101
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Liu C, Leng J, Li Y, Ge T, Li J, Chen Y, Guo C, Qi J. A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Res 2022; 50:9724-9737. [PMID: 36095130 PMCID: PMC9508851 DOI: 10.1093/nar/gkac773] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Leng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yonglong Li
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Tingting Ge
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Jinglong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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102
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Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Amaya I, Usadel B, Mezzetti B. Towards smart and sustainable development of modern berry cultivars in Europe. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1238-1251. [PMID: 35751152 DOI: 10.1111/tpj.15876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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Affiliation(s)
- Elisa Senger
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | | | - Paul Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Béatrice Denoyes
- Université de Bordeaux, UMR BFP, INRAE, Villenave d'Ornon, France
| | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Stefano Predieri
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Nico Lippi
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Monika Höfer
- Institute of Breeding Research on Fruit Crops, Federal Research Centre for Cultivated Plants (JKI), Dresden, Germany
| | - Helen Cockerton
- Genetics, Genomics and Breeding Department, NIAB, East Malling, UK
| | - Christophe Pradal
- CIRAD and UMR AGAP Institute, Montpellier, France
- INRIA and LIRMM, University Montpellier, CNRS, Montpellier, France
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Balcalı, Adana, Turkey
| | | | - Iraida Amaya
- Unidad Asociada deI + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
- Laboratorio de Genómica y Biotecnología, Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Málaga, Spain
| | - Björn Usadel
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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103
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Dreccer MF, Zwart AB, Schmidt RC, Condon AG, Awasi MA, Grant TJ, Galle A, Bourot S, Frohberg C. Wheat yield potential can be maximized by increasing red to far-red light conditions at critical developmental stages. PLANT, CELL & ENVIRONMENT 2022; 45:2652-2670. [PMID: 35815553 DOI: 10.1111/pce.14390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Sensing of neighbours via the Red to Far-Red light ratio (R:FR) may exert a cap to yield potential in wheat. The effects of an increased R:FR inside the canopy were studied in dense wheat mini canopies grown in controlled environments by lowering FR. To distinguish between effects exerted by light sensing and assimilate supply, the treatments were complemented with elevated CO2 , applied between different developmental timepoints to specifically impact tillering, spike growth, floret fertility and grain filling, in different combinations. The yield response to high R:FR was strongly dependent on the developmental stage in all three cultivars and pivoted between positive if applied after the start of stem elongation, and negative or null if applied before. Yield gains of up to 70% and 120% were observed, respectively, in two cultivars, associated with a higher number of tiller spikes and grains per spike in the main shoot. The response to the combination of high R:FR and elevated CO2 or CO2 alone were cultivar dependent. Taken together, our results suggest that R:FR exerts a significant control on yield potential in wheat and achieving a high R:FR from stem elongation to maturity is a promising lever towards a significant increase in grain yield.
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Affiliation(s)
| | - Alec B Zwart
- CSIRO Agriculture and Food, Black Mountain, Australia
| | | | | | - Mary A Awasi
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, Australia
| | - Terry J Grant
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Saint Lucia, Australia
| | - Alexander Galle
- BASF Innovation Center Gent, BASF Belgium Coordination Center CommV, Gent, Belgium
| | - Stephane Bourot
- BASF Innovation Center Gent, BASF Belgium Coordination Center CommV, Gent, Belgium
| | - Claus Frohberg
- BASF Innovation Center Gent, BASF Belgium Coordination Center CommV, Gent, Belgium
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104
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Grünhofer P, Stöcker T, Guo Y, Li R, Lin J, Ranathunge K, Schoof H, Schreiber L. Populus × canescens root suberization in reaction to osmotic and salt stress is limited to the developing younger root tip region. PHYSIOLOGIA PLANTARUM 2022; 174:e13765. [PMID: 36281836 DOI: 10.1111/ppl.13765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
Populus is a valuable and fast-growing tree species commonly cultivated for economic and scientific purposes. But most of the poplar species are sensitive to drought and salt stress. Thus, we compared the physiological effects of osmotic stress (PEG8000) and salt treatment (NaCl) on poplar roots to identify potential strategies for future breeding or genetic engineering approaches. We investigated root anatomy using epifluorescence microscopy, changes in root suberin composition and amount using gas chromatography, transcriptional reprogramming using RNA sequencing, and modifications of root transport physiology using a pressure chamber. Poplar roots reacted to the imposed stress conditions, especially in the developing younger root tip region, with remarkable differences between both types of stress. Overall, the increase in suberin content was surprisingly small, but the expression of key suberin biosynthesis genes was strongly induced. Significant reductions of the radial water transport in roots were only observed for the osmotic and not the hydrostatic hydraulic conductivity. Our data indicate that the genetic enhancement of root suberization processes in poplar might be a promising target to convey increased tolerance, especially against toxic sodium chloride.
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Affiliation(s)
- Paul Grünhofer
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Yayu Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Science and Technology, Beijing Forestry University, Beijing, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, China
| | - Kosala Ranathunge
- UWA School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heiko Schoof
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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105
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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106
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Gao P, Qiu S, Ma X, Parkin IAP, Xiang D, Datla R. Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax. PLANTS 2022; 11:plants11152031. [PMID: 35956508 PMCID: PMC9370790 DOI: 10.3390/plants11152031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/24/2022] [Accepted: 07/30/2022] [Indexed: 11/16/2022]
Abstract
Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8, Canada
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Shuqing Qiu
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Xingliang Ma
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Isobel A. P. Parkin
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4L8, Canada
- Correspondence: (I.A.P.P.); (D.X.); (R.D.); Tel.: +1-306-3859434 (I.A.P.P.); +1-306-9755580 (D.X.); +1-306-2293924 (R.D.)
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107
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Warsame AO, Michael N, O’Sullivan DM, Tosi P. Seed Development and Protein Accumulation Patterns in Faba Bean ( Vicia faba, L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9295-9304. [PMID: 35862501 PMCID: PMC9354250 DOI: 10.1021/acs.jafc.2c02061] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A major objective in faba bean breeding is to improve its protein quality by selecting cultivars with enhanced desirable physicochemical properties. However, the protein composition of the mature seed is determined by a series of biological processes occurring during seed growth. Thus, any attempt to explain the final seed composition must consider the dynamics of the seed proteome during seed development. Here, we investigated the proteomic profile of developing faba bean seeds across 12 growth stages from 20 days after pollination (DAP) to full maturity. We analyzed trypsin-digested total protein extracts from the seeds at different growth stages by liquid chromatography-tandem mass spectrometry (LC-MS/MS), identifying 1217 proteins. The functional clusters of these proteins showed that, in early growth stages, proteins related to cell growth, division, and metabolism were most abundant compared to seed storage proteins that began to accumulate from 45 DAP. Moreover, label-free quantification of the relative abundance of seed proteins, including important globulin proteins, revealed several distinct temporal accumulation trends among the protein classes. These results suggest that these proteins are regulated differently and require further understanding of the impact of the different environmental stresses occurring at different grain filling stages on the expression and accumulation of these seed storage proteins.
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Affiliation(s)
- Ahmed O. Warsame
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
| | - Nicholas Michael
- School
of Chemistry, Food and Pharmacy, University
of Reading, Reading RG6 6AH, U.K.
| | - Donal M. O’Sullivan
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
| | - Paola Tosi
- School
of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, U.K.
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108
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Guerra‐Garcia A, Haile T, Ogutcen E, Bett KE, von Wettberg EJ. An evolutionary look into the history of lentil reveals unexpected diversity. Evol Appl 2022; 15:1313-1325. [PMID: 36051460 PMCID: PMC9423085 DOI: 10.1111/eva.13467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 07/12/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold-season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty-three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were "enzymes," "Cell Wall Organization," and "external stimuli response." All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.
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Affiliation(s)
- Azalea Guerra‐Garcia
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Teketel Haile
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Ezgi Ogutcen
- Conservatoire et Jardin Botaniques de la Ville de GenèveGenevaSwitzerland
| | - Kirstin E. Bett
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Eric J. von Wettberg
- Plant and Soil Science and Gund Institute for the EnvironmentUniversity of VermontBurlingtonVermontUSA
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109
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Coulter M, Entizne JC, Guo W, Bayer M, Wonneberger R, Milne L, Schreiber M, Haaning A, Muehlbauer GJ, McCallum N, Fuller J, Simpson C, Stein N, Brown JWS, Waugh R, Zhang R. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1183-1202. [PMID: 35704392 PMCID: PMC9546494 DOI: 10.1111/tpj.15871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.
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Affiliation(s)
- Max Coulter
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Juan Carlos Entizne
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Wenbin Guo
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Micha Bayer
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Ronja Wonneberger
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Linda Milne
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Miriam Schreiber
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Allison Haaning
- Department of Agronomy and Plant GeneticsUniversity of Minnesota1991 Upper Buford Circle, 542 Borlaug HallSt PaulMinnesota55108USA
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant GeneticsUniversity of Minnesota1991 Upper Buford Circle, 542 Borlaug HallSt PaulMinnesota55108USA
| | - Nicola McCallum
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - John Fuller
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Craig Simpson
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3D‐06466Stadt SeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityGöttingenGermany
| | - John W. S. Brown
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Robbie Waugh
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- School of Agriculture and Wine & Waite Research InstituteUniversity of AdelaideWaite CampusGlen OsmondSouth Australia5064Australia
| | - Runxuan Zhang
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean ( Phaseolus coccineus L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKS7N 5A2Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Environmental GenomicsMax Planck Institute for Evolutionary Biology24306PlönGermany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome CenterUniversity of California, DavisDavisCalifornia95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed AmbientaliUniversità Politecnica delle MarcheAncona60131Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
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111
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Nagy I, Veeckman E, Liu C, Bel MV, Vandepoele K, Jensen CS, Ruttink T, Asp T. Chromosome-scale assembly and annotation of the perennial ryegrass genome. BMC Genomics 2022; 23:505. [PMID: 35831814 PMCID: PMC9281035 DOI: 10.1186/s12864-022-08697-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/14/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well as for evolutionary and comparative genomics. The improvement of long-read sequencing technologies and the advent of optical mapping and chromosome conformation capture technologies in the last few years, significantly promoted the development of chromosome-scale genome assemblies of model plants and crop species. In grasses, chromosome-scale genome assemblies recently became available for cultivated and wild species of the Triticeae subfamily. Development of state-of-the-art genomic resources in species of the Poeae subfamily, which includes important crops like fescues and ryegrasses, is lagging behind the progress in the cereal species. RESULTS Here, we report a new chromosome-scale genome sequence assembly for perennial ryegrass, obtained by combining PacBio long-read sequencing, Illumina short-read polishing, BioNano optical mapping and Hi-C scaffolding. More than 90% of the total genome size of perennial ryegrass (approximately 2.55 Gb) is covered by seven pseudo-chromosomes that show high levels of collinearity to the orthologous chromosomes of Triticeae species. The transposon fraction of perennial ryegrass was found to be relatively low, approximately 35% of the total genome content, which is less than half of the genome repeat content of cultivated cereal species. We predicted 54,629 high-confidence gene models, 10,287 long non-coding RNAs and a total of 8,393 short non-coding RNAs in the perennial ryegrass genome. CONCLUSIONS The new reference genome sequence and annotation presented here are valuable resources for comparative genomic studies in grasses, as well as for breeding applications and will expedite the development of productive varieties in perennial ryegrass and related species.
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Affiliation(s)
- Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, Slagelse, DK-4200 Denmark
| | - Elisabeth Veeckman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, Melle, B-9090 Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, B-9052 Belgium
- Present address: DLF Seeds A/S, Denmark, Højerupvej 31, Store Heddinge, DK-4660 Denmark
| | - Chang Liu
- Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität, Auf der Morgenstelle 32, Tübingen, 72076 Germany
- Present address: Institut für Biologie, Universität Hohenheim, Garbenstr. 30, Stuttgart, 70599 Germany
| | - Michiel Van Bel
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, B-9052 Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052 Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052 Belgium
| | - Klaas Vandepoele
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, B-9052 Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052 Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052 Belgium
| | | | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, Melle, B-9090 Belgium
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, Slagelse, DK-4200 Denmark
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Liu T, Salguero P, Petek M, Martinez-Mira C, Balzano-Nogueira L, Ramšak Ž, McIntyre L, Gruden K, Tarazona S, Conesa A. PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. Nucleic Acids Res 2022; 50:W551-W559. [PMID: 35609982 PMCID: PMC9252773 DOI: 10.1093/nar/gkac352] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/.
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Affiliation(s)
- Tianyuan Liu
- Department of Mechanical Engineering, School of Engineering, Cardiff University, Cardiff, UK
| | - Pedro Salguero
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Lauren McIntyre
- Department of Molecular Genetics and Microbiology, Genetics Institute, University of Florida, Gainesville, USA
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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Irulappan V, Kandpal M, Saini K, Rai A, Ranjan A, Sinharoy S, Senthil-Kumar M. Drought Stress Exacerbates Fungal Colonization and Endodermal Invasion and Dampens Defense Responses to Increase Dry Root Rot in Chickpea. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:583-591. [PMID: 35253477 DOI: 10.1094/mpmi-07-21-0195-fi] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Drought plays a central role in increasing the incidence and severity of dry root rot (DRR) disease in chickpea. This is an economically devastating disease, compromising chickpea yields particularly severely in recent years due to erratic rainfall patterns. Macrophomina phaseolina (formerly Rhizoctonia bataticola) is the causal agent of DRR disease in the chickpea plant. The infection pattern in chickpea roots under well-watered conditions and drought stress are poorly understood at present. This study provides detailed disease symptomatology and the characteristics of DRR fungus at morphological and molecular levels. Using microscopy techniques, the infection pattern of DRR fungus in susceptible chickpea roots was investigated under well-watered and drought-stress conditions. Our observations suggested that drought stress intensifies the progression of already ongoing infection by weakening the endodermal barrier and overall defense. Transcriptomic analysis suggested that the plant's innate immune defense program is downregulated in infected roots when subjected to drought stress. Furthermore, genes involved in hormonal regulation are differentially expressed under drought stress. These findings provide hints in terms of potential chickpea genes to target in crop improvement programs to develop climate-change-resilient cultivars.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Vadivelmurugan Irulappan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Manu Kandpal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Kumud Saini
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Avanish Rai
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
| | - Muthappa Senthil-Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, India
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114
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Barnhart MH, McAssey EV, Dittmar EL, Burke JM. Transcriptomics of developing wild sunflower seeds from the extreme ends of a latitudinal gradient differing in seed oil composition. PLANT DIRECT 2022; 6:e423. [PMID: 35898559 PMCID: PMC9307388 DOI: 10.1002/pld3.423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Seed oil composition, an important agronomic trait in cultivated sunflower, varies latitudinally across the native range of its wild progenitor. This pattern is thought to be driven by selection for a higher proportion of saturated fatty acids in southern populations compared with northern populations, likely due to the different temperatures experienced during seed germination. To investigate whether these differences in fatty acid composition between northern and southern populations correspond to transcriptional variation in the expression of genes involved in fatty acid metabolism, we sequenced RNA from developing seeds of sunflowers from Texas, USA, and Saskatchewan, Canada (the extreme ends of sunflower's latitudinal range) grown in a common garden. We found 4,741 genes to be differentially expressed between Texas and Canada, including several genes involved in lipid metabolism. Several differentially expressed lipid metabolism genes also colocalized with known oil quantitative trait loci (QTL). The genes producing stearoyl-ACP-desaturases (SAD) were of particular interest because of their known role in the conversion of fully saturated into unsaturated fatty acids. Two SAD genes were more highly expressed in seeds from Canadian populations, consistent with the observation of increased levels of unsaturated fatty acids in seeds from that region. We also constructed a gene co-expression network to investigate regional variation in network modules. The results of this analysis revealed regional differentiation for eight of 12 modules but no clear relationship with oil biosynthesis. Overall, the differential expression of SAD genes offers a partial explanation for the observed differences in seed oil composition between Texas and Canada, while the expression patterns of other metabolic genes suggest complex regulation of fatty acid production and usage across latitudes.
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Affiliation(s)
- Max H. Barnhart
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Edward V. McAssey
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- School of Life SciencesUniversity of Hawai'i at MānoaHonoluluHawaiiUSA
| | - Emily L. Dittmar
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - John M. Burke
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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Backer R, Engelbrecht J, van den Berg N. Differing Responses to Phytophthora cinnamomi Infection in Susceptible and Partially Resistant Persea americana (Mill.) Rootstocks: A Case for the Role of Receptor-Like Kinases and Apoplastic Proteases. FRONTIERS IN PLANT SCIENCE 2022; 13:928176. [PMID: 35837458 PMCID: PMC9274290 DOI: 10.3389/fpls.2022.928176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The hemibiotrophic plant pathogen Phytophthora cinnamomi Rands is the most devastating pathogen of avocado (Persea americana Mill.) and, as such, causes significant annual losses in the industry. Although the molecular basis of P. cinnamomi resistance in avocado and P. cinnamomi virulence determinants have been the subject of recent research, none have yet attempted to compare the transcriptomic responses of both pathogen and host during their interaction. In the current study, the transcriptomes of both avocado and P. cinnamomi were explored by dual RNA sequencing. The basis for partial resistance was sought by the inclusion of both susceptible (R0.12) and partially resistant (Dusa®) rootstocks sampled at early (6, 12 and 24 hours post-inoculation, hpi) and late time-points (120 hpi). Substantial differences were noted in the number of differentially expressed genes found in Dusa® and R0.12, specifically at 12 and 24 hpi. Here, the partially resistant rootstock perpetuated defense responses initiated at 6 hpi, while the susceptible rootstock abruptly reversed course. Instead, gene ontology enrichment confirmed that R0.12 activated pathways related to growth and development, essentially rendering its response at 12 and 24 hpi no different from that of the mock-inoculated controls. As expected, several classes of P. cinnamomi effector genes were differentially expressed in both Dusa® and R0.12. However, their expression differed between rootstocks, indicating that P. cinnamomi might alter the expression of its effector arsenal based on the rootstock. Based on some of the observed differences, several P. cinnamomi effectors were highlighted as potential candidates for further research. Similarly, the receptor-like kinase (RLK) and apoplastic protease coding genes in avocado were investigated, focusing on their potential role in differing rootstock responses. This study suggests that the basis of partial resistance in Dusa® is predicated on its ability to respond appropriately during the early stages following P. cinnamomi inoculation, and that important components of the first line of inducible defense, apoplastic proteases and RLKs, are likely to be important to the observed outcome.
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Affiliation(s)
- Robert Backer
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Engelbrecht
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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Lafferty DJ, Espley RV, Deng CH, Dare AP, Günther CS, Jaakola L, Karppinen K, Boase MR, Wang L, Luo H, Allan AC, Albert NW. The Coordinated Action of MYB Activators and Repressors Controls Proanthocyanidin and Anthocyanin Biosynthesis in Vaccinium. FRONTIERS IN PLANT SCIENCE 2022; 13:910155. [PMID: 35812927 PMCID: PMC9263919 DOI: 10.3389/fpls.2022.910155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Vaccinium berries are regarded as "superfoods" owing to their high concentrations of anthocyanins, flavonoid metabolites that provide pigmentation and positively affect human health. Anthocyanin localization differs between the fruit of cultivated highbush blueberry (V. corymbosum) and wild bilberry (V. myrtillus), with the latter having deep red flesh coloration. Analysis of comparative transcriptomics across a developmental series of blueberry and bilberry fruit skin and flesh identified candidate anthocyanin regulators responsible for this distinction. This included multiple activator and repressor transcription factors (TFs) that correlated strongly with anthocyanin production and had minimal expression in blueberry (non-pigmented) flesh. R2R3 MYB TFs appeared key to the presence and absence of anthocyanin-based pigmentation; MYBA1 and MYBPA1.1 co-activated the pathway while MYBC2.1 repressed it. Transient overexpression of MYBA1 in Nicotiana benthamiana strongly induced anthocyanins, but this was substantially reduced when co-infiltrated with MYBC2.1. Co-infiltration of MYBC2.1 with MYBA1 also reduced activation of DFR and UFGT, key anthocyanin biosynthesis genes, in promoter activation studies. We demonstrated that these TFs operate within a regulatory hierarchy where MYBA1 activated the promoters of MYBC2.1 and bHLH2. Stable overexpression of VcMYBA1 in blueberry elevated anthocyanin content in transgenic plants, indicating that MYBA1 is sufficient to upregulate the TF module and activate the pathway. Our findings identify TF activators and repressors that are hierarchically regulated by SG6 MYBA1, and fine-tune anthocyanin production in Vaccinium. The lack of this TF module in blueberry flesh results in an absence of anthocyanins.
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Affiliation(s)
- Declan J. Lafferty
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew P. Dare
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Catrin S. Günther
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian Institute of Bioeconomy Research (NIBIO), Tromsø, Norway
| | - Katja Karppinen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Murray R. Boase
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Lei Wang
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Henry Luo
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Andrew C. Allan
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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Yuan HY, Caron CT, Vandenberg A, Bett KE. RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative. Front Genet 2022; 13:891702. [PMID: 35795209 PMCID: PMC9251359 DOI: 10.3389/fgene.2022.891702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022] Open
Abstract
Lentil is an important pulse crop not only because of its high nutrient value but also because of its ecological advantage in a sustainable agricultural system. Our previous work showed that the cultivated lentil and wild lentil germplasm respond differently to light environments, especially to low R/FR-induced shade conditions. Little is known about how cultivated and wild lentils respond to shade at the level of gene expression and function. In this study, transcriptomic profiling of a cultivated lentil (Lupa, L. culinaris) and a wild lentil (BGE 016880, L. orientalis) at several growth stages is presented. De novo transcriptomes were assembled for both genotypes, and differential gene expression analysis and gene ontology enrichment analysis were performed. The transcriptomic resources generated in this study provide fundamental information regarding biological processes and genes associated with shade responses in lentils. BGE 016880 and Lupa shared a high similarity in their transcriptomes; however, differential gene expression profiles were not consistent between these two genotypes. The wild lentil BGE 016880 had more differentially expressed genes than the cultivated lentil Lupa. Upregulation of genes involved in gibberellin, brassinosteroid, and auxin synthesis and signaling pathways, as well as cell wall modification, in both genotypes explains their similarity in stem elongation response under the shade. Genes involved in jasmonic acid and flavonoid biosynthesis pathways were downregulated in BGE 016880 only, and biological processes involved in defense responses were significantly enriched in the wild lentil BGE 016880 only. Downregulation of WRKY and MYB transcription factors could contribute to the reduced defense response in BGE 016880 but not in Lupa under shade conditions. A better understanding of shade responses of pulse crop species and their wild relatives will play an important role in developing genetic strategies for crop improvement in response to changes in light environments.
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Affiliation(s)
- Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- Aquatic and Crop Resource Development Research Center, National Research Council of Canada, Saskatoon, SK, Canada
| | - Carolyn T. Caron
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Kirstin E. Bett,
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118
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Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. FRONTIERS IN PLANT SCIENCE 2022; 13:867263. [PMID: 35755645 PMCID: PMC9225960 DOI: 10.3389/fpls.2022.867263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.
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Affiliation(s)
- Naoto Sano
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Imen Lounifi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- MBCC Group, Master Builders Construction Chemical, Singapore, Singapore
| | - Gwendal Cueff
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Benoît Valot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, Gif-sur-Yvette, France
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Marc Galland
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [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: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
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Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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Carrell AA, Lawrence TJ, Cabugao KGM, Carper DL, Pelletier DA, Lee JH, Jawdy SS, Grimwood J, Schmutz J, Hanson PJ, Shaw AJ, Weston DJ. Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming. THE NEW PHYTOLOGIST 2022; 234:2111-2125. [PMID: 35266150 PMCID: PMC9310625 DOI: 10.1111/nph.18072] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Travis J. Lawrence
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Kristine Grace M. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee1502 Cumberland Ave.KnoxvilleTN37996USA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Dale A. Pelletier
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jun Hyung Lee
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | | | - David J. Weston
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
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121
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022. [PMID: 35681017 DOI: 10.1101/2020.05.12.090415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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122
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022; 8:670-681. [PMID: 35681017 DOI: 10.1038/s41477-022-01164-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/04/2022] [Indexed: 05/28/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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Powell AF, Feder A, Li J, Schmidt MHW, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B. A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1791-1810. [PMID: 35411592 DOI: 10.1111/tpj.15770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.
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Affiliation(s)
| | - Ari Feder
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Jie Li
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Lance Courtney
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Emma M Jobson
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Alexander Vogel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Yimin Xu
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David Lyon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Kathryn Dumschott
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Marcus McHale
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Kan Bao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Rohit Lal
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asha Duhan
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisandra K Denton
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Sarah R Hind
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA, and
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Cathie Martin
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | | | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
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Hall RD, D'Auria JC, Silva Ferreira AC, Gibon Y, Kruszka D, Mishra P, van de Zedde R. High-throughput plant phenotyping: a role for metabolomics? TRENDS IN PLANT SCIENCE 2022; 27:549-563. [PMID: 35248492 DOI: 10.1016/j.tplants.2022.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/18/2022] [Accepted: 02/02/2022] [Indexed: 05/17/2023]
Abstract
High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype-phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.
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Affiliation(s)
- Robert D Hall
- BU Bioscience, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands; Laboratory of Plant Physiology, Wageningen University, 6700 AA, Wageningen, The Netherlands; Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, The Netherlands.
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Antonio C Silva Ferreira
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal; Faculty of AgriSciences, University of Stellenbosch, Matieland 7602, South Africa; Cork Supply Portugal, S.A., Rua Nova do Fial, 4535, Portugal
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France; Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France PMB-Metabolome, INRAE, Centre INRAE de Nouvelle, Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Dariusz Kruszka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Puneet Mishra
- Food and Biobased Research, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
| | - Rick van de Zedde
- Plant Sciences Group, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
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125
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Shen C, Park M, Warnow T. WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. J Comput Biol 2022; 29:782-801. [PMID: 35575747 DOI: 10.1089/cmb.2021.0585] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Accurate multiple sequence alignment is challenging on many data sets, including those that are large, evolve under high rates of evolution, or have sequence length heterogeneity. While substantial progress has been made over the last decade in addressing the first two challenges, sequence length heterogeneity remains a significant issue for many data sets. Sequence length heterogeneity occurs for biological and technological reasons, including large insertions or deletions (indels) that occurred in the evolutionary history relating the sequences, or the inclusion of sequences that are not fully assembled. Ultra-large alignments using Phylogeny-Aware Profiles (UPP) (Nguyen et al. 2015) is one of the most accurate approaches for aligning data sets that exhibit sequence length heterogeneity: it constructs an alignment on the subset of sequences it considers "full-length," represents this "backbone alignment" using an ensemble of hidden Markov models (HMMs), and then adds each remaining sequence into the backbone alignment based on an HMM selected for that sequence from the ensemble. Our new method, WeIghTed Consensus Hmm alignment (WITCH), improves on UPP in three important ways: first, it uses a statistically principled technique to weight and rank the HMMs; second, it uses k>1 HMMs from the ensemble rather than a single HMM; and third, it combines the alignments for each of the selected HMMs using a consensus algorithm that takes the weights into account. We show that this approach provides improved alignment accuracy compared with UPP and other leading alignment methods, as well as improved accuracy for maximum likelihood trees based on these alignments.
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Affiliation(s)
- Chengze Shen
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Minhyuk Park
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Kumar A, Kaur G, Singh P, Meena V, Sharma S, Tiwari M, Bauer P, Pandey AK. Strategies and Bottlenecks in Hexaploid Wheat to Mobilize Soil Iron to Grains. FRONTIERS IN PLANT SCIENCE 2022; 13:863849. [PMID: 35574143 PMCID: PMC9100831 DOI: 10.3389/fpls.2022.863849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Our knowledge of iron (Fe) uptake and mobilization in plants is mainly based on Arabidopsis and rice. Although multiple players of Fe homeostasis have been elucidated, there is a significant gap in our understanding of crop species, such as wheat. It is, therefore, imperative not only to understand the different hurdles for Fe enrichment in tissues but also to address specifically the knowns/unknowns involved in the plausible mechanism of Fe sensing, signaling, transport, and subsequent storage in plants. In the present review, a unique perspective has been described in light of recent knowledge generated in wheat, an economically important crop. The strategies to boost efficient Fe uptake, transcriptional regulation, and long-distance mobilization in grains have been discussed, emphasizing recent biotechnological routes to load Fe in grains. This article also highlights the new elements of physiological and molecular genetics that underpin the mechanistic insight for the identified Fe-related genes and discusses the bottlenecks in unloading the Fe in grains. The information presented here will provide much-needed resources and directions to overcome challenges and design efficient strategies to enhance the Fe density in wheat grains.
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Affiliation(s)
- Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Palvinder Singh
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Varsha Meena
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Shivani Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Manish Tiwari
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
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Fattel L, Psaroudakis D, Yanarella CF, Chiteri KO, Dostalik HA, Joshi P, Starr DC, Vu H, Wimalanathan K, Lawrence-Dill CJ. Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. Gigascience 2022; 11:6568997. [PMID: 35426911 PMCID: PMC9012101 DOI: 10.1093/gigascience/giac023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/28/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Background Genome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes potentially responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline. Results By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain more GO terms, and are similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets across multiple species could be used together to carry out comparative functional genomics analyses in plants. To test the idea and as a proof of concept, we created dendrograms of functional relatedness based on terms assigned for all 18 genomes. These dendrograms were compared to well-established species-level evolutionary phylogenies to determine whether trees derived were in agreement with known evolutionary relationships, which they largely are. Where discrepancies were observed, we determined branch support based on jackknifing then removed individual annotation sets by genome to identify the annotation sets causing unexpected relationships. Conclusions GOMAP-derived functional annotations used together across multiple species generally retain sufficient biological signal to recover known phylogenetic relationships based on genome-wide functional similarities, indicating that comparative functional genomics across species based on GO data holds promise for generating novel hypotheses about comparative gene function and traits.
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Affiliation(s)
- Leila Fattel
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Dennis Psaroudakis
- Department of Plant Pathology and Microbiology, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Drive, Ames, Iowa 50011, USA
| | - Colleen F Yanarella
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Kevin O Chiteri
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Haley A Dostalik
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Parnal Joshi
- Department of Veterinary Microbiology and Preventive Medicine, 1800 Christensen Drive, Ames, Iowa 50011-1134, USA
| | - Dollye C Starr
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Ha Vu
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Kokulapalan Wimalanathan
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Carolyn J Lawrence-Dill
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
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128
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Song JH, Montes-Luz B, Tadra-Sfeir MZ, Cui Y, Su L, Xu D, Stacey G. High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2022; 13:820348. [PMID: 35498680 PMCID: PMC9048599 DOI: 10.3389/fpls.2022.820348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum. A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.
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Affiliation(s)
- Jae Hyo Song
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Bruna Montes-Luz
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Michelle Zibetti Tadra-Sfeir
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Yaya Cui
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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129
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Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. THE ISME JOURNAL 2022; 16:1074-1085. [PMID: 34845335 PMCID: PMC8941135 DOI: 10.1038/s41396-021-01136-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Interactions between Sphagnum (peat moss) and cyanobacteria play critical roles in terrestrial carbon and nitrogen cycling processes. Knowledge of the metabolites exchanged, the physiological processes involved, and the environmental conditions allowing the formation of symbiosis is important for a better understanding of the mechanisms underlying these interactions. In this study, we used a cross-feeding approach with spatially resolved metabolite profiling and metatranscriptomics to characterize the symbiosis between Sphagnum and Nostoc cyanobacteria. A pH gradient study revealed that the Sphagnum–Nostoc symbiosis was driven by pH, with mutualism occurring only at low pH. Metabolic cross-feeding studies along with spatially resolved matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) identified trehalose as the main carbohydrate source released by Sphagnum, which were depleted by Nostoc along with sulfur-containing choline-O-sulfate, taurine and sulfoacetate. In exchange, Nostoc increased exudation of purines and amino acids. Metatranscriptome analysis indicated that Sphagnum host defense was downregulated when in direct contact with the Nostoc symbiont, but not as a result of chemical contact alone. The observations in this study elucidated environmental, metabolic, and physiological underpinnings of the widespread plant–cyanobacterial symbioses with important implications for predicting carbon and nitrogen cycling in peatland ecosystems as well as the basis of general host-microbe interactions.
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130
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Orduña L, Li M, Navarro-Payá D, Zhang C, Santiago A, Romero P, Ramšak Ž, Magon G, Höll J, Merz P, Gruden K, Vannozzi A, Cantu D, Bogs J, Wong DCJ, Huang SSC, Matus JT. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:529-547. [PMID: 35092714 DOI: 10.1111/tpj.15686] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 05/08/2023]
Abstract
The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
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Affiliation(s)
- Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Pablo Romero
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Gabriele Magon
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Janine Höll
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Patrick Merz
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Jochen Bogs
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
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131
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Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species. Antioxidants (Basel) 2022; 11:antiox11040671. [PMID: 35453356 PMCID: PMC9029244 DOI: 10.3390/antiox11040671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
The plant kingdom contains an enormous diversity of bioactive compounds which regulate plant growth and defends against biotic and abiotic stress. Some of these compounds, like flavonoids, have properties which are health supporting and relevant for industrial use. Many of these valuable compounds are synthesized in various pepper (Capsicum sp.) tissues. Further, a huge amount of biomass residual remains from pepper production after harvest, which provides an important opportunity to extract these metabolites and optimize the utilization of crops. Moreover, abiotic stresses induce the synthesis of such metabolites as a defense mechanism. Two different Capsicum species were therefore exposed to chilling temperature (24/18 ℃ vs. 18/12 ℃), to salinity (200 mM NaCl), or a combination thereof for 1, 7 and 14 days to investigate the effect of these stresses on the metabolome and transcriptome profiles of their leaves. Both profiles in both species responded to all stresses with an increase over time. All stresses resulted in repression of photosynthesis genes. Stress involving chilling temperature induced secondary metabolism whereas stresses involving salt repressed cell wall modification and solute transport. The metabolome analysis annotated putatively many health stimulating flavonoids (apigetrin, rutin, kaempferol, luteolin and quercetin) in the Capsicum biomass residuals, which were induced in response to salinity, chilling temperature or a combination thereof, and supported by related structural genes of the secondary metabolism in the network analysis.
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132
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Fritsche S, Rippel Salgado L, Boron AK, Hanning KR, Donaldson LA, Thorlby G. Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics. Front Genet 2022; 13:815093. [PMID: 35368695 PMCID: PMC8971679 DOI: 10.3389/fgene.2022.815093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.
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Affiliation(s)
- Steffi Fritsche
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
| | - Leonardo Rippel Salgado
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- Molecular and Digital Breeding, The New Zealand Institute for Plant and Food Research, Te Puke, New Zealand
| | | | | | | | - Glenn Thorlby
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- *Correspondence: Glenn Thorlby,
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133
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Eiteneuer C, Velasco D, Atemia J, Wang D, Schwacke R, Wahl V, Schrader A, Reimer JJ, Fahrner S, Pieruschka R, Schurr U, Usadel B, Hallab A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. PLANTS 2022; 11:plants11060745. [PMID: 35336631 PMCID: PMC8952246 DOI: 10.3390/plants11060745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever-growing number of life science research projects. Typically, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed “Gene Expression Plotter” (GXP), an RNAseq and Metabolomics data visualization and analysis tool entirely running in the user’s web browser, thus not needing any custom installation, manual programming or uploading of confidential data to third party servers. Consequently, upon receiving the bioinformatic raw data analysis of RNAseq or other omics results, GXP immediately enables the user to interact with the data according to biological questions by performing knowledge-driven, in-depth data analyses and candidate identification via visualization and data exploration. Thereby, GXP can support and accelerate complex interdisciplinary omics projects and downstream analyses. GXP offers an easy way to publish data, plots, and analysis results either as a simple exported file or as a custom website. GXP is freely available on GitHub (see introduction)
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Affiliation(s)
- Constantin Eiteneuer
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - David Velasco
- Faculty of Natural Sciences, Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, Norway;
| | - Joseph Atemia
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Dan Wang
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Rainer Schwacke
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Vanessa Wahl
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany;
| | - Andrea Schrader
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
| | - Julia J. Reimer
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
- Faculty of Technology, University of Applied Science Emden/Leer, Molecular Biosciences, 26723 Emden, Germany
| | - Sven Fahrner
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Roland Pieruschka
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Ulrich Schurr
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
- Correspondence:
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134
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Zeng C, Wu H, Cao M, Zhou C, Wang X, Fu S. Integrated Analysis of the miRNAome and Transcriptome Reveals miRNA-mRNA Regulatory Networks in Catharanthus roseus Through Cuscuta campestris-Mediated Infection With " Candidatus Liberibacter asiaticus". Front Microbiol 2022; 13:799819. [PMID: 35308338 PMCID: PMC8928264 DOI: 10.3389/fmicb.2022.799819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
Citrus Huanglongbing (HLB) is the most devastating disease of citrus caused by the Gram-negative phloem-limited bacterium "Candidatus Liberibacter asiaticus" (CLas). It can be transmitted by the Asian citrus psyllid "Diaphorina citri," by grafting, and by the holoparasitic dodder. In this study, the non-natural host periwinkle (Catharanthus roseus) was infected via dodder (Cuscuta campestris) from CLas-infected citrus plants, and the asymptomatic leaves (AS) were subjected to transcriptomic and small-RNA profiling. The results were analyzed together with a transcriptome dataset from the NCBI repository that included leaves for which symptoms had just occurred (S) and yellowing leaves (Y). There were 3,675 differentially expressed genes (DEGs) identified in AS, and 6,390 more DEGs in S and further 2109 DEGs in Y. These DEGs were commonly enriched in photosystem, chloroplast, membrane, oxidation-reduction process, metal/zinc ion binding on GO. A total of 14,974 DEGs and 336 DE miRNAs (30 conserved and 301 novel) were identified. Through weighted gene co-expression network and nested network analyses, two critical nested miRNA-mRNA regulatory networks were identified with four conserved miRNAs. The primary miR164-NAC1 network is potentially involved in plant defense responses against CLas from the early infection stage to symptom development. The secondary network revealed the regulation of secondary metabolism and nutrient homeostasis through miR828-MYB94/miR1134-HSF4 and miR827-ATG8 regulatory networks, respectively. The findings discovered new potential mechanisms in periwinkle-CLas interactions, and its confirmation can be done in citrus-CLas system later on. The advantages of periwinkle plants in facilitating the quick establishment and greater multiplication of CLas, and shortening latency for disease symptom development make it a great surrogate for further studies, which could expedite our understanding of CLas pathogenesis.
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Affiliation(s)
| | | | | | | | - Xuefeng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Shimin Fu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
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135
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Comparison of the root, leaf and internode transcriptomes in Sugarcane (Saccharum spp. hybrids). CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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136
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He M, Li X, Mang M, Li Z, Ludewig U, Schulze WX. A systems-biology approach identifies co-expression modules in response to low phosphate supply in maize lines of different breeding history. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1249-1270. [PMID: 34897849 DOI: 10.1111/tpj.15630] [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: 10/14/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Plants cope with low phosphorus availability by adjusting growth and metabolism through transcriptomic and proteomic adaptations. We hypothesize that selected genotypes with distinct phosphorous (P) use efficiency covering the breeding history of European Flint heterotic pool provide a tool to reveal general and genotype-specific molecular responses to P limitation. We reconstructed protein and gene co-expression networks by weighted correlation network analysis and related these to phosphate deficiency-induced traits. In roots, low phosphate supply resulted in a decreasing abundance of proteins in the oxidative pentose phosphate pathway and a negative correlation with root and shoot phosphate content. We observed an increase in abundance and positive correlation with root and shoot phosphate content for proteins in sucrose biosynthesis, lipid metabolism, respiration and RNA processing. Purple acid phosphatases, superoxide dismutase and phenylalanine ammonia lyase were identified as being upregulated under low phosphate in all genotypes. Overall, correlations between protein and mRNA abundance changes were limited, with ribosomal proteins and the ubiquitin protein degradation pathway exclusively responding with protein abundance changes. Carbohydrate, phospho- and sulfo-lipid metabolism showed abundance changes at the protein and mRNA levels. These partially non-overlapping proteomic and transcriptomic adjustments to low phosphate suggest sugar and lipid metabolism as metabolic processes associated with improved P use efficiency specifically in Founder Flint lines. We identified a mitogen-activated protein kinase-kinase as a potential genotype-specific regulator of sucrose metabolism at low phosphate in Founder Flint line EP1. We conclude that, during breedingt of Elite Flint lines, regulation of primary metabolism has changed to result in a distinct low phosphate response in Founder lines.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Xuelian Li
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Melissa Mang
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
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137
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Bawin T, Bruckmüller J, Olsen S, Krause K. A host-free transcriptome for haustoriogenesis in Cuscuta campestris: Signature gene expression identifies markers of successive development stages. PHYSIOLOGIA PLANTARUM 2022; 174:e13628. [PMID: 35048368 PMCID: PMC9313786 DOI: 10.1111/ppl.13628] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 05/10/2023]
Abstract
The development of the infection organ of the parasitic angiosperm genus Cuscuta is a dynamic process that is normally obscured from view as it happens endophytically in its host. We artificially induced haustoriogenesis in Cuscuta campestris by far-red light to define specific morphologically different stages and analyze their transcriptional patterns. This information enabled us to extract sets of high-confidence housekeeping and marker genes for the different stages, validated in a natural infection setting on a compatible host. This study provides a framework for more reproducible investigations of haustoriogenesis and the processes governing host-parasite interactions in shoot parasites, with C. campestris as a model species.
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Affiliation(s)
- Thomas Bawin
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
| | - Julien Bruckmüller
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
| | - Stian Olsen
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
| | - Kirsten Krause
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
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138
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Zhong Y, Chen Y, Zheng D, Pang J, Liu Y, Luo S, Meng S, Qian L, Wei D, Dai S, Zhou R. Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia. DNA Res 2022; 29:6570587. [PMID: 35438173 PMCID: PMC9052405 DOI: 10.1093/dnares/dsac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level genome assembly of Bauhinia variegata to test this hypothesis. The assembled genome is 326.4 Mb with the scaffold N50 of 22.1 Mb and contains 37,996 protein-coding genes. The Ks distribution between gene pairs in the syntenic regions indicates two whole-genome duplications (WGDs): one is B. variegata-specific, and the other is shared among core eudicots. Although Ks between gene pairs generated by the recent WGD in Bauhinia is greater than that between Bauhinia and Cercis, the WGD was not detected in Cercis, which can be explained by an accelerated evolutionary rate in Bauhinia after divergence from Cercis. Ks distribution and phylogenetic analysis for gene pairs generated by the recent WGD in Bauhinia and their corresponding orthologs in Cercis support the allopolyploidy origin hypothesis of Bauhinia. The genome of B. variegata also provides a genomic resource for dissecting genetic basis of its ornamental traits.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Chen
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Danjing Zheng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Jingyi Pang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shukai Luo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Shiyuan Meng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Lei Qian
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Dan Wei
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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139
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Mathur S, Paritosh K, Tandon R, Pental D, Pradhan AK. Comparative Analysis of Seed Transcriptome and Coexpression Analysis Reveal Candidate Genes for Enhancing Seed Size/Weight in Brassica juncea. Front Genet 2022; 13:814486. [PMID: 35281836 PMCID: PMC8907137 DOI: 10.3389/fgene.2022.814486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Seed size/weight is a multigenic trait that is governed by complex transcriptional regulatory pathways. An understanding of the genetic basis of seed size is of great interest in the improvement of seed yield and quality in oilseed crops. A global transcriptome analysis was performed at the initial stages of seed development in two lines of Brassica juncea, small-seeded EH-2 and large-seeded PJ. The anatomical analyses revealed significant differences in cell number and cell size in the outer layer of the seed coat between EH-2 and PJ. Pairwise comparisons at each developmental stage identified 5,974 differentially expressed genes (DEGs) between the two lines, of which 954 genes belong to different families of transcription factors. Two modules were found to be significantly correlated with an increased seed size using weighted gene coexpression network analysis. The DEG and coexpression datasets were integrated with the thousand seed weight (Tsw) quantitative trait loci (QTL) mapped earlier in the EPJ (EH-2 × PJ) doubled haploid (DH) population, which identified forty potential key components controlling seed size. The candidate genes included genes regulating the cell cycle, cell wall biogenesis/modification, solute/sugar transport, and hormone signaling. The results provide a valuable resource to widen the current understanding of regulatory mechanisms underlying seed size in B. juncea.
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Affiliation(s)
- Shikha Mathur
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Kumar Paritosh
- Centre of Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Rajesh Tandon
- Department of Botany, University of Delhi, New Delhi, India
| | - Deepak Pental
- Centre of Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Akshay K. Pradhan
- Centre of Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
- *Correspondence: Akshay K. Pradhan,
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Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold. BMC Genomics 2022; 23:144. [PMID: 35176993 PMCID: PMC8855596 DOI: 10.1186/s12864-022-08312-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. Results In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. Conclusion Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08312-2.
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141
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Staudinger C, Dissanayake BM, Duncan O, Millar AH. The wheat secreted root proteome: Implications for phosphorus mobilisation and biotic interactions. J Proteomics 2022; 252:104450. [PMID: 34890868 DOI: 10.1016/j.jprot.2021.104450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
Root secreted acid phosphatases and organic anions are widely perceived as major players of plant phosphorus (P) mobilisation from the rhizosphere under P limiting growth conditions. Previous research indicated that other mechanisms play a role, especially in species with fine roots, such as wheat. In this study we characterised the plant-derived extracellular proteome of wheat roots by profiling root tip mucilage, soluble root secreted and root tip proteomes. Extracellular acid phosphatases and enzymes of the central carbon metabolism were targeted using selected reaction monitoring. More than 140 proteins with extracellular localisation prediction were identified in mucilage. P starvation induced proteins predicted to be localised to the apoplast which are related to cell wall modification and defence in both, root tip and soluble root-secreted proteomes. Glycolytic enzymes were strongly increased in abundance by P limitation in root tips, as were PEPC and plastidial MDH. Soluble acid phosphatases were not identified in extracellular protein samples. Our results indicate that root tip mucilage contains proteins with the functional potential to actively shape their immediate environment by modification of plant structural components and biotic interactions. Wheat acid phosphatases appear to play a minor role in P mobilisation beyond the immediate root surface. SIGNIFICANCE: Phosphorus (P) is a plant growth limiting nutrient in many agricultural situations and the development of phosphorus efficient crops is of paramount importance for future agricultural management practices. As P is relatively immobile in soils, processes occurring at the root-soil interface, the rhizosphere, are suspected to play a key role in plant-induced P mobilisation. According to the current view, the secretion of extracellular acid phosphatases and organic anions enhances P mobilisation within several millimetres beyond the root surface, either directly or indirectly through the selection and appropriate soil microbes. However, the mechanisms of P mobilisation in species with fine roots, such as wheat, and the role of other secreted root proteins are poorly understood. Here, we carried out the profiling of wheat root tip mucilage, soluble root secreted and root tip proteomes. We analysed proteome changes in response to P starvation. We found that proteins with a predicted localisation to the apoplast made up a major proportion of stress-responsive proteins. Acid phosphatases were not identified within extracellular protein samples, which were enriched in proteins with predicted extracellular localisation. The absence of extracellular APases was further validated by multiple reaction monitoring. Our data indicates that wheat acid phosphatases play a minor role in P mobilisation beyond the immediate root surface and provides a resource for breeding strategies and further investigations of the functional roles of root tip-released proteins in the rhizosphere under P limitation.
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Affiliation(s)
- Christiana Staudinger
- School of Biological Sciences, The University of Western Australia, Australia; The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia; University of Natural Resources and Life Sciences, BOKU-Vienna, Department of Forest and Soil Sciences, Rhizosphere Ecology and Biogeochemistry Group, Austria.
| | - Bhagya M Dissanayake
- The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Owen Duncan
- The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - A Harvey Millar
- The ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
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142
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Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
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Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
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143
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Yang H, Nukunya K, Ding Q, Thompson BE. Tissue-specific transcriptomics reveal functional differences in floral development. PLANT PHYSIOLOGY 2022; 188:1158-1173. [PMID: 34865134 PMCID: PMC8825454 DOI: 10.1093/plphys/kiab557] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/02/2021] [Indexed: 05/22/2023]
Abstract
Flowers are produced by floral meristems, groups of stem cells that give rise to floral organs. In grasses, including the major cereal crops, flowers (florets) are contained in spikelets, which contain one to many florets, depending on the species. Importantly, not all grass florets are developmentally equivalent, and one or more florets are often sterile or abort in each spikelet. Members of the Andropogoneae tribe, including maize (Zea mays), produce spikelets with two florets; the upper and lower florets are usually dimorphic, and the lower floret is greatly reduced compared to the upper floret. In maize ears, early development appears identical in both florets but the lower floret ultimately aborts. To gain insight into the functional differences between florets with different fates, we used laser capture microdissection coupled with RNA-sequencing to globally examine gene expression in upper and lower floral meristems in maize. Differentially expressed genes were involved in hormone regulation, cell wall, sugar, and energy homeostasis. Furthermore, cell wall modifications and sugar accumulation differed between the upper and lower florets. Finally, we identified a boundary domain between upper and lower florets, which we hypothesize is important for floral meristem activity. We propose a model in which growth is suppressed in the lower floret by limiting sugar availability and upregulating genes involved in growth repression. This growth repression module may also regulate floret fertility in other grasses and potentially be modulated to engineer more productive cereal crops.
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Affiliation(s)
- Hailong Yang
- Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
| | - Kate Nukunya
- Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
| | - Queying Ding
- Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
| | - Beth E Thompson
- Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
- Author for communication:
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144
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Apelt F, Mavrothalassiti E, Gupta S, Machin F, Olas JJ, Annunziata MG, Schindelasch D, Kragler F. Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles. PLANT PHYSIOLOGY 2022; 188:861-878. [PMID: 34850215 PMCID: PMC8825464 DOI: 10.1093/plphys/kiab537] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/28/2021] [Indexed: 05/13/2023]
Abstract
Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants' transcriptome substantially changes throughout the day, shaped by the circadian clock, we performed scRNAseq on both Arabidopsis root and above-ground tissues at defined times of the day. For the root scRNAseq analysis, we used tissue-specific reporter lines grown on plates and harvested at the end of the day (ED). In addition, we submitted above-ground tissues from plants grown on soil at ED and end of the night to scRNAseq, which allowed us to identify common cell types/markers between root and shoot and uncover transcriptome changes to above-ground tissues depending on the time of the day. The dataset was also exploited beyond the traditional scRNAseq analysis to investigate non-annotated and di-cistronic transcripts. We experimentally confirmed the predicted presence of some of these transcripts and also addressed the potential function of a previously unidentified marker gene for dividing cells. In summary, this work provides insights into the spatial control of gene expression from nearly 70,000 cells of Arabidopsis for below- and whole above-ground tissue at single-cell resolution at defined time points.
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Affiliation(s)
- Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Eleni Mavrothalassiti
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Saurabh Gupta
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Frank Machin
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Department of Molecular Biology, Karl-Liebknecht-Strasse 24-25, Haus 20, 14476 Potsdam, Germany
| | - Maria Grazia Annunziata
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dana Schindelasch
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
- Author for communication:
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145
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Chaparro-Encinas LA, Parra-Cota FI, Cruz-Mendívil A, Santoyo G, Peña-Cabriales JJ, Castro-Espinoza L, de Los Santos-Villalobos S. Transcriptional regulation of cell growth and reprogramming of systemic response in wheat (Triticum turgidum subsp. durum) seedlings by Bacillus paralicheniformis TRQ65. PLANTA 2022; 255:56. [PMID: 35106645 DOI: 10.1007/s00425-022-03837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Bacillus paralicheniformis TRQ65 reprograms the gene expression patterns associated with systemic response to potentially facilitate its colonization and stimulate cell growth and plant biomass. Plant growth-promoting rhizobacteria (PGPR) carry out numerous mechanisms that enhance growth in seedlings, such as nutrient solubilization, phytohormone production, biocontrol activity, and regulation of induced systemic resistance (ISR) and acquired systemic resistance (ASR). Bacillus paralicheniformis TRQ65 is a biological and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere. In this study, we performed a transcriptomic analysis of wheat seedlings inoculated with the native rhizobacterium Bacillus paralicheniformis TRQ65 (1 × 107 cells∙g -1 of soil) at early development stages (GS15). A morphometrical assay was carried out to confirm growth promotion and after the cultivation period, TRQ65 was re-isolated to define inoculum persistence. Inoculated seedlings showed a significant (P < 0.05) increase in shoot length (93.48%) and dry weight in both shoot (117.02%) and root (48.33%) tissues; also, the strain persisted in the soil at 1.4 × 107 UFC∙g-1 of soil. A total of 228 differentially expressed genes (DEGs) (FDR < 0.05 and |log2 fold change|≥ 1.3) were observed in response to TRQ65 inoculation, of which 185 were down-regulated and 43 were up-regulated. The transcriptional patterns were characterized by the regulation of multidimensional cell growth (ROS, Ca+2 channel, and NADPH oxidases activity), suppression of defense mechanism (PR proteins, PDFs, ROS, transcription factors), induction of central stimuli receptors (RALF, WAK, MAPK), carbohydrate metabolism (invertase activity) and phytohormone-related transport (ABCG transporter and AAAP). These results suggest that B. paralicheniformis TRQ65 is a promising bioinoculant agent for increasing wheat growth and development by reprogramming ISR and ASR simultaneously, suppressing defense mechanisms and inducing central stimuli response.
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Affiliation(s)
- Luis A Chaparro-Encinas
- Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, México
- Universidad Autónoma Agraria Antonio Narro (UAAAN) Unidad Laguna, Periférico Raúl López Sánchez, Valle Verde, 27054, Torreón, Coahuila, México
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug-CIRNO. Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, CP 85000, Valle del Yaqui, Ciudad Obregón, Sonora, México
| | - Abraham Cruz-Mendívil
- Cátedras CONACYT, Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación Para el Desarrollo Integral Regional (CIIDIR) Unidad Sinaloa, Guasave, Sinaloa, México
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Juan J Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Campus Guanajuato, Irapuato Guanajuato, México
| | - Luciano Castro-Espinoza
- Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, México
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146
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Dai X, Tu X, Du B, Dong P, Sun S, Wang X, Sun J, Li G, Lu T, Zhong S, Li P. Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:675-692. [PMID: 34783109 DOI: 10.1111/tpj.15586] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
C4 plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO2 to RuBisCO and to reduce photorespiration. To better understand how C4 photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C4 genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C4 genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C4 genes. Our findings provide deep insight into the architectures associated with C4 gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C4 species.
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Affiliation(s)
- Xiuru Dai
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Baijuan Du
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shilei Sun
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xianglan Wang
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jing Sun
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tiegang Lu
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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147
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Duncan O, Millar AH. Day and night isotope labelling reveal metabolic pathway specific regulation of protein synthesis rates in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:745-763. [PMID: 34997626 DOI: 10.1111/tpj.15661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess the output of the translation process and to estimate the ATP investment involved, the individual rates of protein synthesis and degradation of hundreds of different proteins need to be measured simultaneously. We quantified protein synthesis and degradation through pulse labelling with heavy hydrogen in Arabidopsis thaliana rosettes to allow such an assessment of ATP investment in leaf proteome homeostasis on a gene-by-gene basis. Light-harvesting complex proteins were synthesised and degraded much faster in the day (approximately 10:1), while carbon metabolism and vesicle trafficking components were translated at similar rates day or night. Few leaf proteins changed in abundance between the day and the night despite reduced protein synthesis rates at night, indicating that protein degradation rates are tightly coordinated. The data reveal how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule.
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Affiliation(s)
- Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
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148
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Henninger M, Pedrotti L, Krischke M, Draken J, Wildenhain T, Fekete A, Rolland F, Müller MJ, Fröschel C, Weiste C, Dröge-Laser W. The evolutionarily conserved kinase SnRK1 orchestrates resource mobilization during Arabidopsis seedling establishment. THE PLANT CELL 2022; 34:616-632. [PMID: 34755865 PMCID: PMC8774017 DOI: 10.1093/plcell/koab270] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/28/2021] [Indexed: 05/02/2023]
Abstract
The onset of plant life is characterized by a major phase transition. During early heterotrophic seedling establishment, seed storage reserves fuel metabolic demands, allowing the plant to switch to autotrophic metabolism. Although metabolic pathways leading to storage compound mobilization are well-described, the regulatory circuits remain largely unresolved. Using an inducible knockdown approach of the evolutionarily conserved energy master regulator Snf1-RELATED-PROTEIN-KINASE1 (SnRK1), phenotypic studies reveal its crucial function in Arabidopsis thaliana seedling establishment. Importantly, glucose feeding largely restores growth defects of the kinase mutant, supporting its major impact in resource mobilization. Detailed metabolite studies reveal sucrose as a primary resource early in seedling establishment, in a SnRK1-independent manner. Later, SnRK1 orchestrates catabolism of triacylglycerols and amino acids. Concurrent transcriptomic studies highlight SnRK1 functions in controlling metabolic hubs fuelling gluconeogenesis, as exemplified by cytosolic PYRUVATE ORTHOPHOSPHATE DIKINASE (cyPPDK). Here, SnRK1 establishes its function via phosphorylation of the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63), which directly targets and activates the cyPPDK promoter. Taken together, our results disclose developmental and catabolic functions of SnRK1 in seed storage mobilization and describe a prototypic gene regulatory mechanism. As seedling establishment is important for plant vigor and crop yield, our findings are of agronomical importance.
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Affiliation(s)
- Markus Henninger
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Lorenzo Pedrotti
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Markus Krischke
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Jan Draken
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Theresa Wildenhain
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Agnes Fekete
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, B-3001 Leuven, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, B-3001 Leuven, Belgium
| | - Martin J Müller
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Christian Fröschel
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
| | - Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, 97082 Würzburg, Germany
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149
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Raza A, Tabassum J, Zahid Z, Charagh S, Bashir S, Barmukh R, Khan RSA, Barbosa F, Zhang C, Chen H, Zhuang W, Varshney RK. Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:794373. [PMID: 35058954 PMCID: PMC8764127 DOI: 10.3389/fpls.2021.794373] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 05/17/2023]
Abstract
Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Zainab Zahid
- School of Civil and Environmental Engineering (SCEE), Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Shanza Bashir
- School of Civil and Environmental Engineering (SCEE), Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rao Sohail Ahmad Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Fernando Barbosa
- Department of Clinical Analysis, Toxicology and Food Sciences, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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150
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Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, Qin L, Babic V, Liu L, Cram D, Pasha A, Esteban E, Condie J, Sidebottom C, Zhang Y, Huang Y, Zhang W, Bhowmik P, Kochian LV, Konkin D, Wei Y, Provart NJ, Kagale S, Smith M, Patterson N, Gillmor CS, Datla R, Xiang D. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. THE NEW PHYTOLOGIST 2022; 233:30-51. [PMID: 34687557 DOI: 10.1111/nph.17759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kirby T Nilsen
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Li Qin
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Li Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yan Zhang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Mark Smith
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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