1
|
Peña-Ponton C, Diez-Rodriguez B, Perez-Bello P, Becker C, McIntyre LM, van der Putten WH, De Paoli E, Heer K, Opgenoorth L, Verhoeven KJF. High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5839-5856. [PMID: 38836523 PMCID: PMC11427840 DOI: 10.1093/jxb/erae262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/06/2024]
Abstract
DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
Collapse
Affiliation(s)
- Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Barbara Diez-Rodriguez
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Eva Mayr-Stihl professorship of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098 Freiburg i. Br., Germany
- Natural Resources and Climate Area, CARTIF Technology Centre, 47151 Boecillo, Valladolid, Spain
| | - Paloma Perez-Bello
- IGA Technology Services Srl. Via Jacopo Linussio 51, 33100 Udine UD, Italy
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen 6700 ES, The Netherlands
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Katrin Heer
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Eva Mayr-Stihl professorship of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098 Freiburg i. Br., Germany
| | - Lars Opgenoorth
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
2
|
Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
Collapse
Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
| |
Collapse
|
3
|
Claver A, Luján MÁ, Escuín JM, Schilling M, Jouhet J, Savirón M, López MV, Picorel R, Jarne C, Cebolla VL, Alfonso M. Transcriptomic and lipidomic analysis of the differential pathway contribution to the incorporation of erucic acid to triacylglycerol during Pennycress seed maturation. FRONTIERS IN PLANT SCIENCE 2024; 15:1386023. [PMID: 38736440 PMCID: PMC11082276 DOI: 10.3389/fpls.2024.1386023] [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: 02/14/2024] [Accepted: 04/10/2024] [Indexed: 05/14/2024]
Abstract
Thlaspi arvense (Pennycress) is an emerging feedstock for biofuel production because of its high seed oil content enriched in erucic acid. A transcriptomic and a lipidomic study were performed to analyze the dynamics of gene expression, glycerolipid content and acyl-group distribution during seed maturation. Genes involved in fatty acid biosynthesis were expressed at the early stages of seed maturation. Genes encoding enzymes of the Kennedy pathway like diacylglycerol acyltransferase1 (TaDGAT1), lysophosphatidic acid acyltransferase (TaLPAT) or glycerol 3-phosphate acyltransferase (TaGPAT) increased their expression with maturation, coinciding with the increase in triacylglycerol species containing 22:1. Positional analysis showed that the most abundant triacylglycerol species contained 18:2 at sn-2 position in all maturation stages, suggesting no specificity of the lysophosphatidic acid acyltransferase for very long chain fatty acids. Diacylglycerol acyltransferase2 (TaDGAT2) mRNA was more abundant at the initial maturation stages, coincident with the rapid incorporation of 22:1 to triacylglycerol, suggesting a coordination between Diacylglycerol acyltransferase enzymes for triacylglycerol biosynthesis. Genes encoding the phospholipid-diacylglycerol acyltransferase (TaPDAT1), lysophosphatidylcholine acyltransferase (TaLPCAT) or phosphatidylcholine diacylglycerolcholine phosphotransferase (TaPDCT), involved in acyl-editing or phosphatidyl-choline (PC)-derived diacylglycerol (DAG) biosynthesis showed also higher expression at the early maturation stages, coinciding with a higher proportion of triacylglycerol containing C18 fatty acids. These results suggested a higher contribution of these two pathways at the early stages of seed maturation. Lipidomic analysis of the content and acyl-group distribution of diacylglycerol and phosphatidyl-choline pools was compatible with the acyl content in triacylglycerol at the different maturation stages. Our data point to a model in which a strong temporal coordination between pathways and isoforms in each pathway, both at the expression and acyl-group incorporation, contribute to high erucic triacylglycerol accumulation in Pennycress.
Collapse
Affiliation(s)
- Ana Claver
- Department of Plant Biology, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - María Ángeles Luján
- Department of Plant Biology, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - José Manuel Escuín
- Instituto de Carboquímica-Consejo Superior de Investigaciones Científicas (ICB-CSIC), Zaragoza, Spain
| | - Marion Schilling
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, Centre National de la Recherche Scientifique-Commisariat de l'Energie Atomique-Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (CNRS-CEA-INRAE), Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, Centre National de la Recherche Scientifique-Commisariat de l'Energie Atomique-Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (CNRS-CEA-INRAE), Grenoble, France
| | - María Savirón
- Facultad de Ciencias, Centro de Química y Materiales de Aragón-Consejo Superior de Investigaciones Científicas (CEQMA-CSIC)-Universidad de Zaragoza, Zaragoza, Spain
| | - M. Victoria López
- Department of Soil and Water Conservation, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - Rafael Picorel
- Department of Plant Biology, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - Carmen Jarne
- Departamento de Química Analítica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Vicente L. Cebolla
- Instituto de Carboquímica-Consejo Superior de Investigaciones Científicas (ICB-CSIC), Zaragoza, Spain
| | - Miguel Alfonso
- Department of Plant Biology, Estación Experimental Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| |
Collapse
|
4
|
Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [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: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
Collapse
Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| |
Collapse
|
5
|
Hagelthorn L, Fletcher JC. The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress. FRONTIERS IN PLANT SCIENCE 2023; 14:1240342. [PMID: 37600169 PMCID: PMC10436580 DOI: 10.3389/fpls.2023.1240342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023]
Abstract
CLAVATA3/ESR-related (CLE) peptides perform a variety of important functions in plant development and historically have been targeted during the domestication of existing crops. Pennycress (Thlaspi arvense) is an emerging biofuel crop currently undergoing domestication that offers novel monetary and environmental incentives as a winter cover crop during an otherwise fallow period of the corn/soybean farming rotation. Here we report the characterization of the CLE gene family in pennycress through homology comparison of the CLE motif with other dicot species by conducting a homology comparison and maximum likelihood phylogenetic analysis supplemented with manual annotation. Twenty-seven pennycress CLE genes were identified, and their expression analyzed through transcriptome profiling and RT-qPCR. Our study provides a genome-wide analysis of the CLE gene family in pennycress and carries significant value for accelerating the domestication of this crop through identification of potential key developmental regulatory genes.
Collapse
Affiliation(s)
- Lynne Hagelthorn
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Jennifer C. Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| |
Collapse
|
6
|
Xu L, Wang Y, Dong J, Zhang W, Tang M, Zhang W, Wang K, Chen Y, Zhang X, He Q, Zhang X, Wang K, Wang L, Ma Y, Xia K, Liu L. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:990-1004. [PMID: 36648398 PMCID: PMC10106849 DOI: 10.1111/pbi.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 05/04/2023]
Abstract
High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.
Collapse
Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Weilan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Xiaoli Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xinyu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lun Wang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Yinbo Ma
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Kai Xia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| |
Collapse
|
7
|
Huang Y, Wu D, Huang Z, Li X, Merotto A, Bai L, Fan L. Weed genomics: yielding insights into the genetics of weedy traits for crop improvement. ABIOTECH 2023; 4:20-30. [PMID: 37220539 PMCID: PMC10199979 DOI: 10.1007/s42994-022-00090-5] [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: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 05/25/2023]
Abstract
Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.
Collapse
Affiliation(s)
- Yujie Huang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Zhaofeng Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xiangyu Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School Federal University of Rio Grande do Sul, Porto Alegre, 91540-000 Brazil
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Sciences, Changshang, 410125 China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| |
Collapse
|
8
|
Yang T, Cai B, Jia Z, Wang Y, Wang J, King GJ, Ge X, Li Z. Sinapis genomes provide insights into whole-genome triplication and divergence patterns within tribe Brassiceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:246-261. [PMID: 36424891 DOI: 10.1111/tpj.16043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra, S. alba, and S. arvensis, and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole-genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole-genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba diverged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the divergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea. Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.
Collapse
Affiliation(s)
- Taihua Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bowei Cai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, 2480, Australia
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
9
|
Galanti D, Ramos-Cruz D, Nunn A, Rodríguez-Arévalo I, Scheepens JF, Becker C, Bossdorf O. Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense. PLoS Genet 2022; 18:e1010452. [PMID: 36223399 PMCID: PMC9591053 DOI: 10.1371/journal.pgen.1010452] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/24/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being lower in colder regions and in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylated regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Collapse
Affiliation(s)
- Dario Galanti
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Daniela Ramos-Cruz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Leipzig, Germany
- Institute for Computer Science, University of Leipzig, Leipzig, Germany
| | - Isaac Rodríguez-Arévalo
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - J. F. Scheepens
- Plant Evolutionary Ecology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
- * E-mail:
| |
Collapse
|
10
|
López ME, Roquis D, Becker C, Denoyes B, Bucher E. DNA methylation dynamics during stress response in woodland strawberry ( Fragaria vesca). HORTICULTURE RESEARCH 2022; 9:uhac174. [PMID: 36204205 PMCID: PMC9533225 DOI: 10.1093/hr/uhac174] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/27/2022] [Indexed: 05/29/2023]
Abstract
Environmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes, especially at the level of DNA methylation (5-methylcytosine). DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. We investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable ecologically relevant environmental conditions at the DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in the non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. These findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses.
Collapse
Affiliation(s)
- María-Estefanía López
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
- Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - David Roquis
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
| | - Claude Becker
- LMU BioCenter, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | | |
Collapse
|
11
|
Tandukar Z, Chopra R, Frels K, Heim B, Marks MD, Anderson JA. Genetic dissection of seed characteristics in field pennycress via genome-wide association mapping studies. THE PLANT GENOME 2022; 15:e20211. [PMID: 35484973 DOI: 10.1002/tpg2.20211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Field pennycress (Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome-wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post-harvest with specialized high-throughput imaging and near-infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76-0.79) compared with oil content (0.51) and protein content (0.37). Genotyping-by-sequencing identified 33,606 high quality genome-wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty-nine total marker-trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06-0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker-trait associations that can be incorporated into marker-assisted selection pipelines to accelerate pennycress breeding progress.
Collapse
Affiliation(s)
- Zenith Tandukar
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - Ratan Chopra
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - Katherine Frels
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, Lincoln, NE, USA
| | - Brett Heim
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - M David Marks
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| |
Collapse
|
12
|
García Navarrete T, Arias C, Mukundi E, Alonso AP, Grotewold E. Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense). G3 GENES|GENOMES|GENETICS 2022; 12:6568017. [PMID: 35416986 PMCID: PMC9157065 DOI: 10.1093/g3journal/jkac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.
Collapse
Affiliation(s)
- Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Cintia Arias
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ana Paula Alonso
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|