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Gao J, Qin P, Tang S, Guo L, Dai C, Wen J, Yi B, Ma C, Shen J, Fu T, Zou J, Tu J. A gain-of-function mutation in BnaIAA13 disrupts vascular tissue and lateral root development in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5592-5610. [PMID: 38824403 PMCID: PMC11427839 DOI: 10.1093/jxb/erae245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/31/2024] [Indexed: 06/03/2024]
Abstract
Rapeseed (Brassica napus) is an important oilseed crop worldwide. Plant vascular tissues are responsible for long-distance transport of water and nutrients and for providing mechanical support. The lateral roots absorb water and nutrients. The genetic basis of vascular tissue and lateral root development in rapeseed remains unknown. This study characterized an ethyl methanesulfonate-mutagenized rapeseed mutant, T16, which showed dwarf stature, reduced lateral roots, and leaf wilting. SEM observations showed that the internode cells were shortened. Observations of tissue sections revealed defects in vascular bundle development in the stems and petioles. Genetic analysis revealed that the phenotypes of T16 were controlled by a single semi-dominant nuclear gene. Map-based cloning and genetic complementarity identified BnaA03.IAA13 as the functional gene; a G-to-A mutation in the second exon changed glycine at position 79 to glutamic acid, disrupting the conserved degron motif VGWPP. Transcriptome analysis in roots and stems showed that auxin and cytokinin signaling pathways were disordered in T16. Evolutionary analysis showed that AUXIN/INDOLE-3-ACETIC ACID is conserved during plant evolution. The heterozygote of T16 showed significantly reduced plant height while maintaining other agronomic traits. Our findings provide novel insights into the regulatory mechanisms of vascular tissue and lateral root development, and offer a new germplasm resource for rapeseed breeding.
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Affiliation(s)
- Jinxiang Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Shan Tang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, Hainan, 572025, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
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2
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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Chen Z, Li X, He F, Liu B, Xu W, Chai L, Cheng X, Song L, Guo W, Hu Z, Su Z, Liu J, Xin M, Peng H, Yao Y, Sun Q, Xing J, Ni Z. Positional cloning and characterization reveal the role of TaSRN-3D and TaBSR1 in the regulation of seminal root number in wheat. THE NEW PHYTOLOGIST 2024; 242:2510-2523. [PMID: 38629267 DOI: 10.1111/nph.19740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024]
Abstract
Seminal roots play a critical role in water and nutrient absorption, particularly in the early developmental stages of wheat. However, the genes responsible for controlling SRN in wheat remain largely unknown. Genetic mapping and functional analyses identified a candidate gene (TraesCS3D01G137200, TaSRN-3D) encoding a Ser/Thr kinase glycogen synthase kinase 3 (STKc_GSK3) that regulated SRN in wheat. Additionally, experiments involving hormone treatment, nitrate absorption and protein interaction were conducted to explore the regulatory mechanism of TaSRN-3D. Results showed that the TaSRN-3D4332 allele inhibited seminal roots initiation and development, while loss-of-function mutants showed significantly higher seminal root number (SRN). Exogenous application of epi-brassinolide could increase the SRN in a HS2-allelic background. Furthermore, chlorate sensitivity and 15N uptake assays revealed that a higher number of seminal roots promoted nitrate accumulation. TaBSR1 (BIN2-related SRN Regulator 1, orthologous to OsGRF4/GL2 in rice) acts as an interactor of TaSRN-3D and promotes TaBSR1 degradation to reduce SRN. This study provides valuable insights into understanding the genetic basis and regulatory network of SRN in wheat, highlighting their roles as potential targets for root-based improvement in wheat breeding.
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Affiliation(s)
- Zhaoyan Chen
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Xuanshuang Li
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Fei He
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Bin Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Weiya Xu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Lingling Chai
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Xuejiao Cheng
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Long Song
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhenqi Su
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
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Jafari F, Wang B, Wang H, Zou J. Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:849-864. [PMID: 38131117 DOI: 10.1111/jipb.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Maize is a major staple crop widely used as food, animal feed, and raw materials in industrial production. High-density planting is a major factor contributing to the continuous increase of maize yield. However, high planting density usually triggers a shade avoidance response and causes increased plant height and ear height, resulting in lodging and yield loss. Reduced plant height and ear height, more erect leaf angle, reduced tassel branch number, earlier flowering, and strong root system architecture are five key morphological traits required for maize adaption to high-density planting. In this review, we summarize recent advances in deciphering the genetic and molecular mechanisms of maize involved in response to high-density planting. We also discuss some strategies for breeding advanced maize cultivars with superior performance under high-density planting conditions.
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Affiliation(s)
- Fereshteh Jafari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Junjie Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
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5
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Li Q, Zhang B, Liu W, Zou H. Strigolactones alleviate the toxicity of polystyrene nanoplastics (PS-NPs) in maize (Zea mays L.). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170626. [PMID: 38325482 DOI: 10.1016/j.scitotenv.2024.170626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Nanoplastics are widely used across various fields, yet their uptake can potentially exert adverse effects on plant growth and development, ultimately reducing yields. While there is growing awareness of the phytotoxicity caused by nanoplastics, our understanding of effective strategies to prevent nanoplastic accumulation in plants remains limited. This study explores the role of strigolactones (SLs) in mitigating the toxicity of polystyrene nanoplastics (PS-NPs) in Zea mays L. (maize). SLs application markedly inhibited PS-NPs accumulation in maize roots, thus enhancing the root weight, shoot weight and shoot length of maize. Physiological analysis showed that SLs application activated the activities of antioxidant defence enzymes, superoxide dismutase and catalase, to decrease the malondialdehyde content and electrolyte leakage and alleviate the accumulation of H2O2 and O2.- induced by PS-NPs in maize plants. Transcriptomic analyses revealed that SLs application induced transcriptional reprogramming by regulating the expression of genes related to MAPK, plant hormones and plant-pathogen interaction signal pathways in maize treated with PS-NPs. Notably, the expression of genes, such as ZmAUX/IAA and ZmGID1, associated with phytohormones in maize treated with PS-NPs underwent significant changes. In addition, SLs induced metabolic dynamics changes related to amino acid biosynthesis, ABC transporters, cysteine and methionine metabolism in maize treated with PS-NPs. In summary, these results strongly reveal that SLs could serve as a strategy to mitigate the accumulation and alleviate the stress of PS-NPs in maize, which appears to be a potential approach for mitigating the phytotoxicity induced by PS-NPs in maize.
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Affiliation(s)
- Qiaolu Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Binglin Zhang
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Weijuan Liu
- College of Agriculture, Yangtze University, Jingzhou 434025, China.
| | - Huawen Zou
- College of Agriculture, Yangtze University, Jingzhou 434025, China.
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6
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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7
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Zaman Z, Iqbal R, Jabbar A, Zahra N, Saleem B, Kiran A, Maqbool S, Rasheed A, Naeem MK, Khan MR. Genetic Signature Controlling Root System Architecture in Diverse Spring Wheat Germplasm. PHYSIOLOGIA PLANTARUM 2024; 176:e14183. [PMID: 38343301 DOI: 10.1111/ppl.14183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/30/2023] [Indexed: 02/15/2024]
Abstract
Roots are the main sensing organ, initiating multiple signaling pathways in response to abiotic factors, including nutrients, drought, and salt stress. A focus on improving the root system architecture is a key strategy to mitigate these stresses in wheat crop. In the present study, a diversity panel comprising indigenous landraces and historical cultivars from Pakistan was characterized for the root system architecture (RSA) and important loci were identified using a genome-wide association study (GWAS). RSA of the diversity panel was characterized 30 days after sowing in brunch tubes, and root images were taken. A high-throughput root imaging analysis using Rhizovision software was performed by setting the scale to extract the eight RSA traits and four plant biomass-related traits. GWAS identified 323 association signals for 12 root and biomass traits present on all wheat chromosomes, while the most important and reliable genetic loci (based on pleotropic loci and candidate genes) were identified on chromosomes 2A, 2B, 5A, 5D, 6A, 7B, and 7D for RSA. SNP annotation and transcriptome profiling identified nine candidate genes regulating the RSA and plant biomass traits, including ROOTLESS WITH UNDETECTABLE MERISTEM1, MYB TRANSCRIPTION FACTOR4, BRASSINOSTEROID INSENSITIVE1, SLENDER RICE1, AUXIN-RESPONSIVE FACTOR25, SCARECROW, NARROW LEAF2, PIN-FORMED1 AND PHOSPHATE TRANSCRIPTION FACTOR1. This study provided pre-breeding information for deep-rooting genotypes and associated markers that will accelerate the incorporation of such traits in breeding.
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Affiliation(s)
- Zahra Zaman
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Rubab Iqbal
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- Department of Botany, University of Agriculture, Faisalabad
| | - Abdul Jabbar
- Department of Biotechnology, Mirpur University of Science and Technology (MUST), Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Aysha Kiran
- Department of Botany, University of Agriculture, Faisalabad
| | - Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
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Li X, Wasson AP, Zwart AB, Whan A, Ryan PR, Forrest K, Hayden M, Chin S, Richards R, Delhaize E. Physical Mapping of QTLs for Root Traits in a Population of Recombinant Inbred Lines of Hexaploid Wheat. Int J Mol Sci 2023; 24:10492. [PMID: 37445670 DOI: 10.3390/ijms241310492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals.
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Affiliation(s)
- Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Anton P Wasson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | | | - Alex Whan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Peter R Ryan
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sabrina Chin
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | | | - Emmanuel Delhaize
- Australian Plant Phenomics Facility, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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9
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Ning J, Yamauchi T, Takahashi H, Omori F, Mano Y, Nakazono M. Asymmetric auxin distribution establishes a contrasting pattern of aerenchyma formation in the nodal roots of Zea nicaraguensis during gravistimulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1133009. [PMID: 37152158 PMCID: PMC10154625 DOI: 10.3389/fpls.2023.1133009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Auxin distribution is essential for determining root developmental patterns. The formation of lateral roots and constitutive aerenchyma, which is a gas space developed through cell death, is regulated by auxin in rice (Oryza sativa). However, it is unclear whether the involvement of auxin in constitutive aerenchyma formation is conserved in other species. In this study, we found that constitutive aerenchyma formation was regulated by auxin in the nodal roots of Zea nicaraguensis, a wild relative of maize (Zea mays ssp. mays) grown naturally on frequently flooded coastal plains. Subsequent gravistimulation (root rotation) experiments showed opposite patterns of aerenchyma and lateral root formation. Lateral root formation on the convex side of rotated roots is known to be stimulated by a transient increase in auxin level in the pericycle. We found that aerenchyma formation was accelerated in the cortex on the concave side of the rotated nodal roots of Z. nicaraguensis. A cortex-specific expression analysis of auxin-responsive genes suggested that the auxin level was higher on the concave side than on the convex side. These results suggest that asymmetric auxin distribution underlies the regulation of aerenchyma and lateral root formation in the nodal roots of Z. nicaraguensis. As aerenchyma reduces the respiratory cost of the roots, constitutive aerenchyma on the concave side of the nodal root may balance resource allocation, thereby contributing to the uptake of water and nutrients by newly formed lateral roots. Our study provides insights into auxin-dependent asymmetric root patterning such as that of gravistimulation and hydropatterning response.
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Affiliation(s)
- Jiayang Ning
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - Hirokazu Takahashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Fumie Omori
- Division of Feed and Livestock Research, National Agriculture and Food Research Organization (NARO) Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, Japan
| | - Yoshiro Mano
- Division of Feed and Livestock Research, National Agriculture and Food Research Organization (NARO) Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, Japan
| | - Mikio Nakazono
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- The University of Western Australia (UWA) School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
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10
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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11
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Zheng Z, Guo B, Dutta S, Roy V, Liu H, Schnable PS. The 2020 derecho revealed limited overlap between maize genes associated with root lodging and root system architecture. PLANT PHYSIOLOGY 2023:kiad194. [PMID: 36974884 DOI: 10.1093/plphys/kiad194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Roots anchor plants in soil, and the failure of anchorage (i.e., root lodging) is a major cause of crop yield loss. Anchorage is often assumed to be driven by root system architecture. We made use of a natural experiment to measure the overlap between the genetic regulation of root system architecture and anchorage. After one of the most devastating derechos ever recorded in August 2020, we phenotyped root lodging in a maize (Zea mays) diversity panel consisting of 369 genotypes grown in six environments affected by the derecho. Genome-wide association studies and transcriptome-wide association studies identified 118 candidate genes associated with root lodging. Thirty-four percent (40/118) of these were homologs of genes from Arabidopsis (Arabidopsis thaliana) that affect traits such as root morphology and lignin content, expected to affect root lodging. Finally, Gene Ontology enrichment analysis of the candidate genes and their predicted interaction partners at the transcriptional and translational levels revealed the complex regulatory networks of physiological and biochemical pathways underlying root lodging in maize. Limited overlap between genes associated with lodging resistance and root system architecture in this diversity panel suggests that anchorage depends in part on factors other than gross characteristics of root system architecture.
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Affiliation(s)
- Zihao Zheng
- Department of Agronomy, Iowa State University, Ames, IA 50011-1051, USA
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011-3650, USA
| | - Bufei Guo
- Department of Statistics, Iowa State University, Ames, IA, 50011-1090, USA
| | - Somak Dutta
- Department of Statistics, Iowa State University, Ames, IA, 50011-1090, USA
| | - Vivekananda Roy
- Department of Statistics, Iowa State University, Ames, IA, 50011-1090, USA
| | - Huyu Liu
- Department of Agronomy, Iowa State University, Ames, IA 50011-1051, USA
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011-3650, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011-1051, USA
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011-3650, USA
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12
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Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
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13
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Li L, Cheng X, Kong X, Jia P, Wang X, Zhang L, Zhang X, Zhang Y, Zhang Z, Zhang B. Comparative Transcriptomic Analysis Reveals the Negative Response Mechanism of Peanut Root Morphology and Nitrate Assimilation to Nitrogen Deficiency. PLANTS (BASEL, SWITZERLAND) 2023; 12:732. [PMID: 36840080 PMCID: PMC9960604 DOI: 10.3390/plants12040732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Root architecture plays a fundamental role in crop yield, which is sensitive to nitrogen fertilizer. Although it is well studied that nitrogen fertilizer significantly promotes peanut (Arachis hypogaea L.) growth and yield, less information was available on how its root development responds to nitrogen deficiency. In this study, the growth and development of roots were inhibited, as indicated by the significantly decreased root dry weight and length and the lateral root number, especially under 10 days of nitrogen deficiency treatment. The activities and the expression of the genes related to nitrogen assimilation enzymes including nitrate reductase, glutamine synthetase, glutamate dehydrogenase, and glutamine oxoglutarate aminotransferase and the genes encoding the nitrate transporters were significantly decreased under 10 days of nitrogen deficiency treatment, which may lead to a decrease in nitrate content, as indicated by the significantly decreased nitrogen balance index. Transcriptome sequencing revealed a total of 293 (119 up- and 174 downregulated) and 2271 (1165 up- and 1106 downregulated) differentially expressed genes (DEGs) identified after five and ten days of nitrogen deficiency treatments, respectively. Bioinformatic analysis showed that these DEGs were mainly involved in nitrate transportation and assimilation, phytohormone signal transduction, and the lignin biosynthesis pathway. Furthermore, a putative schematic diagram of nitrogen deficiency inhibiting root growth was established, which gives us a better understanding of nitrogen metabolism in peanut roots and a theoretical basis for improving nitrogen use efficiency.
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Affiliation(s)
- Lijie Li
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiangguo Cheng
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiangjun Kong
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Peipei Jia
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaohui Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lei Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaotian Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yi Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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14
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Wang K, Zhang Z, Sha X, Yu P, Li Y, Zhang D, Liu X, He G, Li Y, Wang T, Guo J, Chen J, Li C. Identification of a new QTL underlying seminal root number in a maize-teosinte population. FRONTIERS IN PLANT SCIENCE 2023; 14:1132017. [PMID: 36824192 PMCID: PMC9941338 DOI: 10.3389/fpls.2023.1132017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Seminal roots play an important role in acquisition of water and nutrients by maize seedlings. Compared with its teosinte ancestor, maize underwent a change in seminal root number (SRN). Although several key genes controlling SRN have been cloned, identification and utilization of new genes from teosinte would be useful for improving maize root architecture. In this study, a maize-teosinte BC2F6 population containing 206 individuals genotyped by resequencing was used to conduct high-resolution quantitative trait locus (QTL) mapping of SRN. A new major QTL on chromosome 7 (qSRN7) was identified. Differentially expressed genes (DEGs) based on RNA-Seq were identified between two inbred lines with no SRN and multiple SRN at two periods of seminal roots primordia formation. A total of 116 DEGs detected in at least one period were identified within the qSRN7 interval. Three DEGs (Zm00001d021572, Zm00001d021579 and Zm00001d021861) associated with SRN were identified through regional association mapping. When compared with reported domestication-related selective sweeps, Zm00001d021572 was selected during maize domestication. Our findings provide important insights into the genetic basis of SRN and identify a promising candidate gene for further studies on SRN.
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Affiliation(s)
- Kailiang Wang
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Zhen Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiaoQian Sha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Yu
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanhua He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Guo
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Jiafa Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Baer M, Taramino G, Multani D, Sakai H, Jiao S, Fengler K, Hochholdinger F. Maize lateral rootless 1 encodes a homolog of the DCAF protein subunit of the CUL4-based E3 ubiquitin ligase complex. THE NEW PHYTOLOGIST 2023; 237:1204-1214. [PMID: 36345913 DOI: 10.1111/nph.18599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
In maize (Zea mays L.), lateral roots are formed in the differentiation zone of all root types in a multi-step process. The maize mutant lateral rootless 1 (lrt1) is defective in lateral root formation in primary and seminal roots but not in shoot-borne roots. We cloned the lrt1 gene by mapping in combination with BSA-seq and subsequent validation via CRISPR/Cas9. The lrt1 gene encodes a 209 kDa homolog of the DDB1-CUL4-ASSOCIATED FACTOR (DCAF) subunit of the CUL4-based E3 ubiquitin ligase (CRL4) complex localized in the nucleus. DDB1-CUL4-ASSOCIATED FACTOR proteins are encoded by an evolutionary old gene family already present in nonseed plants. They are adaptors that bind substrate proteins and promote their ubiquitylation, thus typically marking them for subsequent degradation in the 26S proteasome. Gene expression studies demonstrated that lrt1 transcripts are expressed preferentially in the meristematic zone of all root types of maize. Downregulation of the rum1 gene in lrt1 mutants suggests that lrt1 acts upstream of the lateral root regulator rum1. Our results demonstrate that DCAF proteins play a key role in root-type-specific lateral root formation in maize. Together with its role in nitrogen acquisition in nitrogen-poor soil, lrt1 could be a promising target for maize improvement.
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Affiliation(s)
- Marcel Baer
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | | | | | | | | | | | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
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16
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Ren W, Zhao L, Liang J, Wang L, Chen L, Li P, Liu Z, Li X, Zhang Z, Li J, He K, Zhao Z, Ali F, Mi G, Yan J, Zhang F, Chen F, Yuan L, Pan Q. Genome-wide dissection of changes in maize root system architecture during modern breeding. NATURE PLANTS 2022; 8:1408-1422. [PMID: 36396706 DOI: 10.1038/s41477-022-01274-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 10/12/2022] [Indexed: 05/12/2023]
Abstract
Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.
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Affiliation(s)
- Wei Ren
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Longfei Zhao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jiaxing Liang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Lifeng Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Limei Chen
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Pengcheng Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhigang Liu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Xiaojie Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhihai Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jieping Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Kunhui He
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Zheng Zhao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Farhan Ali
- Cereal Crops Research Institute, Pirsabak, Nowshera, Pakistan
| | - Guohua Mi
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fusuo Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Fanjun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
| | - Lixing Yuan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
| | - Qingchun Pan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
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17
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Ma H, Li P, Xiao N, Xia T. Poly-γ-glutamic acid promoted maize root development by affecting auxin signaling pathway and the abundance and diversity of rhizosphere microbial community. BMC PLANT BIOLOGY 2022; 22:521. [PMID: 36352394 PMCID: PMC9647955 DOI: 10.1186/s12870-022-03908-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The root systems of higher plants play an important role in plant growth and development. In our present study, it was found that poly-γ-glutamic acid (γ-PGA), an environmentally friendly biomacromolecule, significantly improved root development in maize. RESULTS After treatment with γ-PGA for 7 days, the fresh weight of maize roots was significantly increased and the differences between γ-PGA treated group and control group were mainly caused by the number (higher by 71.87% compared to the control) and length of lateral roots. RNAseq and RT-PCR analyses showed that γ-PGA treatment upregulated the expression of genes related to the synthesis of auxins and auxin signal in maize roots. In addition, γ-PGA promoted the accumulation of plant growth-promoting bacteria, such as Azospirillum, Azohydromonas, Ramlibacter, and Sphingobium (Proteobacteria), Streptomyces (Actinobacteria), Parasegetibacter (Bacteroidetes), and Gemmatimonas (Gemmatimonadetes) in rhizosphere soil and the secretion of auxins. The results of this study deepened our understanding of the effects and mechanism of γ-PGA on maize root development, and as well as highlighted the possibility of using γ-PGA to improve crop growth and soil environment. CONCLUSIONS γ-PGA promotes early growth and development of maize roots by inducing the secretion and accumulation of auxin in roots and in rhizosphere soil, and increasing the abundance of plant growth promoting bacteria.
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Affiliation(s)
- Haizhen Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, PR China
| | - Panpan Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, PR China
| | - Ning Xiao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, PR China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China.
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, PR China.
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18
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McReynolds MR, Dash L, Montes C, Draves MA, Lang MG, Walley JW, Kelley DR. Temporal and spatial auxin responsive networks in maize primary roots. QUANTITATIVE PLANT BIOLOGY 2022; 3:e21. [PMID: 37077976 PMCID: PMC10095944 DOI: 10.1017/qpb.2022.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 05/03/2023]
Abstract
Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin-regulated networks underlying maize root development, we have characterized auxin-responsive transcription across two time points (30 and 120 min) and four regions of the primary root: the meristematic zone, elongation zone, cortex and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin-regulated genes are region unique and are predominantly observed in differentiated tissues compared with the root meristem. Auxin gene regulatory networks were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin-Response Factor subnetworks were generated to identify target genes that exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.
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Affiliation(s)
- Maxwell R. McReynolds
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Linkan Dash
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Melissa A. Draves
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Michelle G. Lang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
- Corteva Agriscience, Johnston, Iowa50131, USA
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Dior R. Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
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19
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Abstract
Despite their importance in supplying nutrients, root traits related to maize domestication are scarce. We used laser ablation tomography to characterize the root architecture and anatomy of 5,300-y-old maize specimens recovered from San Marcos (Tehuacán, Mexico), revealing exquisite preservation of their cellular organization. Outer cortical cells contained thick and lignified walls typical of extant maize adapted to hard soils. By contrast, the absence of seminal roots is only found in the maize ancestor, teosinte. Two genes important for seminal root development had mutations that could relate to their absence. Our results indicate that some traits related to drought adaptation were not fully present in the earliest maize from Tehuacán, providing clues to conditions prevailing during early maize cultivation. Efforts to understand the phenotypic transition that gave rise to maize from teosinte have mainly focused on the analysis of aerial organs, with little insights into possible domestication traits affecting the root system. Archeological excavations in San Marcos cave (Tehuacán, Mexico) yielded two well-preserved 5,300 to 4,970 calibrated y B.P. specimens (SM3 and SM11) corresponding to root stalks composed of at least five nodes with multiple nodal roots and, in case, a complete embryonic root system. To characterize in detail their architecture and anatomy, we used laser ablation tomography to reconstruct a three-dimensional segment of their nodal roots and a scutellar node, revealing exquisite preservation of the inner tissue and cell organization and providing reliable morphometric parameters for cellular characteristics of the stele and cortex. Whereas SM3 showed multiple cortical sclerenchyma typical of extant maize, the scutellar node of the SM11 embryonic root system completely lacked seminal roots, an attribute found in extant teosinte and in two specific maize mutants: root with undetectable meristem1 (rum1) and rootless concerning crown and seminal roots (rtcs). Ancient DNA sequences of SM10—a third San Marcos specimen of equivalent age to SM3 and SM11—revealed the presence of mutations in the transcribed sequence of both genes, offering the possibility for some of these mutations to be involved in the lack of seminal roots of the ancient specimens. Our results indicate that the root system of the earliest maize from Tehuacán resembled teosinte in traits important for maize drought adaptation.
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20
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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21
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Xu J, Wang X, Zhu H, Yu F. Identification and Analysis of Zinc Efficiency-Associated Loci in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:739282. [PMID: 34868123 PMCID: PMC8634756 DOI: 10.3389/fpls.2021.739282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Zinc (Zn) deficiency, a globally predominant micronutrient disorder in crops and humans, reduces crop yields and adversely impacts human health. Despite numerous studies on the physiological mechanisms underlying Zn deficiency tolerance, its genetic basis of molecular mechanism is still poorly understood. Thus, the Zn efficiency of 20 maize inbred lines was evaluated, and a quantitative trait locus (QTL) analysis was performed in the recombination inbred line population derived from the most Zn-efficient (Ye478) and Zn-inefficient inbred line (Wu312) to identify the candidate genes associated with Zn deficiency tolerance. On this basis, we analyzed the expression of ZmZIP1-ZmZIP8. Thirteen QTLs for the traits associated with Zn deficiency tolerance were detected, explaining 7.6-63.5% of the phenotypic variation. The genes responsible for Zn uptake and transport across membranes (ZmZIP3, ZmHMA3, ZmHMA4) were identified, which probably form a sophisticated network to regulate the uptake, translocation, and redistribution of Zn. Additionally, we identified the genes involved in the indole-3-acetic acid (IAA) biosynthesis (ZmIGPS) and auxin-dependent gene regulation (ZmIAA). Notably, a high upregulation of ZmZIP3 was found in the Zn-deficient root of Ye478, but not in that of Wu312. Additionally, ZmZIP4, ZmZIP5, and ZmZIP7 were up-regulated in the Zn-deficient roots of Ye478 and Wu312. Our findings provide a new insight into the genetic basis of Zn deficiency tolerance.
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Affiliation(s)
| | | | | | - Futong Yu
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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22
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Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice. Int J Mol Sci 2021; 22:ijms22189868. [PMID: 34576034 PMCID: PMC8465104 DOI: 10.3390/ijms22189868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Crown roots are essential for plants to obtain water and nutrients, perceive environmental changes, and synthesize plant hormones. In this study, we identified and characterized short crown root 8 (scr8), which exhibited a defective phenotype of crown root and vegetative development. Temperature treatment showed that scr8 was sensitive to temperature and that the mutant phenotypes were rescued when grown under low temperature condition (20 °C). Histological and EdU staining analysis showed that the crown root formation was hampered and that the root meristem activity was decreased in scr8. With map-based cloning strategy, the SCR8 gene was fine-mapped to an interval of 126.4 kb on chromosome 8. Sequencing analysis revealed that the sequence variations were only found in LOC_Os08g14850, which encodes a CC-NBS-LRR protein. Expression and inoculation test analysis showed that the expression level of LOC_Os08g14850 was significantly decreased under low temperature (20 °C) and that the resistance to Xanthomonas oryzae pv. Oryzae (Xoo) was enhanced in scr8. These results indicated that LOC_Os08g14850 may be the candidate of SCR8 and that its mutation activated the plant defense response, resulting in a crown root growth defect.
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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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24
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Moussa AA, Mandozai A, Jin Y, Qu J, Zhang Q, Zhao H, Anwari G, Khalifa MAS, Lamboro A, Noman M, Bakasso Y, Zhang M, Guan S, Wang P. Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages. BMC Genomics 2021; 22:558. [PMID: 34284723 PMCID: PMC8290564 DOI: 10.1186/s12864-021-07874-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/05/2021] [Indexed: 01/26/2023] Open
Abstract
Background Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study. Results Using inclusive composite interval mapping, 8 QTLs accounting for 6.44–8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDWv3-1-1 and qRDW/SDWv3-1-1), 2 (qRBNv1-2-1), 4 (qSUAv1-4-1, qSUAv2-4-1, and qROVv2-4-1), and 10 (qTRLv1-10-1, qRBNv1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages. Conclusions This study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07874-x.
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Affiliation(s)
- Abdourazak Alio Moussa
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China.
| | - Ajmal Mandozai
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Yukun Jin
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Jing Qu
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Qi Zhang
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - He Zhao
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Gulaqa Anwari
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | | | - Abraham Lamboro
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Muhammad Noman
- College of Life Sciences, Jilin Agricultural University, Jilin, 130118, Changchun, China
| | - Yacoubou Bakasso
- Biology Department, Faculty of Sciences and Techniques, Abdou Moumouni University of Niamey, 10662, Niamey, Niger
| | - Mo Zhang
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Shuyan Guan
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Piwu Wang
- College of Agronomy, Plant Biotechnology Center, Jilin Agricultural University, 130118, Changchun, Jilin, China.
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25
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Yue K, Lingling L, Xie J, Coulter JA, Luo Z. Synthesis and regulation of auxin and abscisic acid in maize. PLANT SIGNALING & BEHAVIOR 2021; 16:1891756. [PMID: 34057034 PMCID: PMC8205056 DOI: 10.1080/15592324.2021.1891756] [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] [Indexed: 05/12/2023]
Abstract
Indole-3-acetic acid (IAA), the primary auxin in higher plants, and abscisic acid (ABA) play crucial roles in the ability of maize (Zea mays L.) to acclimatize to various environments by mediating growth, development, defense and nutrient allocation. Although understanding the biochemical reactions for IAA and ABA biosynthesis and signal transduction has progressed, the mechanisms by which auxin and ABA are synthesized and transduced in maize have not been fully elucidated to date. The synthesis and signal transduction pathway of IAA and ABA in maize can be analyzed using an existing model. This article focuses on the research progress toward understanding the synthesis and signaling pathways of IAA and ABA, as well as IAA and ABA regulation of maize growth, providing insight for future development and the significance of IAA and ABA for maize improvement.
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Affiliation(s)
- Kai Yue
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Li Lingling
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- CONTACT Lingling Li College of Agronomy/Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Junhong Xie
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jeffrey A. Coulter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Zhuzhu Luo
- College of Resource and Environment, Gansu Agricultural University, Lanzhou, China
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26
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Ober ES, Alahmad S, Cockram J, Forestan C, Hickey LT, Kant J, Maccaferri M, Marr E, Milner M, Pinto F, Rambla C, Reynolds M, Salvi S, Sciara G, Snowdon RJ, Thomelin P, Tuberosa R, Uauy C, Voss-Fels KP, Wallington E, Watt M. Wheat root systems as a breeding target for climate resilience. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1645-1662. [PMID: 33900415 PMCID: PMC8206059 DOI: 10.1007/s00122-021-03819-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
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Affiliation(s)
- Eric S Ober
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Cristian Forestan
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Josefine Kant
- Forschungszentrum Jülich, IBG-2, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Emily Marr
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Charlotte Rambla
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Kai P Voss-Fels
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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27
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Alaguero-Cordovilla A, Gran-Gómez FJ, Jadczak P, Mhimdi M, Ibáñez S, Bres C, Just D, Rothan C, Pérez-Pérez JM. A quick protocol for the identification and characterization of early growth mutants in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110673. [PMID: 33218638 DOI: 10.1016/j.plantsci.2020.110673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Root system architecture (RSA) manipulation may improve water and nutrient capture by plants under normal and extreme climate conditions. With the aim of initiating the genetic dissection of RSA in tomato, we established a defined ontology that allowed the curated annotation of the observed phenotypes on 12 traits at four consecutive growth stages. In addition, we established a quick approach for the molecular identification of the mutations associated with the trait-of-interest by using a whole-genome sequencing approach that does not require the building of an additional mapping population. As a proof-of-concept, we screened 4543 seedlings from 300 tomato M3 lines (Solanum lycopersicum L. cv. Micro-Tom) generated by chemical mutagenesis with ethyl methanesulfonate. We studied the growth and early development of both the root system (primary and lateral roots) and the aerial part of the seedlings as well as the wound-induced adventitious roots emerging from the hypocotyl. We identified 659 individuals (belonging to 203 M3 lines) whose early seedling and RSA phenotypes differed from those of their reference background. We confirmed the genetic segregation of the mutant phenotypes affecting primary root length, seedling viability and early RSA in 31 M4 families derived from 15 M3 lines selected in our screen. Finally, we identified a missense mutation in the SlCESA3 gene causing a seedling-lethal phenotype with short roots. Our results validated the experimental approach used for the identification of tomato mutants during early growth, which will allow the molecular identification of the genes involved.
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Affiliation(s)
| | | | - Paula Jadczak
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain.
| | - Mariem Mhimdi
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain.
| | - Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain.
| | - Cécile Bres
- INRAE and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Daniel Just
- INRAE and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
| | - Christophe Rothan
- INRAE and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France.
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28
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Ma L, Qing C, Frei U, Shen Y, Lübberstedt T. Association mapping for root system architecture traits under two nitrogen conditions in germplasm enhancement of maize doubled haploid lines. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Guo J, Li C, Zhang X, Li Y, Zhang D, Shi Y, Song Y, Li Y, Yang D, Wang T. Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110380. [PMID: 32005385 DOI: 10.1016/j.plantsci.2019.110380] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Water deficits are a major constraint on maize growth and yield, and deep roots are one of the major mechanisms of drought tolerance. In this study, four root and shoot traits were evaluated within an association panel consisting of 209 diverse maize accessions under well-watered (WW) and water-stressed (WS) conditions. A significant positive correlation was observed between seminal root length (SRL) under WS treatment and the drought tolerance index (DI) of maize seedlings. The transcriptome profiles of maize seminal roots were compared between four drought-tolerant lines and four drought-sensitive lines under both water conditions to identify genes associated with the drought stress response. After drought stress, 343 and 177 common differentially expressed genes (DEGs) were identified in the drought-tolerant group and drought-sensitive group, respectively. In parallel, a coexpression network underlying SRL was constructed on the basis of transcriptome data, and 10 hub genes involved in two significant associated modules were identified. Additionally, a genome-wide association study (GWAS) of the SRL revealed 62 loci for the two water treatments. By integrating the results of the GWAS, the common DEGs and the coexpression network analysis, 7 promising candidate genes were prioritized for further research. Together, our results provide a foundation for the enhanced understanding of seminal root changes in response to drought stress in maize.
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Affiliation(s)
- Jian Guo
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | | | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Deguang Yang
- College of Agriculture, Northeast Agricultural University, Harbin, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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30
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Shorinola O, Kaye R, Golan G, Peleg Z, Kepinski S, Uauy C. Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform. G3 (BETHESDA, MD.) 2019; 9:2799-2809. [PMID: 31352407 PMCID: PMC6723138 DOI: 10.1534/g3.119.400537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022]
Abstract
Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.
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Affiliation(s)
- Oluwaseyi Shorinola
- Bioscience Eastern and Central Africa - International Livestock Research Institute, Nairobi, PO Box 30709, Kenya
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ryan Kaye
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, and
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Matthes MS, Best NB, Robil JM, Malcomber S, Gallavotti A, McSteen P. Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling. MOLECULAR PLANT 2019; 12:298-320. [PMID: 30590136 DOI: 10.1016/j.molp.2018.12.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/02/2018] [Accepted: 12/16/2018] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin has been shown to be of pivotal importance in growth and development of land plants. The underlying molecular players involved in auxin biosynthesis, transport, and signaling are quite well understood in Arabidopsis. However, functional characterizations of auxin-related genes in economically important crops, specifically maize and rice, are still limited. In this article, we comprehensively review recent functional studies on auxin-related genes in both maize and rice, compared with what is known in Arabidopsis, and highlight conservation and diversification of their functions. Our analysis is illustrated by phylogenetic analysis and publicly available gene expression data for each gene family, which will aid in the identification of auxin-related genes for future research. Current challenges and future directions for auxin research in maize and rice are discussed. Developments in gene editing techniques provide powerful tools for overcoming the issue of redundancy in these gene families and will undoubtedly advance auxin research in crops.
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Affiliation(s)
- Michaela Sylvia Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Norman Bradley Best
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Janlo M Robil
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA.
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Li P, Pan T, Wang H, Wei J, Chen M, Hu X, Zhao Y, Yang X, Yin S, Xu Y, Fang H, Liu J, Xu C, Yang Z. Natural variation of ZmHKT1 affects root morphology in maize at the seedling stage. PLANTA 2019; 249:879-889. [PMID: 30460404 DOI: 10.1007/s00425-018-3043-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/12/2018] [Indexed: 05/25/2023]
Abstract
Eight variants in ZmHKT1 promoter were significantly associated with root diameter, four haplotypes based on these significant variants were found, and Hap2 has the largest root diameter. Roots play an important role in uptake of water, nutrients and plant anchorage. Identification of gene and corresponding SNPs associated with root traits would enable develop maize lines with better root traits that might help to improve capacity for absorbing nutrients and water acquisition. The genomic sequences of a salt tolerance gene ZmHKT1 was resequenced in 349 maize inbred lines, and the association between nucleotide polymorphisms and seedling root traits was detected. A total of 269 variants in ZmHKT1 were identified, including 226 single nucleotide polymorphisms and 43 insertions and deletions. The gene displayed high level of nucleotide diversity, especially in non-genic regions. A total of 19 variations in untranslated region of ZmHKT1 were found to be associated with six seedling traits. Eight variants in promoter region were significantly associated with average root diameter (ARD), four haplotypes were found based on these significant variants, and Hap2 has the largest ARD. Two SNPs in high-linkage disequilibrium (SNP-415 and SNP 2169) with pleiotropic effects were significantly associated with plant height, root surface area, root volume, and shoot dry weight. This result revealed that ZmHKT1 was an important contributor to the phenotypic variations of seedling root traits in maize, these significant variants could use to develop functional markers to improve root traits.
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Affiliation(s)
- Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Ting Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Houmiao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jie Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Minjun Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaohong Hu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyi Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Shuangyi Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Huimin Fang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
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33
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Lu C, Chen MX, Liu R, Zhang L, Hou X, Liu S, Ding X, Jiang Y, Xu J, Zhang J, Zhao X, Liu YG. Abscisic Acid Regulates Auxin Distribution to Mediate Maize Lateral Root Development Under Salt Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:716. [PMID: 31231407 PMCID: PMC6560076 DOI: 10.3389/fpls.2019.00716] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/15/2019] [Indexed: 05/20/2023]
Abstract
Roots are important plant organs. Lateral root (LR) initiation (LRI) and development play a central role in environmental adaptation. The mechanism of LR development has been well investigated in Arabidopsis. When we evaluated the distribution of auxin and abscisic acid (ABA) in maize, we found that the mechanism differed from that in Arabidopsis. The distribution of ABA and auxin within the primary roots (PRs) and LRs was independent of each other. Auxin localization was observed below the quiescent center of the root tips, while ABA localized at the top of the quiescent center. Furthermore, NaCl inhibited LRI by increasing ABA accumulation, which mainly regulates auxin distribution, while auxin biosynthesis was inhibited by ABA in Arabidopsis. The polar localization of ZmPIN1 in maize was disrupted by NaCl and exogenous ABA. An inhibitor of ABA biosynthesis, fluridone (FLU), and the ABA biosynthesis mutant vp14 rescued the phenotype under NaCl treatment. Together, all the evidence suggested that NaCl promoted ABA accumulation in LRs and that ABA altered the polar localization of ZmPIN1, disrupted the distribution of auxin and inhibited LRI and development.
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Affiliation(s)
- Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Mo-Xian Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Rui Liu
- School of Life Sciences, Shandong University, Jinan, China
| | - Lin Zhang
- Department of Agronomy, Northeast Agricultural University, Harbin, China
| | - Xuanxuan Hou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Shouxu Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Yong Jiang
- National Oceanography Centre, Qingdao, China
| | - Jiandi Xu
- Rice Research Institute, Shandong Agricultural Research Institute, Jinan, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- *Correspondence: Ying-Gao Liu, ;
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34
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Bray AL, Topp CN. The Quantitative Genetic Control of Root Architecture in Maize. PLANT & CELL PHYSIOLOGY 2018; 59:1919-1930. [PMID: 30020530 PMCID: PMC6178961 DOI: 10.1093/pcp/pcy141] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 05/07/2023]
Abstract
Roots remain an underexplored frontier in plant genetics despite their well-known influence on plant development, agricultural performance and competition in the wild. Visualizing and measuring root structures and their growth is vastly more difficult than characterizing aboveground parts of the plant and is often simply avoided. The majority of research on maize root systems has focused on their anatomy, physiology, development and soil interaction, but much less is known about the genetics that control quantitative traits. In maize, seven root development genes have been cloned using mutagenesis, but no genes underlying the many root-related quantitative trait loci (QTLs) have been identified. In this review, we discuss whether the maize mutants known to control root development may also influence quantitative aspects of root architecture, including the extent to which they overlap with the most recent maize root trait QTLs. We highlight specific challenges and anticipate the impacts that emerging technologies, especially computational approaches, may have toward the identification of genes controlling root quantitative traits.
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Affiliation(s)
- Adam L Bray
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christopher N Topp
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Corresponding author: E-mail, ; Fax, 314 587 1501
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35
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Jia X, Liu P, Lynch JP. Greater lateral root branching density in maize improves phosphorus acquisition from low phosphorus soil. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4961-4970. [PMID: 30295904 PMCID: PMC6137997 DOI: 10.1093/jxb/ery252] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/03/2018] [Indexed: 05/03/2023]
Abstract
The development of crops with better growth under suboptimal phosphorus availability would improve food security in developing countries while reducing environmental pollution in developed countries. We tested the hypothesis that maize (Zea mays) phenotypes with greater lateral root branching density have greater phosphorus acquisition from low phosphorus soils. Recombinant inbred lines with either 'many short' (MS) or 'few long' (FL) lateral root phenotypes were grown under high and low phosphorus conditions in greenhouse mesocosms and in the field. Under low phosphorus in mesocosms, lines with the MS phenotype had 89% greater phosphorus acquisition and 48% more shoot biomass than FL lines. Under low phosphorus in the field, MS lines had 16% shallower rooting depth (D95), 81% greater root length density in the top 20 cm of the soil, 49% greater shoot phosphorus content, 12% greater leaf photosynthesis, 19% greater shoot biomass, and 14% greater grain yield than FL lines. These results are consistent with the hypothesis that the phenotype of many, shorter lateral roots improves phosphorus acquisition under low phosphorus availability and merits consideration for genetic improvement of phosphorus efficiency in maize and other crops.
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Affiliation(s)
- Xucun Jia
- College of Agronomy, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong Province, China
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Peng Liu
- College of Agronomy, Shandong Agricultural University/State Key Laboratory of Crop Biology, Tai’an, Shandong Province, China
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
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36
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Ju C, Zhang W, Liu Y, Gao Y, Wang X, Yan J, Yang X, Li J. Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize. BMC PLANT BIOLOGY 2018; 18:171. [PMID: 30111287 PMCID: PMC6094888 DOI: 10.1186/s12870-018-1383-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/01/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Root systems play important roles in crop growth and stress responses. Although genetic mechanism of root traits in maize (Zea mays L.) has been investigated in different mapping populations, root traits have rarely been utilized in breeding programs. Elucidation of the genetic basis of maize root traits and, more importantly, their connection to other agronomic trait(s), such as grain yield, may facilitate root trait manipulation and maize germplasm improvement. In this study, we analyzed genome-wide genetic loci for maize seedling root traits at three time-points after seed germination to identify chromosomal regions responsible for both seedling root traits and other agronomic traits in a recombinant inbred line (RIL) population (Zong3 × Yu87-1). RESULTS Eight seedling root traits were examined at 4, 9, and 14 days after seed germination, and thirty-six putative quantitative trait loci (QTLs), accounting for 9.0-23.2% of the phenotypic variation in root traits, were detected. Co-localization of root trait QTLs was observed at, but not between, the three time-points. We identified strong or moderate correlations between root traits controlled by each co-localized QTL region. Furthermore, we identified an overlap in the QTL locations of seedling root traits examined here and six other traits reported previously in the same RIL population, including grain yield-related traits, plant height-related traits, and traits in relation to stress responses. Maize chromosomal bins 1.02-1.03, 1.07, 2.06-2.07, 5.05, 7.02-7.03, 9.04, and 10.06 were identified QTL hotspots for three or four more traits in addition to seedling root traits. CONCLUSIONS Our identification of co-localization of root trait QTLs at, but not between, each of the three time-points suggests that maize seedling root traits are regulated by different sets of pleiotropic-effect QTLs at different developmental stages. Furthermore, the identification of QTL hotspots suggests the genetic association of seedling root traits with several other traits and reveals maize chromosomal regions valuable for marker-assisted selection to improve root systems and other agronomic traits simultaneously.
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Affiliation(s)
- Chuanli Ju
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wei Zhang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ya Liu
- Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097 China
| | - Yufeng Gao
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaofan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jiansheng Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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37
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Hochholdinger F, Marcon C, Baldauf JA, Yu P, Frey FP. Proteomics of Maize Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:143. [PMID: 29556242 PMCID: PMC5844967 DOI: 10.3389/fpls.2018.00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.
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38
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Qiao L, Zhang W, Li X, Zhang L, Zhang X, Li X, Guo H, Ren Y, Zheng J, Chang Z. Characterization and Expression Patterns of Auxin Response Factors in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1395. [PMID: 30283490 PMCID: PMC6157421 DOI: 10.3389/fpls.2018.01395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 09/03/2018] [Indexed: 05/22/2023]
Abstract
Auxin response factors (ARFs) are important transcription factors involved in both the auxin signaling pathway and the regulatory development of various plant organs. In this study, 23 TaARF members encoded by a total of 68 homeoalleles were isolated from 18 wheat chromosomes (excluding chromosome 4). The TaARFs, including their conserved domains, exon/intron structures, related microRNAs, and alternative splicing (AS) variants, were then characterized. Phylogenetic analysis revealed that members of the TaARF family share close homology with ARFs in other grass species. qRT-PCR analyses revealed that 20 TaARF members were expressed in different organs and tissues and that the expression of some members significantly differed in the roots, stems, and leaves of wheat seedlings in response to exogenous auxin treatment. Moreover, protein network analyses and co-expression results showed that TaTIR1-TaARF15/18/19-TaIAA13 may interact at both the protein and genetic levels. The results of subsequent evolutionary analyses showed that three transcripts of TaARF15 in the A subgenome of wheat exhibited high evolutionary rate and underwent positive selection. Transgenic analyses indicated that TaARF15-A.1 promoted the growth of roots and leaves of Arabidopsis thaliana and was upregulated in the overexpression plants after auxin treatment. Our results will provide reference information for subsequent research and utilization of the TaARF gene family.
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Affiliation(s)
- Linyi Qiao
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyan Li
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital Affiliated with the Capital Medical University, Beijing, China
| | - Lei Zhang
- Department of Plant Protection, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Xiaojun Zhang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xin Li
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Huijuan Guo
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yuan Ren
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Jun Zheng
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- *Correspondence: Jun Zheng, Zhijian Chang,
| | - Zhijian Chang
- Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture, Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- *Correspondence: Jun Zheng, Zhijian Chang,
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39
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Hochholdinger F, Yu P, Marcon C. Genetic Control of Root System Development in Maize. TRENDS IN PLANT SCIENCE 2018; 23:79-88. [PMID: 29170008 DOI: 10.1016/j.tplants.2017.10.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/21/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
The maize root system comprises structurally and functionally different root types. Mutant analyses have revealed that root-type-specific genetic regulators intrinsically determine the maize root system architecture. Molecular cloning of these genes has demonstrated that key elements of auxin signal transduction, such as LOB domain (LBD) and Aux/IAA proteins, are instrumental for seminal, shoot-borne, and lateral root initiation. Moreover, genetic analyses have demonstrated that genes related to exocytotic vesicle docking, cell wall loosening, and cellulose synthesis and organization control root hair elongation. The identification of upstream regulators, protein interaction partners, and downstream targets of these genes together with cell-type-specific transcriptome analyses have provided novel insights into the regulatory networks controlling root development and architecture in maize.
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Affiliation(s)
- Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany.
| | - Peng Yu
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
| | - Caroline Marcon
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany
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40
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Wu W, Liu Y, Wang Y, Li H, Liu J, Tan J, He J, Bai J, Ma H. Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals. Int J Mol Sci 2017; 18:E2107. [PMID: 28991190 PMCID: PMC5666789 DOI: 10.3390/ijms18102107] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 11/28/2022] Open
Abstract
The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.
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Affiliation(s)
- Wentao Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Yaxue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Yuqian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Huimin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiaxi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiaxin Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiadai He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jingwen Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
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41
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Wang J, Pei L, Jin Z, Zhang K, Zhang J. Overexpression of the protein phosphatase 2A regulatory subunit a gene ZmPP2AA1 improves low phosphate tolerance by remodeling the root system architecture of maize. PLoS One 2017; 12:e0176538. [PMID: 28448624 PMCID: PMC5407761 DOI: 10.1371/journal.pone.0176538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/12/2017] [Indexed: 11/21/2022] Open
Abstract
Phosphate (Pi) limitation is a constraint for plant growth and development in many natural and agricultural ecosystems. In this study, a gene encoding Zea mays L. protein phosphatase 2A regulatory subunit A, designated ZmPP2AA1, was induced in roots by low Pi availability. The function of the ZmPP2AA1 gene in maize was analyzed using overexpression and RNA interference. ZmPP2AA1 modulated root gravitropism, negatively regulated primary root (PR) growth, and stimulated the development of lateral roots (LRs). A detailed characterization of the root system architecture (RSA) in response to different Pi concentrations with or without indole-3-acetic acid and 1-N-naphthylphthalamic acid revealed that auxin was involved in the RSA response to low Pi availability. Overexpression of ZmPP2AA1 enhanced tolerance to Pi starvation in transgenic maize in hydroponic and soil pot experiments. An increased dry weight (DW), root-to-shoot ratio, and total P content and concentration, along with a delayed and reduced accumulation of anthocyanin in overexpressing transgenic maize plants coincided with their highly branched root system and increased Pi uptake capability under low Pi conditions. Inflorescence development of the ZmPP2AA1 overexpressing line was less affected by low Pi stress, resulting in higher grain yield per plant under Pi deprivation. These data reveal the biological function of ZmPP2AA1, provide insights into a linkage between auxin and low Pi responses, and drive new strategies for the efficient utilization of Pi by maize.
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Affiliation(s)
- Jiemin Wang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Laming Pei
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
- Department of Biotechnology, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhe Jin
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Kewei Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Juren Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
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42
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Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F. Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:403-414. [PMID: 28204533 PMCID: PMC5444478 DOI: 10.1093/jxb/erw422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise comparisons of rtcs and wild-type embryo transcriptomes identified 131 transcription factors among 3526 differentially expressed genes [false discovery rate (FDR) <5% and |log2Fc|≥1]. Among those, functional annotation highlighted genes involved in cell cycle control and phytohormone action, particularly auxin signaling. Moreover, in silico promoter analyses identified putative RTCS target genes associated with transcription factor action and hormone metabolism and signaling. Significantly, non-syntenic genes that emerged after the separation of maize and sorghum were over-represented among genes displaying RTCS-dependent expression during seminal root primordia formation. This might suggest that these non-syntenic genes came under the transcriptional control of the syntenic gene rtcs during seminal root evolution. Taken together, this study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
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43
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Yu P, Gutjahr C, Li C, Hochholdinger F. Genetic Control of Lateral Root Formation in Cereals. TRENDS IN PLANT SCIENCE 2016; 21:951-961. [PMID: 27524642 DOI: 10.1016/j.tplants.2016.07.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/19/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Cereals form complex root systems composed of different root types. Lateral root formation is a major determinant of root architecture and is instrumental for the efficient uptake of water and nutrients. Positioning and patterning of lateral roots and cell types involved in their formation are unique in monocot cereals. Recent discoveries advanced the molecular understanding of the intrinsic genetic control of initiation and elongation of lateral roots in cereals by distinct, in part root-type-specific genetic programs. Moreover, molecular networks modulating the plasticity of lateral root formation in response to water and nutrient availability and arbuscular mycorrhizal fungal colonization have been identified. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in cereals.
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Affiliation(s)
- Peng Yu
- China Agricultural University, College of Resources and Environmental Science, Department of Plant Nutrition, 100193 Beijing, China; University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, 53113 Bonn, Germany
| | | | - Chunjian Li
- China Agricultural University, College of Resources and Environmental Science, Department of Plant Nutrition, 100193 Beijing, China.
| | - Frank Hochholdinger
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, 53113 Bonn, Germany.
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44
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Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth. Sci Rep 2016; 6:34395. [PMID: 27708345 PMCID: PMC5052636 DOI: 10.1038/srep34395] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/13/2016] [Indexed: 11/08/2022] Open
Abstract
Root hairs are tubular extensions of the epidermis. Root hairs of the monogenic recessive maize mutant roothairless 6 (rth6) are arrested after bulge formation during the transition to tip growth and display a rough cell surface. BSR-Seq in combination with Seq-walking and subsequent analyses of four independently generated mutant alleles established that rth6 encodes CSLD5 a plasma membrane localized 129 kD D-type cellulose synthase with eight transmembrane domains. Cellulose synthases are required for the biosynthesis of cellulose, the most abundant biopolymer of plant cell walls. Phylogenetic analyses revealed that RTH6 is part of a monocot specific clade of D-type cellulose synthases. D-type cellulose synthases are highly conserved in the plant kingdom with five gene family members in maize and homologs even among early land plants such as the moss Physcomitrella patens or the clubmoss Selaginella moellendorffii. Expression profiling demonstrated that rth6 transcripts are highly enriched in root hairs as compared to all other root tissues. Moreover, in addition to the strong knock down of rth6 expression in young primary roots of the mutant rth6, the gene is also significantly down-regulated in rth3 and rth5 mutants, while it is up-regulated in rth2 mutants, suggesting that these genes interact in cell wall biosynthesis.
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45
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Li P, Zhuang Z, Cai H, Cheng S, Soomro AA, Liu Z, Gu R, Mi G, Yuan L, Chen F. Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:242-53. [PMID: 26269087 DOI: 10.1111/jipb.12384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/10/2015] [Indexed: 05/26/2023]
Abstract
Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.
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Affiliation(s)
- Pengcheng Li
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhongjuan Zhuang
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Leading Bio-agricultural Co., Ltd., Qinhuangdao, 066000, China
| | - Hongguang Cai
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Shuai Cheng
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ayaz Ali Soomro
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhigang Liu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Riliang Gu
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Lixing Yuan
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Fanjun Chen
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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46
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Salvi S, Giuliani S, Ricciolini C, Carraro N, Maccaferri M, Presterl T, Ouzunova M, Tuberosa R. Two major quantitative trait loci controlling the number of seminal roots in maize co-map with the root developmental genes rtcs and rum1. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1149-59. [PMID: 26880748 PMCID: PMC4753855 DOI: 10.1093/jxb/erw011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genetic dissection of root architecture and functions allows for a more effective and informed design of novel root ideotypes and paves the way to evaluate their effects on crop resilience to a number of abiotic stresses. In maize, limited attention has been devoted to the genetic analysis of root architecture diversity at the early stage. The difference in embryonic (including seminal and primary) root architecture between the maize reference line B73 (which mostly develops three seminal roots) and the landrace Gaspé Flint (with virtually no seminal roots) was genetically dissected using a collection of introgression lines grown in paper rolls and pots. Quantitative trait locus (QTL) analysis identified three QTLs controlling seminal root number (SRN) on chromosome bins 1.02, 3.07, and 8.04-8.05, which collectively explained 66% of the phenotypic variation. In all three cases, Gaspé Flint contributed the allele for lower SRN. Primary root dry weight was negatively correlated with SRN (r= -0.52), and QTLs for primary root size co-mapped with SRN QTLs, suggesting a pleiotropic effect of SRN QTLs on the primary root, most probably caused by competition for seed resources. Interestingly, two out of three SRN QTLs co-mapped with the only two known maize genes (rtcs and rum1) affecting the number of seminal roots. The strong additive effect of the three QTLs and the development of near isogenic lines for each QTL in the elite B73 background provide unique opportunities to characterize functionally the genes involved in root development and to evaluate how root architecture affects seedling establishment, early development, and eventually yield in maize.
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Affiliation(s)
- Silvio Salvi
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Silvia Giuliani
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | - Nicola Carraro
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Marco Maccaferri
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Roberto Tuberosa
- DipSA University of Bologna, viale Fanin 44, 40127 Bologna, Italy
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47
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Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F. Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1123-35. [PMID: 26628518 PMCID: PMC4753849 DOI: 10.1093/jxb/erv513] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, D-93053 Regensburg, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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48
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Zhang Y, Marcon C, Tai H, von Behrens I, Ludwig Y, Hey S, Berendzen KW, Hochholdinger F. Conserved and unique features of the homeologous maize Aux/IAA proteins ROOTLESS WITH UNDETECTABLE MERISTEM 1 and RUM1-like 1. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1137-47. [PMID: 26672614 PMCID: PMC4753850 DOI: 10.1093/jxb/erv519] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The maize (Zea mays L.) Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEM 1) is a key regulator of lateral and seminal root formation. An ancient maize genome duplication resulted in the emergence of its homeolog rum1-like1 (rul1), which displays 92% amino acid sequence identity with RUM1. Both, RUL1 and RUM1 exhibit the canonical four domain structure of Aux/IAA proteins. Moreover, both are localized to the nucleus, are instable and have similar short half-lives of ~23min. Moreover, RUL1 and RUM1 can be stabilized by specific mutations in the five amino acid degron sequence of domain II. In addition, proteins encoded by both genes interact in vivo with auxin response factors (ARFs) such as ZmARF25 and ZmARF34 in protoplasts. Although it was demonstrated that RUL1 and RUM1 can homo and heterodimerize in vivo, rul1 expression is independent of rum1. Moreover, on average rul1 expression is ~84-fold higher than rum1 in the 12 tested tissues and developmental stages, although the relative expression levels in different root tissues are very similar. While RUM1 and RUL1 display conserved biochemical properties, yeast-two-hybrid in combination with BiFC experiments identified a RUM1-associated protein 1 (RAP1) that specifically interacts with RUM1 but not with RUL1. This suggests that RUM1 and RUL1 are at least in part interwoven into different molecular networks.
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Affiliation(s)
- Yanxiang Zhang
- Center for Molecular Cell and Systems Biology, College of Life Science, Fujian Agriculture & Forestry University, 350002 Fuzhou, China Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Caroline Marcon
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Huanhuan Tai
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Inga von Behrens
- ZMBP, Center for Plant Molecular Biology, General Genetics, University of Tuebingen, 72076 Tuebingen, Germany
| | - Yvonne Ludwig
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Stefan Hey
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
| | - Kenneth W Berendzen
- ZMBP, Center for Plant Molecular Biology, Central Facilities, University of Tuebingen, 72076 Tuebingen, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
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49
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Xu C, Tai H, Saleem M, Ludwig Y, Majer C, Berendzen KW, Nagel KA, Wojciechowski T, Meeley RB, Taramino G, Hochholdinger F. Cooperative action of the paralogous maize lateral organ boundaries (LOB) domain proteins RTCS and RTCL in shoot-borne root formation. THE NEW PHYTOLOGIST 2015; 207:1123-33. [PMID: 25902765 DOI: 10.1111/nph.13420] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/18/2015] [Indexed: 05/24/2023]
Abstract
The paralogous maize (Zea mays) LBD (Lateral Organ Boundaries Domain) genes rtcs (rootless concerning crown and seminal roots) and rtcl (rtcs-like) emerged from an ancient whole-genome duplication. RTCS is a key regulator of crown root initiation. The diversity of expression, molecular interaction and phenotype of rtcs and rtcl were investigated. The rtcs and rtcl genes display highly correlated spatio-temporal expression patterns in roots, despite the significantly higher expression of rtcs. Both RTCS and RTCL proteins bind to LBD downstream promoters and act as transcription factors. In line with its auxin inducibility and binding to auxin response elements of rtcs and rtcl promoters, ARF34 (AUXIN RESPONSE FACTOR 34) acts as transcriptional activator. Yeast two-hybrid screening combined with bimolecular fluorescence complementation (BiFC) experiments revealed conserved and unique interaction partners of RTCS and RTCL. The rtcl mutation leads to defective shoot-borne root elongation early in development. Cooperative action of RTCS and RTCL during shoot-borne root formation was demonstrated by rtcs-dependent repression of rtcl transcription in coleoptilar nodes. Although RTCS is instrumental in shoot-borne root initiation, RTCL controls shoot-borne root elongation early in development. Their conserved role in auxin signaling, but diverse function in shoot-borne root formation, is underscored by their conserved and unique interaction partners.
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Affiliation(s)
- Changzheng Xu
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
- RCBB, Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest University, 400716, Chongqing, China
| | - Huanhuan Tai
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Muhammad Saleem
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Yvonne Ludwig
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Christine Majer
- ZMBP, Center for Plant Molecular Biology, General Genetics, University of Tübingen, 72076, Tübingen, Germany
| | - Kenneth W Berendzen
- ZMBP, Center for Plant Molecular Biology, Central Facilities, University of Tübingen, 72076, Tübingen, Germany
| | - Kerstin A Nagel
- IBG-2, Plant Sciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | | | - Robert B Meeley
- DuPont Pioneer Ag Biotech Research, Johnston, IA, 50131-1004, USA
| | - Graziana Taramino
- DuPont Crop Genetics Research, Experimental Station, Wilmington, DE, 19880-0353, USA
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
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50
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Zhang Y, von Behrens I, Zimmermann R, Ludwig Y, Hey S, Hochholdinger F. LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signalling downstream of the Aux/IAA gene rootless with undetectable meristem 1. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3855-63. [PMID: 25911745 PMCID: PMC4473986 DOI: 10.1093/jxb/erv187] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Only little is known about target genes of auxin signalling downstream of the Aux/IAA-ARF module. In the present study, it has been demonstrated that maize lateral root primordia 1 (lrp1) encodes a transcriptional activator that is directly regulated by the Aux/IAA protein ROOTLESS WITH UNDETECTABLE MERISTEM 1 (RUM1). Expression of lrp1 is confined to early root primordia and meristems and is auxin-inducible. Based on its primary protein structure, LRP1 is predicted to be a transcription factor. This notion is supported by exclusive LRP1 localization in the nucleus and its ability to activate downstream gene activity. Based on the observation that lrp1 transcription is completely repressed in the semi-dominant gain of function mutant rum1, it was demonstrated that the lrp1 promoter is a direct target of RUM1 proteins. Subsequently, promoter activation assays indicated that RUM1 represses the expression of a GFP reporter fused to the native promoter of lrp1. Constitutive repression of lrp1 in rum1 mutants is a consequence of the stability of mutated rum1 proteins which cannot be degraded by the proteasome and thus constitutively bind to the lrp1 promoter and repress transcription. Taken together, the repression of the transcriptional activator lrp1 by direct binding of RUM1 to its promoter, together with specific expression of lrp1 in root meristems, suggests a function in maize root development via the RUM1-dependent auxin signalling pathway.
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Affiliation(s)
- Yanxiang Zhang
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany Center for Molecular Cell and Systems Biology, College of Life Science, Fujian Agriculture & Forestry University, 350002 Fuzhou, China
| | - Inga von Behrens
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Roman Zimmermann
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Yvonne Ludwig
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
| | - Stefan Hey
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
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