, Rht16, and Rht15 performed best for early seedling growth parameters. Considering all traits collectively, Rht15 showed the most promise for utilization in marginal environments followed by Rht19 and Rht16. These wheat mutants may be useful for deciphering the underlying molecular mechanisms of understudied traits and breeding programs in arid and semiarid regions where deep planting is practiced.
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Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan P Grant
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
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31
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Lekshmy VS, Vijayaraghavareddy P, Nagashree AN, Ramu VS, Ramegowda V, Makarla U, Sreeman S. Induction of Acquired Tolerance Through Gradual Progression of Drought Is the Key for Maintenance of Spikelet Fertility and Yield in Rice Under Semi-irrigated Aerobic Conditions. FRONTIERS IN PLANT SCIENCE 2021; 11:632919. [PMID: 33679820 PMCID: PMC7930615 DOI: 10.3389/fpls.2020.632919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/22/2020] [Indexed: 06/01/2023]
Abstract
Plants have evolved several adaptive mechanisms to cope with water-limited conditions. While most of them are through constitutive traits, certain "acquired tolerance" traits also provide significant improvement in drought adaptation. Most abiotic stresses, especially drought, show a gradual progression of stress and hence provide an opportunity to upregulate specific protective mechanisms collectively referred to as "acquired tolerance" traits. Here, we demonstrate a significant genetic variability in acquired tolerance traits among rice germplasm accessions after standardizing a novel gradual stress progress protocol. Two contrasting genotypes, BPT 5204 (drought susceptible) and AC 39000 (tolerant), were used to standardize methodology for capturing acquired tolerance traits at seedling phase. Seedlings exposed to gradual progression of stress showed higher recovery with low free radical accumulation in both the genotypes compared to rapid stress. Further, the gradual stress progression protocol was used to examine the role of acquired tolerance at flowering phase using a set of 17 diverse rice genotypes. Significant diversity in free radical production and scavenging was observed among these genotypes. Association of these parameters with yield attributes showed that genotypes that managed free radical levels in cells were able to maintain high spikelet fertility and hence yield under stress. This study, besides emphasizing the importance of acquired tolerance, explains a high throughput phenotyping approach that significantly overcomes methodological constraints in assessing genetic variability in this important drought adaptive mechanism.
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Affiliation(s)
- V. S. Lekshmy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Preethi Vijayaraghavareddy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Department of Plant Sciences, Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, Netherlands
| | - A. N. Nagashree
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | | | | | - Udayakumar Makarla
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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Uga Y. Challenges to design-oriented breeding of root system architecture adapted to climate change. BREEDING SCIENCE 2021; 71:3-12. [PMID: 33762871 PMCID: PMC7973499 DOI: 10.1270/jsbbs.20118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 05/12/2023]
Abstract
Roots are essential organs for capturing water and nutrients from the soil. In particular, root system architecture (RSA) determines the extent of the region of the soil where water and nutrients can be gathered. As global climate change accelerates, it will be important to improve belowground plant parts, as well as aboveground ones, because roots are front-line organs in the response to abiotic stresses such as drought, flooding, and salinity stress. However, using conventional breeding based on phenotypic selection, it is difficult to select breeding lines possessing promising RSAs to adapted to abiotic stress because roots remain hidden underground. Therefore, new breeding strategies that do not require phenotypic selection are necessary. Recent advances in molecular biology and biotechnology can be applied to the design-oriented breeding of RSA without phenotypic selection. Here I summarize recent progress in RSA ideotypes as "design" and RSA-related gene resources as "materials" that will be needed in leveraging these technologies for the RSA breeding. I also highlight the future challenges to design-oriented breeding of RSA and explore solutions to these challenges.
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Affiliation(s)
- Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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Lucob-Agustin N, Sugiura D, Kano-Nakata M, Hasegawa T, Suralta RR, Niones JM, Inari-Ikeda M, Yamauchi A, Inukai Y. The promoted lateral root 1 (plr1) mutation is involved in reduced basal shoot starch accumulation and increased root sugars for enhanced lateral root growth in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110667. [PMID: 33218634 DOI: 10.1016/j.plantsci.2020.110667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Lateral roots (LRs) are indispensable for plant growth, adaptability and productivity. We previously reported a rice mutant, exhibiting a high density of thick and long LRs (L-type LRs) with long parental roots and herein referred to as promoted lateral root1 (plr1). In this study, we describe that the mutant exhibited decreased basal shoot starch accumulation, suggesting that carbohydrates might regulate the mutant root phenotype. Further analysis revealed that plr1 mutation gene regulated reduced starch accumulation resulting in increased root sugars for the regulation of promoted LR development. This was supported by the exogenous glucose application that promoted L-type LRs. Moreover, nitrogen (N) application was found to reduce basal shoot starch accumulation in both plr1 mutant and wild-type seedlings, which was due to the repressed expression of starch biosynthesis genes. However, unlike the wild-type that responded to N treatment only at seedling stage, the plr1 mutant regulated LR development under low to increasing N levels, both at seedling and higher growth stages. These results suggest that plr1 mutation gene is involved in reduced basal shoot starch accumulation and increased root sugar level for the promotion of L-type LR development, and thus would be very useful in improving rice root architecture.
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Affiliation(s)
- Nonawin Lucob-Agustin
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Daisuke Sugiura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tomomi Hasegawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Roel R Suralta
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija 3119, Philippines.
| | - Jonathan M Niones
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija 3119, Philippines.
| | - Mayuko Inari-Ikeda
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan.
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Guimarães PHR, de Lima IP, de Castro AP, Lanna AC, Guimarães Santos Melo P, de Raïssac M. Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought? RICE (NEW YORK, N.Y.) 2020; 13:67. [PMID: 32930888 PMCID: PMC7492358 DOI: 10.1186/s12284-020-00404-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology. RESULTS High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought. CONCLUSIONS This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.
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Affiliation(s)
| | - Isabela Pereira de Lima
- Universidade Federal de Lavras, Departamento de Agricultura, Campus Universitário, Lavras, MG, 37200-000, Brazil
| | | | - Anna Cristina Lanna
- Embrapa Arroz e Feijão, Rodovia GO-462, km 12, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | | | - Marcel de Raïssac
- Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, AGAP, Montpellier, France.
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Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci U S A 2020; 117:21242-21250. [PMID: 32817523 PMCID: PMC7474696 DOI: 10.1073/pnas.2005911117] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The root system architecture (RSA) of crops can affect their production, particularly in abiotic stress conditions, such as with drought, waterlogging, and salinity. Salinity is a growing problem worldwide that negatively impacts on crop productivity, and it is believed that yields could be improved if RSAs that enabled plants to avoid saline conditions were identified. Here, we have demonstrated, through the cloning and characterization of qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), that a shallower root growth angle (RGA) could enhance rice yields in saline paddies. qSOR1 is negatively regulated by auxin, predominantly expressed in root columella cells, and involved in the gravitropic responses of roots. qSOR1 was found to be a homolog of DRO1 (DEEPER ROOTING 1), which is known to control RGA. CRISPR-Cas9 assays revealed that other DRO1 homologs were also involved in RGA. Introgression lines with combinations of gain-of-function and loss-of-function alleles in qSOR1 and DRO1 demonstrated four different RSAs (ultra-shallow, shallow, intermediate, and deep rooting), suggesting that natural alleles of the DRO1 homologs could be utilized to control RSA variations in rice. In saline paddies, near-isogenic lines carrying the qSOR1 loss-of-function allele had soil-surface roots (SOR) that enabled rice to avoid the reducing stresses of saline soils, resulting in increased yields compared to the parental cultivars without SOR. Our findings suggest that DRO1 homologs are valuable targets for RSA breeding and could lead to improved rice production in environments characterized by abiotic stress.
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Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM. A balancing act: how plants integrate nitrogen and water signals. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4442-4451. [PMID: 31990028 PMCID: PMC7382378 DOI: 10.1093/jxb/eraa054] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
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Affiliation(s)
- Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jose M Alvarez
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Amelia Henry
- International Rice Research Institute, Metro Manila, Philippines
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Correspondence:
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Oo AZ, Tsujimoto Y, Rakotoarisoa NM, Kawamura K, Nishigaki T. P-dipping of rice seedlings increases applied P use efficiency in high P-fixing soils. Sci Rep 2020; 10:11919. [PMID: 32681148 PMCID: PMC7368074 DOI: 10.1038/s41598-020-68977-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Applied phosphorus (P) use efficiency is generally low due to the low mobility of P in soil and its affinity to form insoluble complexes. Localized P application nearby the root zone is a potential approach to overcome this issue in crop production. However, the interaction with soil conditions is little understood, which results in less effective application of this approach. Using root-box experiments and changing P-retention capacity of soils, we revealed that applied P use efficiency of rice can be substantially improved by dipping seedlings in P-enriched slurry at transplanting (P-dipping) even in highly P-fixing soils. Spatial analysis of soluble P in soils indicated that P-dipping creates a P hotspot because the P-enriched slurry is transferred with seedling roots. The P hotspot could have induced vigorous surface root and facilitated further P uptake from the spot. In contrast, the effect of conventional P incorporation depended on P-retention capacity of soils; no increases in soluble P content in soils or plant P uptakes were observed when P-retention capacity was high. Our finding of significant interaction between localized P application and a specific soil property should help improving applied P use efficiency and achieving sustainable rice production against depleting P fertilizer resources.
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Affiliation(s)
- Aung Zaw Oo
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Yasuhiro Tsujimoto
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan.
| | - Njato Mickaël Rakotoarisoa
- Département de Recherche Rizicoles (DRR), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), BP 1690, Tsimbazaza, Antananarivo, Madagascar
| | - Kensuke Kawamura
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
| | - Tomohiro Nishigaki
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 3058686, Japan
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38
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Falk KG, Jubery TZ, O'Rourke JA, Singh A, Sarkar S, Ganapathysubramanian B, Singh AK. Soybean Root System Architecture Trait Study through Genotypic, Phenotypic, and Shape-Based Clusters. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:1925495. [PMID: 33313543 PMCID: PMC7706349 DOI: 10.34133/2020/1925495] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/16/2020] [Indexed: 05/24/2023]
Abstract
We report a root system architecture (RSA) traits examination of a larger scale soybean accession set to study trait genetic diversity. Suffering from the limitation of scale, scope, and susceptibility to measurement variation, RSA traits are tedious to phenotype. Combining 35,448 SNPs with an imaging phenotyping platform, 292 accessions (replications = 14) were studied for RSA traits to decipher the genetic diversity. Based on literature search for root shape and morphology parameters, we used an ideotype-based approach to develop informative root (iRoot) categories using root traits. The RSA traits displayed genetic variability for root shape, length, number, mass, and angle. Soybean accessions clustered into eight genotype- and phenotype-based clusters and displayed similarity. Genotype-based clusters correlated with geographical origins. SNP profiles indicated that much of US origin genotypes lack genetic diversity for RSA traits, while diverse accession could infuse useful genetic variation for these traits. Shape-based clusters were created by integrating convolution neural net and Fourier transformation methods, enabling trait cataloging for breeding and research applications. The combination of genetic and phenotypic analyses in conjunction with machine learning and mathematical models provides opportunities for targeted root trait breeding efforts to maximize the beneficial genetic diversity for future genetic gains.
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Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | - Jamie A. O'Rourke
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
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Lucob-Agustin N, Kawai T, Takahashi-Nosaka M, Kano-Nakata M, Wainaina CM, Hasegawa T, Inari-Ikeda M, Sato M, Tsuji H, Yamauchi A, Inukai Y. WEG1, which encodes a cell wall hydroxyproline-rich glycoprotein, is essential for parental root elongation controlling lateral root formation in rice. PHYSIOLOGIA PLANTARUM 2020; 169:214-227. [PMID: 31925781 DOI: 10.1111/ppl.13063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 05/25/2023]
Abstract
Lateral roots (LRs) determine the overall root system architecture, thus enabling plants to efficiently explore their underground environment for water and nutrients. However, the mechanisms regulating LR development are poorly understood in monocotyledonous plants. We characterized a rice mutant, wavy root elongation growth 1 (weg1), that produced higher number of long and thick LRs (L-type LRs) formed from the curvatures of its wavy parental roots caused by asymmetric cell growth in the elongation zone. Consistent with this phenotype, was the expression of the WEG1 gene, which encodes a putative member of the hydroxyproline-rich glycoprotein family that regulates cell wall extensibility, in the root elongation zone. The asymmetric elongation growth in roots is well known to be regulated by auxin, but we found that the distribution of auxin at the apical region of the mutant and the wild-type roots was symmetric suggesting that the wavy root phenotype in rice is independent of auxin. However, the accumulation of auxin at the convex side of the curvatures, the site of L-type LR formation, suggested that auxin likely induced the formation of L-type LRs. This was supported by the need of a high amount of exogenous auxin to induce the formation of L-type LRs. These results suggest that the MNU-induced weg1 mutated gene regulates the auxin-independent parental root elongation that controls the number of likely auxin-induced L-type LRs, thus reflecting its importance in improving rice root architecture.
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Affiliation(s)
- Nonawin Lucob-Agustin
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Tsubasa Kawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Misuzu Takahashi-Nosaka
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Cornelius M Wainaina
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Tomomi Hasegawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Mayuko Inari-Ikeda
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Moeko Sato
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- PREST, JST, Kawaguchi, Saitama, 332-0012, Japan
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40
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Thabet SG, Moursi YS, Karam MA, Börner A, Alqudah AM. Natural Variation Uncovers Candidate Genes for Barley Spikelet Number and Grain Yield under Drought Stress. Genes (Basel) 2020; 11:genes11050533. [PMID: 32403266 PMCID: PMC7290517 DOI: 10.3390/genes11050533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 01/01/2023] Open
Abstract
Drought stress can occur at any growth stage and can affect crop productivity, which can result in large yield losses all over the world. In this respect, understanding the genetic architecture of agronomic traits under drought stress is essential for increasing crop yield potential and harvest. Barley is considered the most abiotic stress-tolerant cereal, particularly with respect to drought. In the present study, worldwide spring barley accessions were exposed to drought stress beginning from the early reproductive stage with 35% field capacity under field conditions. Drought stress had significantly reduced the agronomic and yield-related traits such as spike length, awn length, spikelet per spike, grains per spike and thousand kernel weight. To unravel the genetic factors underlying drought tolerance at the early reproductive stage, genome-wide association scan (GWAS) was performed using 121 spring barley accessions and a 9K single nucleotide polymorphisms (SNPs) chip. A total number of 101 significant SNPs, distributed over all seven barley chromosomes, were found to be highly associated with the studied traits, of which five genomic regions were associated with candidate genes at chromosomes 2 and 3. On chromosome 2H, the region between 6469300693-647258342 bp includes two candidate drought-specific genes (HORVU2Hr1G091030 and HORVU2Hr1G091170), which are highly associated with spikelet and final grain number per spike under drought stress conditions. Interestingly, the gene expression profile shows that the candidate genes were highly expressed in spikelet, grain, spike and leaf organs, demonstrating their pivotal role in drought tolerance. To the best of our knowledge, we reported the first detailed study that used GWAS with bioinformatic analyses to define the causative alleles and putative candidate genes underlying grain yield-related traits under field drought conditions in diverse barley germplasm. The identified alleles and candidate genes represent valuable resources for future functional characterization towards the enhancement of barley cultivars for drought tolerance.
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Affiliation(s)
- Samar G. Thabet
- Department of Botany, Faculty of Science, University of Fayoum, Fayoum 63514, Egypt; (S.G.T.); (Y.S.M.); (M.A.K.)
| | - Yasser S. Moursi
- Department of Botany, Faculty of Science, University of Fayoum, Fayoum 63514, Egypt; (S.G.T.); (Y.S.M.); (M.A.K.)
| | - Mohamed A. Karam
- Department of Botany, Faculty of Science, University of Fayoum, Fayoum 63514, Egypt; (S.G.T.); (Y.S.M.); (M.A.K.)
| | - Andreas Börner
- Research Group Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland OT Gatersleben, Germany;
| | - Ahmad M. Alqudah
- Research Group Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Seeland OT Gatersleben, Germany;
- Correspondence: or
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41
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Waidmann S, Sarkel E, Kleine-Vehn J. Same same, but different: growth responses of primary and lateral roots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2397-2411. [PMID: 31956903 PMCID: PMC7178446 DOI: 10.1093/jxb/eraa027] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.
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Affiliation(s)
- Sascha Waidmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Elizabeth Sarkel
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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42
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Moisseyev G, Park K, Cui A, Freitas D, Rajagopal D, Konda AR, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama EN, Cahoon EB, Zhang C. RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5851117. [PMID: 32500918 PMCID: PMC7273057 DOI: 10.1093/database/baaa038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/02/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Root-associated genes play an important role in plants. Despite the fact that there have been studies on root biology, information on genes that are specifically expressed or upregulated in roots is poorly collected. There exist very few databases dedicated to genes and promoters associated with root biology, preventing effective root-related studies. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and constructed a comprehensive online database of these genes and their promoter sequences. This database creates a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.
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Affiliation(s)
- Gleb Moisseyev
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kiyoul Park
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Cui
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Daniel Freitas
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Divith Rajagopal
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | | | - Mackenzie Mcham
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
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43
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Correa J, Postma JA, Watt M, Wojciechowski T. Soil compaction and the architectural plasticity of root systems. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6019-6034. [PMID: 31504740 PMCID: PMC6859514 DOI: 10.1093/jxb/erz383] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/15/2019] [Indexed: 05/18/2023]
Abstract
Soil compaction is a serious global problem, and is a major cause of inadequate rooting and poor yield in crops around the world. Root system architecture (RSA) describes the spatial arrangement of root components within the soil and determines the plant's exploration of the soil. Soil strength restricts root growth and may slow down root system development. RSA plasticity may have an adaptive value, providing environmental tolerance to soil compaction. However, it is challenging to distinguish developmental retardation (apparent plasticity) or responses to severe stress from those root architectural changes that may provide an actual environmental tolerance (adaptive plasticity). In this review, we outline the consequences of soil compaction on the rooting environment and extensively review the various root responses reported in the literature. Finally, we discuss which responses enhance root exploration capabilities in tolerant genotypes, and to what extent these responses might be useful for breeding. We conclude that RSA plasticity in response to soil compaction is complex and can be targeted in breeding to increase the performance of crops under specific agronomical conditions.
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Affiliation(s)
- José Correa
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, Jülich,Germany
| | - Johannes A Postma
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, Jülich,Germany
| | - Michelle Watt
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, Jülich,Germany
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44
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Verma H, Borah JL, Sarma RN. Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers. Sci Rep 2019; 9:16513. [PMID: 31712622 PMCID: PMC6848176 DOI: 10.1038/s41598-019-52884-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/23/2019] [Indexed: 11/16/2022] Open
Abstract
The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.
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Affiliation(s)
- H Verma
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India.
| | - J L Borah
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - R N Sarma
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India.
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45
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Zheng X, Wen X, Qiao L, Zhao J, Zhang X, Li X, Zhang S, Yang Z, Chang Z, Chen J, Zheng J. A novel QTL QTrl.saw-2D.2 associated with the total root length identified by linkage and association analyses in wheat (Triticum aestivum L.). PLANTA 2019; 250:129-143. [PMID: 30944981 DOI: 10.1007/s00425-019-03154-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
In wheat, a QTL QTrl.saw-2D.2 associated with the total root length was identified, presumably containing genes closely related to root development. A mapping population of 184 recombinant inbred lines derived from the cross SY95-71 × CH7034 was used to map QTL for seedling root characteristics in hydroponic culture (HC) and in soil-filled pot (SP) methods. Four traits, including maximum root length (MRL), root number (RN), total length (TRL), and root diameter (RD) were measured and used in QTL analyses. A total of 33 QTL for the four root traits were detected, 17 QTLs for TRL, six for RN, seven for MRL, and three for RD. Seven QTL were detected in both HC and SP methods, which explained 7-18% phenotypic variation. One QTL QTrl.saw-2D.2 detected in both HC and SP methods was also validated in another population comprised of 215 diverse lines. This QTL is a novel QTL that explained the highest phenotypic variation 18% in all QTL identified in the present study. Based on candidate gene and comparative genomics analyses, the QTL QTrl.saw-2D.2 may contain genes closely related to root development in wheat (Triticum aestivum L.). The two candidate genes were proposed to explore in future studies.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China
| | - Xiaojie Wen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China
| | - Xiaojun Zhang
- The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Xin Li
- The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Shuwei Zhang
- The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Zujun Yang
- The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Zhijian Chang
- The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA.
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen, China.
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46
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Climate change and abiotic stress mechanisms in plants. Emerg Top Life Sci 2019; 3:165-181. [DOI: 10.1042/etls20180105] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
Abstract
Predicted global climatic change will perturb the productivity of our most valuable crops as well as detrimentally impact ecological fitness. The most important aspects of climate change with respect to these effects relate to water availability and heat stress. Over multiple decades, the plant research community has amassed a highly comprehensive understanding of the physiological mechanisms that facilitate the maintenance of productivity in response to drought, flooding, and heat stress. Consequently, the foundations necessary to begin the development of elite crop varieties that are primed for climate change are in place. To meet the food and fuel security concerns of a growing population, it is vital that biotechnological and breeding efforts to harness these mechanisms are accelerated in the coming decade. Despite this, those concerned with crop improvement must approach such efforts with caution and ensure that potentially harnessed mechanisms are viable under the context of a dynamically changing environment.
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47
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Alahmad S, El Hassouni K, Bassi FM, Dinglasan E, Youssef C, Quarry G, Aksoy A, Mazzucotelli E, Juhász A, Able JA, Christopher J, Voss-Fels KP, Hickey LT. A Major Root Architecture QTL Responding to Water Limitation in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:436. [PMID: 31024600 PMCID: PMC6468307 DOI: 10.3389/fpls.2019.00436] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r 2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.
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Affiliation(s)
- Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Khaoula El Hassouni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chvan Youssef
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Georgia Quarry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alpaslan Aksoy
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | | | - Angéla Juhász
- School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Jason A. Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA, Australia
| | - Jack Christopher
- Leslie Research Facility, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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48
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Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements. PLoS One 2019; 14:e0214145. [PMID: 30947257 PMCID: PMC6448822 DOI: 10.1371/journal.pone.0214145] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Root growth angle (RGA) in response to gravity controlled by auxin is a pertinent target trait for obtainment of higher yield in cereals. But molecular basis of this root architecture trait remain obscure in wheat and barley. We selected four cultivars two each for wheat and barley to unveil the molecular genetic mechanism of Deeper Rooting 1-like gene which controls RGA in rice leading to higher yield under drought imposition. Morphological analyses revealed a deeper and vertically oriented root growth in “NARC 2009” variety of wheat than “Galaxy” and two other barley cultivars “Scarlet” and “ISR42-8”. Three new homoeologs designated as TaANDRO1-like, TaBNDRO1-like and TaDNDRO1-like corresponding to A, B and D genomes of wheat could be isolated from “NARC 2009”. Due to frameshift and intronization/exonization events the gene structures of these paralogs exhibit variations in size. DRO1-like genes with five distinct domains prevail in diverse plant phyla from mosses to angiosperms but in lower plants their differentiation from LAZY, NGR and TAC1 (root and shoot angle genes) is enigmatic. Instead of IGT as denominator motif of this family, a new C-terminus motif WxxTD in the V-domain is proposed as family specific motif. The EAR-like motif IVLEM at the C-terminus of the TaADRO1-like and TaDDRO1-like that diverged to KLHTLIPNK in TaBDRO1-like and HvDRO1-like is the hallmark of these proteins. Split-YFP and yeast two hybrid assays complemented the interaction of TaDRO1-like with TOPLESS—a repressor of auxin regulated root promoting genes in plants—through IVLEM/KLHTLIPNK motif. Quantitative RT-PCR revealed abundance of DRO1-like RNA in root tips and spikelets while transcript signals were barely detectable in shoot and leaf tissues. Interestingly, wheat exhibited stronger expression of TaBDRO1-like than barley (HvDRO1-like), but TaBDRO1-like was the least expressing among three paralogs. The underlying cause of this expression divergence seems to be the presence of AuxRE motif TGTCTC and core TGTC with a coupling AuxRE-like motif ATTTTCTT proximal to the transcriptional start site in TaBDRO1-like and HvDRO1-like promoters. This is evident from binding of ARF1 to TGTCTC and TGTC motifs of TaBDRO1-like as revealed by yeast one-hybrid assay. Thus, evolution of DRO1-like wheat homoeologs might incorporate the C-terminus mutations as well as gain and loss of AuxREs and other cis-regulatory elements during expression divergence. Since root architecture is an important target trait for wheat crop improvement, therefore DRO1-like genes have potential applications in plant breeding for enhancement of plant productivity by the use of modern genome editing approaches.
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49
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Zhu Y, Weiner J, Yu M, Li F. Evolutionary agroecology: Trends in root architecture during wheat breeding. Evol Appl 2019; 12:733-743. [PMID: 30976306 PMCID: PMC6439874 DOI: 10.1111/eva.12749] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/16/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022] Open
Abstract
Root system characteristics determine soil space exploration and resource acquisition, and these characteristics include competitive traits that increase individual fitness but reduce population performance. We hypothesize that crop breeding for increased yield is often a form of "group selection" that reduces such "selfish" traits to increase population yield. To study trends in root architecture resulting from plant breeding and test the hypothesis that increased yields result in part from group selection on root traits, we investigated root growth and branching behavior in a historical sequence of wheat (Triticum aestivum) cultivars that have been widely grown in northwestern China. Plants were grown in gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resource levels for fractal analysis of root system architecture. Yield in field was evaluated at standard and low planting densities. Newer cultivars produced higher yields than older ones only at the higher sowing density, showing that increased yield results from changes in competitive behavior. Seminal root number and growth angles were negatively correlated with yield, while primary seminal root length was positively correlated with yield. Roots of higher-yielding modern varieties were simpler and less branched, grew deeper but spread less laterally than modern varieties. The fractal dimension of root branching was negatively correlated with the yield of cultivars at all resource levels. Root:shoot ratio was negatively correlated with yield under high soil resource levels. The results are consistent with the hypothesis that the success of wheat breeding for higher yields over past 100 years in northwestern China has been in part due to unconscious group selection on root traits, resulting in smaller, less branched, and deeper roots, suggesting a direction for further increases in crop yield in the future.
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Affiliation(s)
- Yong‐He Zhu
- State Key Laboratory of Grassland Agro‐ecosystems, Institute of Arid Agroecology, School of Life SciencesLanzhou UniversityLanzhouGansu ProvinceChina
| | - Jacob Weiner
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Ming‐Xi Yu
- State Key Laboratory of Grassland Agro‐ecosystems, Institute of Arid Agroecology, School of Life SciencesLanzhou UniversityLanzhouGansu ProvinceChina
| | - Feng‐Min Li
- State Key Laboratory of Grassland Agro‐ecosystems, Institute of Arid Agroecology, School of Life SciencesLanzhou UniversityLanzhouGansu ProvinceChina
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50
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Sial TA, Liu J, Zhao Y, Khan MN, Lan Z, Zhang J, Kumbhar F, Akhtar K, Rajpar I. Co-Application of Milk Tea Waste and NPK Fertilizers to Improve Sandy Soil Biochemical Properties and Wheat Growth. Molecules 2019; 24:E423. [PMID: 30682802 PMCID: PMC6384766 DOI: 10.3390/molecules24030423] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 11/20/2022] Open
Abstract
Desert soil is one of the most severe conditions which negatively affect the environment and crop growth production in arid land. The application of organic amendments with inorganic fertilizers is an economically viable and environmentally comprehensive method to develop sustainable agriculture. The aim of this study was to assess whether milk tea waste (TW) amendment combined with chemical fertilizer (F) application can be used to improve the biochemical properties of sandy soil and wheat growth. The treatments included control without amendment (T1), chemical fertilizers (T2), TW 2.5% + F (T3), TW 5% + F (T4) and TW 10% + F (T5). The results showed that the highest chlorophyll (a and b) and carotenoids, shoot and root dry biomass, and leaf area index (LAI) were significantly (p < 0.05) improved with all amendment treatments. However, the highest root total length, root surface area, root volume and diameter were recorded for T4 among all treatments. The greater uptake of N, P, and K contents for T4 increased for the shoot by 68.9, 58.3, and 57.1%, and for the root by 65.7, 34.3, and 47.4% compared to the control, respectively. Compared with the control, T5 treatment decreased the soil pH significantly (p < 0.05) and increased soil enzyme activities such as urease (95.2%), β-glucosidase (81.6%) and dehydrogenase (97.2%), followed by T4, T3, and T2. Our findings suggested that the integrated use of milk tea waste and chemical fertilizers is a suitable amendment method for improving the growth and soil fertility status of sandy soils.
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Affiliation(s)
- Tanveer Ali Sial
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
- Department of Soil Science, Sindh Agriculture University, Tandojam 70060, Pakistan.
| | - Jiao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Ying Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
- College of Resources and Environmental Engineering, Ludong University, Yantai 264025, China.
| | - Muhammad Numan Khan
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Zhilong Lan
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Jianguo Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Farhana Kumbhar
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Kashif Akhtar
- Department of Agronomy, The University of Agriculture, Peshawar 25000, Pakistan.
| | - Inayatullah Rajpar
- Department of Soil Science, Sindh Agriculture University, Tandojam 70060, Pakistan.
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